# ent

id: cord-006556-hmzoxqu3
type: DISEASE
entity:
  influenza A H1N1 pandemic preparation for severe respiratory emergency outbreaks Extracorporeal membrane oxygenation ECMO in patients with


id: cord-017566-dvxrwzqw
type: PROTEIN
entity:
  picornavirus 2B and 3A alphavirus 6K retrovirus Vpu paramyxovirus SH orthomyxovirus M2 reovirus p10 flavivirus p7 phycodnavirus Kcv coronavirus E


id: cord-017566-dvxrwzqw
type: DNA
entity:
  human immunodeficiency virus type 1 transmembrane glycoprotein gp41 A human virus protein poliovirus protein 2BC


id: cord-017566-dvxrwzqw
type: DNA
entity:
  rat 28S ribosomal ribonucleic acid Membrane permeabilization by small hydrophobic nonstructural proteins


id: cord-006947-nrzjedhi
type: CELL_LINE
entity:
  human red blood cell membrane Proc Equilibrium physics breakdown reveals the active nature of red blood cell flickering Receptor


id: cord-006947-nrzjedhi
type: WORK_OF_ART
entity:
  Math On the attraction of floating particles Effective capillary interaction of spherical particles at fluid interfaces Force


id: cord-009371-ub4p4ngr
type: GGP
entity:
  Intubitlon of mternahzatlon arylsulfatase 63 lmmunoglobulln 76 a 2 macroglobuhn 77 semlikl forest varus


id: cord-022504-tk7v4hoj
type: CELL_TYPE
entity:
  anterior nasal passage posterior nasal passage pharynx larynx trachea main bronchi bronchi bronchioles terminal bronchioles alveolar duct


id: cord-022504-tk7v4hoj
type: ORG
entity:
  Occupational Exposure Limits WHO Environmental Health Series 4 World Health Organization Summaries Evaluations Nickel and


id: cord-011888-3mvzkff6
type: ORG
entity:
  the Risks of Death Cardiovascular Events and Hospitalization Behavioral Counseling to Promote a Healthful Diet


id: cord-011888-3mvzkff6
type: ORG
entity:
  the Future Front Public Health Hemodialysis Prescription and Assessment of Adequacy Renal Urology News


id: cord-011888-3mvzkff6
type: ORG
entity:
  Impact of Blood and Dialysate Flow and Surface on Performance of New Polysulfone Hemodialysis Dialyzers


id: cord-016938-pk76snuy
type: ORG
entity:
  Various Pore Sizes A Bone Replaceable Artificial Bone Substitute Morphological and Physicochemical Characterization Behavior of Osteoblasts


id: cord-016938-pk76snuy
type: ORG
entity:
  Osteogenesis Ex Vivo Mechanical Evaluation of Carbonate Apatite Collagen Grafted Porous PLLA Membrane in Rabbit Calvarial Bone Type


id: cord-008480-p41oae8e
type: PROTEIN
entity:
  detergent concentration Proteins markers alcohol deshydrogenase 7 4S Boehringer catalase 11 3S Boehringer and fl galactosidase 16S Sigma


id: cord-014685-ihh30q6f
type: PROTEIN
entity:
  hydrophobic helical peptide P Chetal V Chauhan D Sahal International Centre For Genetic Engineering Biotechnology


id: cord-014685-ihh30q6f
type: PROTEIN
entity:
  post termination complex P Guo L Zhang Y Feng G Jing Institute of Biophysics Chinese Academy of Sciences National Laboratory of Biomacromolecules Beijing China Ribosome recycling factor RRF


id: cord-014685-ihh30q6f
type: PROTEIN
entity:
  L chain apoferritin K Yoshizawa 1 K Iwahori 3 Y Mishima 1 I Yamashita 2 1 CREST JST 2 ATRL Matsushita 3 Nara Institute of Science and Technology The denaturation of apoferritin


id: cord-014685-ihh30q6f
type: PROTEIN
entity:
  carbonic anhydrase H M Becker J W Deitmer Abt Allgem Zoologie TU Kaiserslautern 67663 Kaiserslautern


id: cord-014685-ihh30q6f
type: PROTEIN
entity:
  prostaglandin endoperoxide H2 synthase Prostaglandin endoperoxide H 2 synthases 1 and 2 PGHS 1 and 2


id: cord-014685-ihh30q6f
type: PROTEIN
entity:
  nucleoprotein complex K Zupán 1 L Herényi 1 K Tóth 2 Z Majer 3 G Csík 1 1 Institute of Biophysics and Radiation Biology Semmelweis Univ Budapest Hungary 2 Biophysics of Macromolecules German Cancer Research Center Heidelberg Germany 3 Department of Organic Chemistry Eötvös Loránd


id: cord-014685-ihh30q6f
type: DNA
entity:
  HIV 1 genomic RNA S Bernacchi 2 E Ennifar 1 K Toth 2 P Walter 1 J Langowski 2 P Dumas 1 1 CNRS UPR 9002 Strasbourg France 2 DKFZ Heidelberg Germany


id: cord-014685-ihh30q6f
type: DNA
entity:
  CUG repeats Y Sato K Kimura A Takénaka Graduate School of Bioscience and Biotechnology Tokyo Institute of Technology Yokohama Japan


id: cord-014685-ihh30q6f
type: GGP
entity:
  Refs 1 2 3 XAS spectroscopy results show that there are two different structures of the metal binding site


id: cord-014685-ihh30q6f
type: CHEBI
entity:
  cholesterol proteoliposomes M Berchel 1 J Jeftic 1 T Benvegnu 1 J Y Thepot 2 D Plusquellec 1 1 ENSCR


id: cord-014685-ihh30q6f
type: GGP
entity:
  speci c conductance s of aqueous solution of electrolytes viz NaF NaCl NaNO 3 Na2SO 4 KF KCl KNO 3 K 2 SO 4 MgCl 2 CaCl 2 FeCl 3 MnCl 2 CrCl 3 CuCl 2 CoCl 2


id: cord-014685-ihh30q6f
type: CL
entity:
  stem bulge stem region of DIS39 and the solution structures of DIS39 in the kissing loop and extendedduplex


id: cord-014685-ihh30q6f
type: PRODUCT
entity:
  J C Holyoake M S Sansom Biochemistry Department University of Oxford South Parks Road Oxford OX1 3QU


id: cord-014685-ihh30q6f
type: ORG
entity:
  Department of Animal Physiology and Biophysics Faculty of Biology University of Bucharest 2 Department of Biochemistry Faculty of Biology University of Bucharest Bucharest Romania Hypericin Hyp


id: cord-014685-ihh30q6f
type: WORK_OF_ART
entity:
  Faculty of Science and Technology Keio University Japan 2 Japan Synchrotron Radiation Research Institute


id: cord-014685-ihh30q6f
type: ORG
entity:
  NMR 2 Department of Surgery 3 Department of Radiotherapy All India Institute of Medical Sciences New Delhi India Diffusion


id: cord-014685-ihh30q6f
type: ORG
entity:
  Applied Physics College of Humanities and Sciences Nihon University 2 Department of Biophysics and Life


id: cord-014685-ihh30q6f
type: ORG
entity:
  University of Helsinki Finland 2 Institute of Biotechnology University of Helsinki Finland Molecular


id: cord-014685-ihh30q6f
type: CHEMICAL
entity:
  Ruysshaert 2 B Bechinger 1 1 ULP CNRS Chemistry 4 rue Blaise Pascal 67070 Strasbourg 2 Université Libre Campus Plaine


id: cord-015866-65zrbo1w
type: PROTEIN
entity:
  channel ionotropic GABA A and G receptor protein family GABA B The N methyl D aspartate NMDA receptors


id: cord-015866-65zrbo1w
type: PROTEIN
entity:
  K ATPases type IB soft transition metal translocating ATPases type IIA sarcoplasmic reticulum SR Ca 2 ATPases type IIB plasma membrane Ca 2 ATPases type IIC Na K ATPases


id: cord-015866-65zrbo1w
type: PROTEIN
entity:
  H K ATPases type IID eukaryotic Na ATPases type IIIA H ATPases type IIIB bacterial Mg 2 ATPases type IV lipid flippases


id: cord-015866-65zrbo1w
type: CHEMICAL
entity:
  light blue Methanobacterium thermoautotrophicum yellow Methanococcus jannaschii purple Synechocystis PCC6803


id: cord-015866-65zrbo1w
type: CHEMICAL
entity:
  Color blue N terminus red C terminus with approximate molecular dimensions The first and last b strands b1


id: cord-020712-l9cn0n99
type: PROTEIN
entity:
  Yoshimura C I ol 1985 3 Yoshimtiria c rrl 19x2 4 Kitdniilc c d 19x2 Chicken Germany 34 strains Mutants


id: cord-253366-03cg831z
type: ORG
entity:
  Peptide Membrane Interaction of Severe Acute Respiratory Syndrome Coronavirus Fusion Peptide Organization


id: cord-020714-h1fevqcw
type: PROTEIN
entity:
  neuraminidase inhibitor 2 deoxy 2 3 dehydro Ntrifluoracetylneuraminic acid FANA Influenza virus grown


id: cord-020714-h1fevqcw
type: DISEASE
entity:
  herpes simplex virus XII The virion polypeptides of type 1 strains Protein composition of coronavirus OC


id: cord-020714-h1fevqcw
type: DISEASE
entity:
  herpes simplex virus IV The site of glycosylation and accumulation of viral membrane proteins The polypeptides of influenza virus VII


id: cord-022354-aqtceqqo
type: PROTEIN
entity:
  VSV G protein Bergmann 1982 1983 Rose et al 1984 Adams and Rose 1985a b the influenza virus hemagglutinin protein Sveda


id: cord-022354-aqtceqqo
type: DNA
entity:
  leu leu lysjgly leu leu leu gly leu val val ile leu leu leu leu val cys leu pro cys leu leu gin phe val ser ser ser ile arg lys met μΆ his leu leu lys gly leu leu leu gly leu val val ile leu leu leu leu val cys arg pro cys leu leu gin phe val ser ser ser ile arg lys met T24 his leu leu lys gly leu leu leu gly leu val val ile leu leu leu leu val cysj i leu leu gin phe val ser ser ser ile arg lys met T18 his leu leu lys gly leu leu leu gly leu val val ile leu leu leu leu val ser ser se7Üe arg lys met T16 his leu leu lys gly leu leu leu gly leu val val ile leu


id: cord-022354-aqtceqqo
type: DNA
entity:
  T11 his leu leu lys gly leu leu leu gly leu val ser ser ser ile arg lys met T5 his leu leu lys gJ7leu ser ser ile arg lys


id: cord-022354-aqtceqqo
type: CHEMICAL
entity:
  Sindbis virus glycoproteins Defects in functional expression of an influenza virus hemagglutinin lacking the signal peptide sequences Analysis of the hemagglutinin glycoprotein


id: cord-279463-bli8hwda
type: CHEMICAL
entity:
  N linked glycosylation in the CAT protein After protease digestion in the presence of microsomal membranes


id: cord-287093-9mertwj7
type: DISEASE
entity:
  enteroviruses of the picornavirus supergroup and the flavivirus HCV 25 31 The membrane vesicles generated by picornaviruses are most heterogeneous and varied between subgroups and may be derived from membrane compartments that fragment


id: cord-276456-oa6hh7ky
type: PROTEIN
entity:
  SNARE soluble N ethylmaleimidesensitive factor attachment protein SNAP receptor and synaptotagmin complexes


id: cord-274101-vm9nh8lc
type: PROTEIN
entity:
  heparan c 2012 Institute of Food Technologists Vol 11 2012 r Comprehensive Reviews in Food Science and Food Safety 193 sulfate molecules


id: cord-274101-vm9nh8lc
type: CL
entity:
  monocytogenes E coli O157 H7 and Salmonella Typhimurium Sivarooban and others 2008 The activity of bacteriocins incorporated into polymeric materials in synergy with other conservation technologies has also been reported Films incorporated with enterocins A and B bacteriocins produced by Enterococcus faecium


id: cord-020788-a33vcapl
type: CELL_LINE
entity:
  polarized MDCK cells Madin Darby Canine Kidney Rodriguez Boulan and Sabatini 1978 spawned an extensive search in which chimeric and deletion analyses were applied to the problem of identifying the underlying apical and basolateral sorting signals reviewed in Caplan and Matlin 1989 These efforts to characterize sorting signals have generally involved the generation of chimeric or truncated contructs prepared from portions of apical and basolateral membrane proteins


id: cord-020788-a33vcapl
type: CELL_LINE
entity:
  polarized epithelial cell Madin Darby canine kidney Tissue specific sorting of the human LDL receptor


id: cord-265887-g5zhoyo9
type: WORK_OF_ART
entity:
  Research and Development on Therapeutic Agents and Vaccines for COVID 19 and Related Human Coronavirus Diseases Identification


id: cord-265887-g5zhoyo9
type: ORG
entity:
  Peptide Membrane Interaction of Severe Acute Respiratory Syndrome Coronavirus Fusion Peptide Structure Function and Evolution of Coronavirus


id: cord-272666-3uidpr79
type: PROTEIN
entity:
  coronavirus nonstructural proteins 3 and 4 Virology Mobility and Interactions of Coronavirus Nonstructural Protein 4 Severe Acute Respiratory Syndrome Coronavirus Nonstructural Proteins 3 4 and 6 Induce Double Membrane Vesicles Targeting Membrane Bound Viral RNA


id: cord-272666-3uidpr79
type: ORG
entity:
  Associated Nuclear Transport Machinery Limit Access of Pattern Recognition Receptors to Viral Replication Sites Ultrastructure


id: cord-272666-3uidpr79
type: ORG
entity:
  Zippered Endoplasmic Reticulum Membranes Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus


id: cord-269756-tid8a464
type: PROTEIN
entity:
  phospholipids 1 palmitoyl 2 hydroxy sn glycero 3 phosphocholine LPC 1 2 dipalmitoyl snglycero phosphatidylcholine DPPC 1 2 dipalmitoyl sn glycero 3 phospho 1


id: cord-269756-tid8a464
type: GGP
entity:
  POPA S 0 0 29 Those differences in the TMA orientation are likely due to distinct orienting forces that arise from the particular hydrogen bonding


id: cord-269756-tid8a464
type: ORG
entity:
  Membrane Surface Order An Electron Spin Resonance Study HIV gp41 Fusion Peptide Increases Membrane Ordering


id: cord-269756-tid8a464
type: ORG
entity:
  Pulsed Electron Paramagnetic Resonance of Spin Labels Investigation of Model Membrane Disruption Mechanism


id: cord-269756-tid8a464
type: ORG
entity:
  Kinetics and Activation Thermodynamics of Stalk and Pore Formation Differently Mechanistic Implications Conformation


id: cord-269756-tid8a464
type: CHEMICAL
entity:
  glycerol POPG 1 palmitoyl 2 oleoyl sn glycero 3 phospho L serine POPS 1 palmitoyl 2 oleoyl sn glycero 3 phosphate POPA


id: cord-319754-5isw53wl
type: DNA
entity:
  HCoV 229E fusion core Hepatitis C Virus Entry In Hepatitis C Virus From Molecular Virology to Antiviral Therapy How hepatitis C


id: cord-319754-5isw53wl
type: ORG
entity:
  Peptide Membrane Interaction of Severe Acute Respiratory Syndrome Coronavirus Fusion Peptide Target Membrane Cholesterol


id: cord-319754-5isw53wl
type: ORG
entity:
  The Major Cellular Sterol Regulatory Pathway Is Required for Andes Virus Infection Haploid Genetic Screen


id: cord-264996-og3sg0qw
type: DISEASE
entity:
  human immunodeficiency virus Induction of p38 mitogen activated protein kinase reduces early endosome autoantigen 1 EEA1 recruitment to phagosomal membranes Caveolin 3


id: cord-325915-dw989txm
type: DNA
entity:
  VSV G pseudotyped retroviral vector AC Fractogel EMD heparin S 61 66 Filtration UF DF AC SEC Fractogel EMD heparin S Sepharose CL 4B Retroviridae vector MoMLV


id: cord-325915-dw989txm
type: DISEASE
entity:
  abnormal cervical cytology A correlation with histological study The pH stability of the papilloma virus protein The removal of phages T1 and PP7 and poliovirus from fluids with hollow fiber


id: cord-323319-u5hfkjv8
type: WORK_OF_ART
entity:
  Cleaning and Disinfection for Community Facilities Interim Recommendations for U S 339 Community Facilities


id: cord-294842-aesiff1f
type: CHEMICAL
entity:
  N terminal amphipathic α helices a highly hydrophobic central core domain composed of four putative transmembrane segments


id: cord-314402-kjzkk51t
type: GGP
entity:
  STAR Singapore 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 Targeting non multiplying organisms


id: cord-330110-pamxy4av
type: CHEMICAL
entity:
  carboxylic acid 6 bromo 4 dimethylamino methyl 5hydroxy 1 methyl 2 phenylthio methyl ethyl ester monohydrochloride CAS


id: cord-314604-w61sqy17
type: ORG
entity:
  Loops that Mediate Protein Protein Interactions and Translation into Submicromolar Inhibitors Intramolecular


id: cord-314604-w61sqy17
type: WORK_OF_ART
entity:
  Helix Folding A Joint Experimental and Simulation Study Design of a Short Thermally Stable Helix Embedded in a Macrocycle


id: cord-300429-b0zev8zb
type: CHEMICAL
entity:
  N terminal cysteine residue of hedgehog proteins sonic Indian and desert in mammals It determines secretion of these proteins


id: cord-300429-b0zev8zb
type: DISEASE
entity:
  acute respiratory syndrome virus the fusion F protein of paramyxoviruses e g measles virus Env of retroviruses e g HIV 1 feline immunodeficiency virus FIV


id: cord-300429-b0zev8zb
type: CHEMICAL
entity:
  Sindbis virus glycoproteins S acylation of the hemagglutinin of influenza viruses mass spectrometry reveals site specific attachment of stearic acid


id: cord-300429-b0zev8zb
type: DISEASE
entity:
  human immunodeficiency virus type 1 transmembrane protein gp41 harbors lipid raft association determinants Bioorthogonal


id: cord-339172-210dwhgj
type: PROTEIN
entity:
  indocarbocyanine Cy3 conjugated donkey anti rabbit immunoglobulin Ig and Alexa Fluor 488 conjugated goat anti mouse Ig secondary antibodies


id: cord-346446-i7gpxcyo
type: PROTEIN
entity:
  beta poly L malate Natural and synthetic poly malic acid based derivates a family of versatile biopolymers for the design of drug nanocarriers Covalent nano delivery systems for selective imaging and treatment of brain tumors Specific inhibition of Physarum polycephalum DNA polymerase alpha primase


id: cord-356090-oj3d9ail
type: CELL_LINE
entity:
  HMMM model Fig 1C 30 31 33 Symmetric conventional full membranes were first constructed using CHARMM GUI 52


id: cord-356090-oj3d9ail
type: PROTEIN
entity:
  Plasma Membrane Membrane Cholesterol Modulates Oligomeric Status and Peptide Membrane Interaction of Severe Acute Respiratory Syndrome Coronavirus Fusion Peptide


id: cord-317430-uvx8si42
type: CELL_TYPE
entity:
  primary mouse bone marrow dendritic cells BMDCs B cells dendritic cells DCs macrophages MΦs natural killer NK cells


id: cord-004584-bcw90f5b
type: CELL_LINE
entity:
  G361 tumour cell lines Binder S Kolarova H Bajgar R Tomankova K Daskova A Deparment of Medical Biophysics Faculty of Medicine


id: cord-004584-bcw90f5b
type: DNA
entity:
  double helix Pietro Parisse 1 Matteo Castronovo 2 Bojana Lucic 3 Alessandro Vindigni 3 Giacinto Scoles 2 and Loredana Casalis 1 1 Sincrotrone Trieste S C p A Trieste Italy 2 Temple University Philadelphia USA 3 Protein DNA


id: cord-004584-bcw90f5b
type: PROTEIN
entity:
  voltage gated ion channels Zoltan Nusser Institute of Experimental Medicine Hungarian Academy of Sciences Budapest Hungary Voltage gated Na Nav channels


id: cord-004584-bcw90f5b
type: PROTEIN
entity:
  bacterial light harvesting complexes Katia Duquesne 1 Edward O Reilly 2 Cecile Blanchard 1 Alexandra Olaya Castro 2


id: cord-004584-bcw90f5b
type: PROTEIN
entity:
  helical membrane protein Jana Broecker Sebastian Fiedler Sandro Keller Molecular Biophysics University


id: cord-004584-bcw90f5b
type: WORK_OF_ART
entity:
  The diacylglycerolacyltransferase1 DGAT1 is an integral protein from the reticulum endoplasmic membrane that


id: cord-004584-bcw90f5b
type: ORG
entity:
  Department of Medical Physics and Informatics University of Szeged Hungary 2 Department of Experimental Physics University of Szeged Hungary


id: cord-004584-bcw90f5b
type: WORK_OF_ART
entity:
  Applied and Environmental Chemistry University of Szeged Hungary 5 Institute of Biophysics HAS Biological Research Center


id: cord-004584-bcw90f5b
type: ORG
entity:
  Ahmet Yildiz Department of Physics and Department of Molecular and Cell Biology University of California Berkeley CA


id: cord-313599-5j19stye
type: DISEASE
entity:
  influenza A H1N1 virus severe acute respiratory syndrome SARS virus and Escherichia coli 105 however further verify its feasibility by experiments is imperative None of these challenges


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  H1 A M Polyanichko 1 H Wieser 2 1 Faculty of Physics Saint Petersburg State University Russia 2 Dept


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  antitumor nonclassical platinum complexes O Vrana V Kohoutkova V Brabec Institute of Biophysics AS CR Královopolská 135 CZ 61265


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  CYP450 L S Goto 2 C O Hokka 1 J F Lima 2 O R Nascimento 2 A P U Araújo 2 1 Grupo de Engenharia Bioquímica UFSCar BR 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  Complex I A L Maniero 1 C Bergamini 2 M Bortolus 1 R Fato 2 S Leoni 2 G Lenaz 2 1 Università degli Studi di Padova Padova Italy 2 Università degli studi di Bologna Bologna Italy Complex I NADH Dehydrogenase


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  arXiv 0805 0696v1 S Soria 1 F Quercioli 3 R Mercatelli 3 F Bianco 2 I Cacciari 2 G Righini 2 1 Centro Studi e Ricerche E Fermi P Del Viminale 2 00184 Rome Italy 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  plague F1 capsular antigen A Soliakov 1 J R Harris 1 M R Hicks 2 A Rodger 2 R Woody 3 A Watkinson 4 J H Lakey 1 1 Cell


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  membrane proteins C V Kulkarni 3 O Ces 1 S Iwata 2 R H Templer 1 1 Chemical Biology Centre and Department of Chemistry Imperial College London United Kingdom 2 Division of Molecular


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  lambda bacteriophage epigenetic switch L Finzi Physics Department emory University 400 dowman Dr Atlanta GA 30322 USA


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  topoisomerase II activity H Seidel 1 T Klose 2 H Lilie 2 C G Hübner 1 1 Institute of Physics Ratzeburger Allee 160 23538 Lübeck Germany 2 Institute of Biochemistry and Biotechnology Kurt Mothes Str 3 06120 Halle Germany One essential element


id: cord-004534-jqm1hxps
type: DNA
entity:
  human MEF2D gene W Zhou 1 L Ying 2 1 Molecular Medicine National Heart and Lung Institute Imperial College London London SW7 2AZ UK 2 Chemical Biology


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  OmpF channel E Hajjar 1 A Kumar 1 M Winterhalter 2 P Ruggerone 1 M Ceccarelli 1 1 Department of Physics University of Cagliari Italy 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  protein N Maghelli 1 V Krstic 2 N Pavin 2 F Julicher 2 I Tolic Norrelykke 1 1 MPI CBG Dresden Germany 2 MPI PKS Dresden Germany


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  integrin αIIbβ3 M Rocco 1 C Rosano 1 J W Weisel 2 D Horita 3 R R Hantgan 3 1 Istituto Nazionale per la Ricerca sul Cancro IST Genova Italy 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  redox cofactor L Erokhova 1 P Kügler 2 P Pohl 1 1 Institute of Biophysics Johannes Kepler University Linz Austria 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  cation channels Y Sawada 1 M Murase 2 M Sokabe 1 1 Dept Physiol Nagoya Univ Grad Sch Med Nagoya Japan 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  Na K ATPase C H Chang 1 T Y Tsong 2 1 Institute of Physics National Chiao Tung university Physics Division National Center for Theoretical Sciences Hsinchu Taiwan 2 Institute of Physics Academy of Sciences Taipei 115 Taiwan Na K ATPase


id: cord-004534-jqm1hxps
type: CELL_TYPE
entity:
  permeabilized skeletal muscle fibres D S Ushakov D Ibanez Garcia T G West P M W French M A Ferenczi Imperial College London UK


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  extracellular matrix molecule hyaluronic acid modulates L type voltage dependent Ca2 channels E Dvoretskova 1 G Kochlamazashvili 2 O Bukalo 2 C Henneberger 3 D Rusakov 3 M Schachner 2 A Dityatev 1 1 Italian Institute of Technology Genova Italy 2


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  colicin translocon C L Johnson 1 A Solovyova 1 P Callow 2 S A Holt 3 L A Clifton 3 K Weiss 4 J H Lakey 1 1


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  human 3 phosphoglycerate kinase P Lallemand 1 J Rouhana 1 L Chaloin 1 B Roy 2 S Arold 3 T Barman 1 C Lionne 1 1 CPBS UMR 5236 4 bd Henri IV


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  Green Fluorescent Protein G Jung Biophysical Chemistry Saarland University 66123 Saarbruecken Germany Biotechnological design of the Green Fluorescent Protein GFP


id: cord-004534-jqm1hxps
type: PROTEIN
entity:
  J Strömqvist 1 S Johansson 1 Y Ohsugi 3 K Andersson 2 L Xu 1 M Kinjo 3 P Höglund 2 J Widengren 1 1 Experimental biomolecular Physics KTH Stockholm Sweden 2


id: cord-004534-jqm1hxps
type: GGP
entity:
  Alzheimer s disease Some diabetes drugs appear to decrease the cognitive decline associated with Alzheimer s


id: cord-004534-jqm1hxps
type: GGP
entity:
  human 3 phosphoglycerate kinase P Lallemand 1 J Rouhana 1 L Chaloin 1 B Roy 2 S Arold 3 T Barman 1 C Lionne 1 1


id: cord-004534-jqm1hxps
type: ORG
entity:
  Institute for Problems of Cryobiology and Cryomedicine National Academy of Sciences of Ukraine Kharkov Ukraine


id: cord-004534-jqm1hxps
type: ORG
entity:
  Physics Department University of Genoa Italy 2 Biochemical Sciences Department University of Florence Italy Short


id: cord-004534-jqm1hxps
type: ORG
entity:
  Molski Adam Mickiewicz University Laboratory for Dynamics of Physicochemical Processes Poznan Poland RNAzymes


id: cord-004534-jqm1hxps
type: ORG
entity:
  Department of Physics Faculty of Science Messina University Italy 2 Department of Physics Faculty of Science Perugia University Italy Important


id: cord-004534-jqm1hxps
type: ORG
entity:
  Chemistry University of Oxford Oxford U K 2 Department of Electronics Computer Science and Systems University of Bologna Bologna Italy Potassium


id: cord-004534-jqm1hxps
type: ORG
entity:
  Institute of Physics National Chiao Tung university Physics Division National Center for Theoretical Sciences Hsinchu


id: cord-004534-jqm1hxps
type: ORG
entity:
  Department of Physics University of Warwick U K 2 Department of Chemistry University of Warwick U K Information


id: cord-004534-jqm1hxps
type: ORG
entity:
  Biotechnology Jagiellonian University 2 Department of Pharmacodynamics Medical College Jagiellonian University


id: cord-004534-jqm1hxps
type: LAW
entity:
  A Isvoran 1 E Quiniou 2 C Craescu 2 L Mouawad 2 1 West University of Timisoara Department of Chemistry Pestalozzi


id: cord-004534-jqm1hxps
type: WORK_OF_ART
entity:
  A Martino D Crane I M Feavers B Bolgiano Division of Bacteriology National Institute for Biological Standards and Control Potters


id: cord-004534-jqm1hxps
type: CHEMICAL
entity:
  E Del Favero 1 G Di Fede 2 F Tagliavini 2 M Salmona 3 L Cantù 1 1 University of Milan Segrate Italy 2 Carlo


id: cord-004534-jqm1hxps
type: CHEMICAL
entity:
  L D Alfonso 1 M Collini 1 M Caccia 1 G Tallarida 2 S Caprioli 2 G Chirico 1 1 Dipartimento di Fisica Università di Milano Bicocca Italy 2 Laboratorio


id: cord-004534-jqm1hxps
type: CHEMICAL
entity:
  1 D Magatti 1 B Cardinali 2 A Profumo 2 M Rocco 2 1 Dipartimento di Fisica e Matematica Università dell Insubria


id: cord-001835-0s7ok4uw
type: PROTEIN
entity:
  villin headpiece miniprotein Stanislaw Oldziej 1 Wioletta _ Zmudzi nska 1 Anna Hałabis 1 1 The C terminal subdomain


id: cord-001835-0s7ok4uw
type: PROTEIN
entity:
  human glucose 6 phosphate dehydrogenase G6PD Nurriza Ab Latif 1 2 Paul Engel 1 1 Conway Institute Univerversity College Dublin 2 Faculty of Biosciences and Medical Engineering Universiti Teknologi Malaysia Human glucose 6 phosphate dehydrogenase G6PD


id: cord-001835-0s7ok4uw
type: PROTEIN
entity:
  coagulation factor VIIa Jais R Bjelke 1 Gorm Andersen 1 Henrik Østergaard 1 Laust B Johnsen 1 Anette A Pedersen 1 Tina H Glue 1 1


id: cord-001835-0s7ok4uw
type: PROTEIN
entity:
  enoyl CoA hydratase family Fernandes 1 Teresa Sorbo 2 Ivan Duka 2 Lia Christina Appold 3 Marianne Ilbert 4 Fabian Kiessling 3 CNRS UMR 7281 5 UCiBio REQUIMTE


id: cord-001835-0s7ok4uw
type: GGP
entity:
  Biryukova 1 Elizaveta Kostanova 1 Alexey Kononikhin 0 Anna Bugrova 1 Evgeny Nikolaev 0 Mark Rosenfeld 1 1 N M


id: cord-001835-0s7ok4uw
type: ORG
entity:
  School of Chemistry National University of Ireland Galway 2 School of Biochemistry and Immunology Trinity College


id: cord-001835-0s7ok4uw
type: WORK_OF_ART
entity:
  Destabilizing the Transient Helical Conformation of Islet Amyloid Polypeptide Hastens Peptide Self Assembly and Potentiates Cytotoxicity Carole Anne de Carufel 1


id: cord-001835-0s7ok4uw
type: EVENT
entity:
  Physical and Engineering Biology Yale University 3 Mechanical Engineering and Materials Science Yale University 4 Applied Physics Yale University


id: cord-001835-0s7ok4uw
type: ORG
entity:
  Department of Biology Stanford University 2 Department of Pediatrics Stanford University 3 Department of Pharmacology University of California San Diego 4 Department of Pediatrics Emory University 5 Institute for Biomedical Sciences


id: cord-001835-0s7ok4uw
type: ORG
entity:
  Graduate School of Science and Engineering Ibaraki University 3 Department of Life Science Graduate School of Life Science University of Hyogo 4


id: cord-001835-0s7ok4uw
type: ORG
entity:
  The New York Structural Biology Center 5 Department of Biochemistry Faculty of Medicine University of Montreal


id: cord-001835-0s7ok4uw
type: ORG
entity:
  University of Southern California Keck School of Medicine 2 Developing a Technique to Detect Deamidated Proteins


id: cord-001835-0s7ok4uw
type: ORG
entity:
  the Ethical Committee for Animal Experimentation from Center of Health and Science of the Federal University of Rio de Janeiro


id: cord-001835-0s7ok4uw
type: ORG
entity:
  1 National Autonomous University of Mexico Faculty of Medicine 2 National Autonomous University of Mexico Faculty of Chemistry 3


id: cord-001835-0s7ok4uw
type: WORK_OF_ART
entity:
  Deartment of Biology Wilfrid Laurier University 2 Department of Biology University of Waterloo Chloroplast


id: cord-001835-0s7ok4uw
type: ORG
entity:
  University of Greenwich Faculty of Engineering and Sciene 2 University of Greenwich Centre of Sports Science and Human Performance


id: cord-001835-0s7ok4uw
type: CHEMICAL
entity:
  N terminal recognition element In addition expressed protein ligation is being used to incorporate backbone modifications such as the thioamide


id: cord-001835-0s7ok4uw
type: CHEMICAL
entity:
  N terminal catalytic module 2 This module shows the capacity of recognize the GlcNAc MurNAc L Ala D isoGln muropeptide GMDP


id: cord-001835-0s7ok4uw
type: DISEASE
entity:
  acute myeloid leukemia mutations Daniela Marasco 1 Concetta Di Natale 1 Valentina Punzo 1 Domenico Riccardi 1 Pasqualina Scognamiglio 1 Roberta Cascella 2 Cristina Cecchi 2 Fabrizio Chiti 2 Marilisa Leone


id: cord-001835-0s7ok4uw
type: DISEASE
entity:
  human immunodeficiency virus type 1 subtype C based on Envelope V3 sequences Available http istree bioprotection org Signal processing based Bioinformatics methods


# bib

id: cord-000884-zq8kqf6h
author: Shen, Hsin-Hui
date: 2013-01-14
txt: ./txt/cord-000884-zq8kqf6h.txt
cache: ./cache/cord-000884-zq8kqf6h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565336/
doi: 10.3390/ijms14011589
summary:
  This review will discuss the reconstitution of membrane protein activities in four different types of model membrane—monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. To simplify cell membrane systems, model membranes such as monolayers, bilayers, liposomes and nanodiscs have been developed, enabling detailed investigation of membrane protein structure in lipid membranes. There are a number of approaches used to create a model membrane in order to mimic properties of the native cell membrane, and we will review these various approaches for reconstituting membrane proteins into different types of model membrane-monolayers [5] , supported planar lipid bilayer [6] and liposomes [7] as shown in Figure 1A -C. By using this approach, it appears that both PLA2 and PLC are active at the monolayer model membrane, indicating that the kinetics of phospholipid hydrolysis at the air-water interface can be monitored by biophysical characterization techniques in situ such as PM-IRRAS and infrared reflection adsorption spectroscopy [22] .

title:
  Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities

abstract:
  The function of any given biological membrane is determined largely by the specific set of integral membrane proteins embedded in it, and the peripheral membrane proteins attached to the membrane surface. The activity of these proteins, in turn, can be modulated by the phospholipid composition of the membrane. The reconstitution of membrane proteins into a model membrane allows investigation of individual features and activities of a given cell membrane component. However, the activity of membrane proteins is often difficult to sustain following reconstitution, since the composition of the model phospholipid bilayer differs from that of the native cell membrane. This review will discuss the reconstitution of membrane protein activities in four different types of model membrane—monolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. Variation in the surrounding model environments for these four different types of membrane layer can affect the three-dimensional structure of reconstituted proteins and may possibly lead to loss of the proteins activity. We also discuss examples where the same membrane proteins have been successfully reconstituted into two or more model membrane systems with comparison of the observed activity in each system. Understanding of the behavioral changes for proteins in model membrane systems after membrane reconstitution is often a prerequisite to protein research. It is essential to find better solutions for retaining membrane protein activities for measurement and characterization in vitro.


id: cord-001835-0s7ok4uw
title: Abstracts of the 29th Annual Symposium of The Protein Society
author: nan
date: 2015-10-01
txt: ./txt/cord-001835-0s7ok4uw.txt
cache: ./cache/cord-001835-0s7ok4uw.txt
extension: .txt
mime: text/plain
url: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.2823
doi: 10.1002/pro.2823
abstract: nan
summary:
  Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues.


id: cord-004584-bcw90f5b
title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary
author: nan
date: 2011-08-06
txt: ./txt/cord-004584-bcw90f5b.txt
cache: ./cache/cord-004584-bcw90f5b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080017/
doi: 10.1007/s00249-011-0734-z
abstract: nan
summary:
  Our goals are two-fold: (1) to monitor conformational changes in each domain upon its binding to specific ligands and then to correlate the observed changes with structural differences between the CRDs and (2) to investigate the interaction between the CRDs and lipid model membranes. Cholesterol-assisted lipid and protein interactions such as the integration into lipid nanodomains are considered to play a functional part in a whole range of membrane-associated processes, but their direct and non-invasive observation in living cells is impeded by the resolution limit of [200nm of a conventional far-field optical microscope. Therefore, to investigate the dynamic and complex membrane lateral organization in living cells, we have developed an original approach based on molecule diffusion measurements performed by fluorescence correlation spectroscopy at different spatial scales (spot variable FCS, svFCS) (1).


id: cord-006556-hmzoxqu3
title: Extracorporeal Life Support: Four Decades and Counting
author: Alibrahim, Omar S.
date: 2017-04-12
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102020/
doi: 10.1007/s40140-017-0210-0
abstract:
  Extracorporeal membrane oxygenation (ECMO) or extracorporeal life support (ECLS) is a form of heart lung bypass that is used to support neonates, pediatrics, and adult patients with cardiorespiratory failure for days or weeks till organ recovery or transplantation. Venoarterial (VA) and venovenous (VV) ECLS are the most common modes of support. ECLS circuit components and monitoring have been evolving over the last 40 years. The technology is safer, simpler, and more durable with fewer complications. The use of neonatal respiratory ECLS use has been declining over the last two decades, while adult respiratory ECLS is growing especially since the H1N1 influenza pandemic in 2009. This review provides an overview of ECLS evolution over the last four decades, its use in neonatal, pediatric and adults, description of basic principles, circuit components, complications, and outcomes as well as a quick look into the future.


id: cord-006947-nrzjedhi
title: Nano- and microparticles at fluid and biological interfaces
author: Dasgupta, S
date: 2017-09-20
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104866/
doi: 10.1088/1361-648x/aa7933
abstract:
  Systems with interfaces are abundant in both technological applications and biology. While a fluid interface separates two fluids, membranes separate the inside of vesicles from the outside, the interior of biological cells from the environment, and compartmentalize cells into organelles. The physical properties of interfaces are characterized by interface tension, those of membranes are characterized by bending and stretching elasticity. Amphiphilic molecules like surfactants that are added to a system with two immiscible fluids decrease the interface tension and induce a bending rigidity. Lipid bilayer membranes of vesicles can be stretched or compressed by osmotic pressure; in biological cells, also the presence of a cytoskeleton can induce membrane tension. If the thickness of the interface or the membrane is small compared with its lateral extension, both can be described using two-dimensional mathematical surfaces embedded in three-dimensional space. We review recent work on the interaction of particles with interfaces and membranes. This can be micrometer-sized particles at interfaces that stabilise emulsions or form colloidosomes, as well as typically nanometer-sized particles at membranes, such as viruses, parasites, and engineered drug delivery systems. In both cases, we first discuss the interaction of single particles with interfaces and membranes, e.g. particles in external fields, non-spherical particles, and particles at curved interfaces, followed by interface-mediated interaction between two particles, many-particle interactions, interface and membrane curvature-induced phenomena, and applications.


id: cord-008480-p41oae8e
title: Characterization of aminopeptidase N from Torpedo marmorata kidney
author: O''Callaghan, Barbara
date: 2004-11-12
txt: ./txt/cord-008480-p41oae8e.txt
cache: ./cache/cord-008480-p41oae8e.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131328/
doi: 10.1016/s0248-4900(94)80003-0
summary:
  Depending on solubilization conditions, both the antigen and peptidase activity were recovered either as a broad peak with a sedimentation coefficient of 18S (2% CHAPS) or as a single peak of 7.8S (1% CHAPS plus 0.2 % C(12)E(9)), showing that Torpedo aminopeptidase N behaves as an oligomer stabilized by hydrophobic interactions, easily converted into a 160 kDa monomer. The antigen is highly concentrated in the apical membrane of proximal tubule epithelial cells (600 gold particles/μm(2) of brush border membrane) whereas no labeling could be detected in other cell types or in other membranes of the same cells (basolatéral membranes, vacuoles or vesicles). Hybrids were selected in hypoxanthine, aminopterin and thymidine medium and superuatants from the culture wefts containing hybrid cells were tested for the presence of antibodies binding to the apical membrane of tubular epithelial cells on Torpedo kidney frozen sections.

abstract:
  A major antigen of the brush border membrane of Torpedo marmorata kidney was identified and purified by immunoprecipitation. The sequence of its 18 N terminal amino acids was determined and found to be very similar to that of mammalian aminopeptidase N (EC 3.4.11.2). Indeed aminopeptidase N activity was efficiently immunoprecipitated by monoclonal antibody 180K1. The purified antigen gives a broad band at 180 kDa after SDS-gel electrophoresis, which, after treatment by endoglycosidase F, is converted to a thinner band at 140 kDa. This antigen is therefore heavily glycosylated. Depending on solubilization conditions, both the antigen and peptidase activity were recovered either as a broad peak with a sedimentation coefficient of 18S (2% CHAPS) or as a single peak of 7.8S (1% CHAPS plus 0.2 % C(12)E(9)), showing that Torpedo aminopeptidase N behaves as an oligomer stabilized by hydrophobic interactions, easily converted into a 160 kDa monomer. The antigen is highly concentrated in the apical membrane of proximal tubule epithelial cells (600 gold particles/μm(2) of brush border membrane) whereas no labeling could be detected in other cell types or in other membranes of the same cells (basolatéral membranes, vacuoles or vesicles). Monoclonal antibodies prepared here will be useful tools for further functional and structural studies of Torpedo kidney aminopeptidase N.


id: cord-009371-ub4p4ngr
author: Mollenhauer, Hilton H.
date: 1990-05-07
txt: ./txt/cord-009371-ub4p4ngr.txt
cache: ./cache/cord-009371-ub4p4ngr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148783/
doi: 10.1016/0304-4157(90)90008-z
title:
  Alteration of intracellular traffic by monensin; mechanism, specificity and relationship to toxicity

abstract:
  Monensin, a monovalent ion-selective ionophore, facilitates the transmembrane exchange of principally sodium ions for protons. The outer surface of the ionophore-ion comples is composed largely of nonpolar hydrocarbon, which imparts a high solubility to the complexes in nonpolar solvents. In biological systems, these complexes are freely soluble in the lipid components of membranes and, presumably, diffuse or shuttle through the membranes from one aqueous membrane interface to the other. The net effect for monensin is a trans-membrane exchange of sodium ions for protons. However, the interaction of an ionophore with biological membranes, and its ionophoric expression, is highly dependent on the biochemical configuration of the membrane itself. One apparent consequence of this exchange is the neutralization of acidic intracellular compartments such as the trans Golgi apparatus cisternae and associated elements, lysosomes, and certain endosomes. This is accompanied by a disruption of trans Golgi apparatus cisternae and of lysosome and acidic endosome function. At the same time, Golgi apparatus cisternae appear to swell, presumably due to osmotic uptake of water resulting from the inward movement of ions. Monensin effects on Golgi apparatus are observed in cells from a wide range of plant and animal species. The action of monensin is most often exerted on the trans half of the stacked cisternae, often near the point of exit of secretory vesicles at the trans face of the stacked cisternae, or, especially at low monensin concentrations or short exposure times, near the middle of the stacked cisternae. The effects of monensin are quite rapid in both animal and plant cells; i.e., changes in Golgi apparatus may be observed after only 2–5 min of exposure. It is implicit in these observations that the uptake of osmotically active cations is accompanied by a concomitant efflux of H(+) and that a net influx of protons would be required to sustain the ionic exchange long enough to account for the swelling of cisternae observed in electron micrographs. In the Golgi apparatus, late processing events such as terminal glycosylation and proteolytic cleavages are most susceptible to inhibition by monensin. Yet, many incompletely processed molecules may still be secreted via yet poorly understood mechanisms that appear to bypass the Golgi apparatus. In endocytosis, monensin does not prevent internalization. However, intracellular degradation of internalized ligands may be prevented. It is becoming clear that endocytosis involves both acidic and non-acidic compartments and that monensin inhibits those processes that normally occur in acidic compartments. Thus, monensin, which is capable of collapsing Na(+) and H(+) gradients, has gained wide-spread acceptance as a tool for studying Golgi apparatus function and for localizing and identifying the molecular pathways of subcellular vesicular traffic involving acid compartments. Among its advantages are the low concentrations at which inhibitions are produced (0.01–1.0 μM), a minimum of troublesome side effects (e.g., little or no change of protein synthesis or ATP levels) and a reversible action. Because the affinity of monensin for Na(+) is ten times that for K(+), its nearest competitor, monensin mediates primarily a Na(+)-H(+) exchange. Monensin has little tendency to bind calcium. Not only is monensin of importance as an experimental tool, it is of great commercial value as a coccidiostat for poultry and to promote more efficient utilization of feed in cattle. The mechanisms by which monensin interact with coccidia and rumen microflora to achieved these benefits are reasonably well documented. However, the interactions between monensin and the tissues of the host animal are not well understood although the severe toxicological manifestations of monensin poisoning are well known. Equine species are particularly susceptible to monensin poisoning, and a common effect of monensin poisoning is vacuolization and/or swelling of mitochondria in striated muscle. Other pathological injuries to striated muscle, spleen, lung, liver and kidney also have been noted. A consistent observation is cardiac myocyte degeneration as well as vacuolization. Differences in cellular response resulting from exposure to monensin (i.e., Golgi apparatus swelling in cultured cells, isolated tissues, and plants vs.mitochondrial swelling in animals fed monensin) suggest that myocardial damage is due either to a monensin metabolite or is a secondary response to some other derivation. However, as pointed out by Bergen and Bates [26], the underlying mode of action of ionophores is on transmembrane ion fluxes which dissipate cation and proton gradients. Consequently, some or all of the observed monensin effects in vivo in animals could be secondary phenomena caused by disruption of normal membrane physiology resulting from altered ion fluxes.


id: cord-011888-3mvzkff6
author: Moore, John P.
date: 2020-06-15
txt: ./txt/cord-011888-3mvzkff6.txt
cache: ./cache/cord-011888-3mvzkff6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7361684/
doi: 10.3390/polym12061348
summary:
  title: Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes Ultrafiltration and dialysis were performed using bovine serum albumin (BSA), lysozyme, and urea to analyze various properties of each hollow fiber membrane type. Utilizing the procedure from Moore et al., OTO-CNMs Form I and Form II were synthesized and used in conjunction with cellulose triacetate (CTA) from Acros Organics (Fair Lawn, NJ, USA), N-methyl pyrrolidone (NMP) from VWR (Radnor, PA, USA), and deionized water to create novel membranes for filtration [21] . In this study on the implementation of two derivatives of cellulose nanomaterials into hollow fiber membranes for ultrafiltration and dialysis, OTO-CNM Form I and Form II mixed-matrix membranes have been quantitatively evaluated for the first time by determining model molecule selectivity (BSA, urea, and lysozyme), as well as transport rates (flux and diffusion rates).

title:
  Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterial Ultrafiltration and Dialysis Mixed-Matrix Hollow Fiber Membranes

abstract:
  Recent exploration of cellulose nanomaterials has resulted in the creation of Oxone(®)-Mediated TEMPO-Oxidized Cellulose Nanomaterials (OTO-CNMs). These materials, when incorporated into a polymer matrix, have properties showing increased flux, decreased membrane resistance, and improved clearance, making them an ideal material for dialysis. This study is the first to focus on the implementation of OTO-CNMs into hollow fiber membranes and a comparison of these membranes for ultrafiltration and dialysis. Ultrafiltration and dialysis were performed using bovine serum albumin (BSA), lysozyme, and urea to analyze various properties of each hollow fiber membrane type. The results presented in this study provide the first quantitative evaluation of the clearance and sieving characteristics of Oxone(®)-Mediated TEMPO-Oxidized Cellulose-Nanomaterial-doped cellulose triacetate mixed-matrix hemodialyzers. While the cellulose nanomaterials increased flux (10–30%) in ultrafiltration mode, this was offset by increased removal of albumin. However, in dialysis mode, these materials drastically increased the mass transfer of components (50–100%), which could lead to significantly lower dialysis times for patients. This change in the performance between the two different modes is most likely due to the increased porosity of the cellulose nanomaterials.


id: cord-013223-f43hks44
title: Emerging role of bacterial extracellular vesicles in cancer
author: Chronopoulos, Antonios
date: 2020-10-15
txt: ./txt/cord-013223-f43hks44.txt
cache: ./cache/cord-013223-f43hks44.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7557313/
doi: 10.1038/s41388-020-01509-3
summary:
  The increasing appreciation that microbiota-derived EV can enter the systemic circulation and be detected in human body fluids is likely to stimulate completely new areas of investigation in microbiome research, biomarkers and liquid biopsies, BEV-based therapeutics, onco-immunology, as well as fundamental microbial EV biology. In addition to potentially modulating the innate immune response via or more cytosolic DNA sensors, the possibility that pathogenic BEV-derived DNA can be transferred and detected in the nucleus of non-phagocytic cells (e.g. epithelial cells) [30] , raises the intriguing possibility that bacterial genetic material could be transferred to human somatic cells and integrated into the host genome. BEVs released by bacteria in the gut lumen can cross the epithelial barrier to gain access into the underlying submucosa enabling them to interact with various resident immune cell populations (dendritic cells, neutrophils and macrophages) as well as potentially disseminate more widely around the body via the systemic or lymphatic circulation to reach distant tissues and organs or even the brain (Fig. 2) .

abstract:
  Shedding of microbial extracellular vesicles constitutes a universal mechanism for inter-kingdom and intra-kingdom communication that is conserved among prokaryotic and eukaryotic microbes. In this review we delineate fundamental aspects of bacterial extracellular vesicles (BEVs) including their biogenesis, cargo composition, and interactions with host cells. We critically examine the evidence that BEVs from the host gut microbiome can enter the circulatory system to disseminate to distant organs and tissues. The potential involvement of BEVs in carcinogenesis is evaluated and future research ideas explored. We further discuss the potential of BEVs in microbiome-based liquid biopsies for cancer diagnostics and bioengineering strategies for cancer therapy.


id: cord-014685-ihh30q6f
title: Posters P788 - P999
author: nan
date: 2005-09-21
txt: ./txt/cord-014685-ihh30q6f.txt
cache: ./cache/cord-014685-ihh30q6f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080055/
doi: 10.1007/s00249-005-0504-x
abstract: nan
summary:
  This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes.


id: cord-015866-65zrbo1w
title: Membrane Transport
author: Wardhan, Rashmi
date: 2018-01-12
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119958/
doi: 10.1007/978-981-10-7101-0_6
abstract:
  Every living cell has to exchange molecules across the membrane for cellular functions. The hydrophobic or lipophilic molecules do not require energy for crossing the membrane. They can diffuse freely from higher to lower concentration till equilibrium is established. This process is called passive transport or diffusion.


id: cord-016938-pk76snuy
title: Collagen Fabrication for the Cell-based Implants in Regenerative Medicine
author: Suh, Hwal (Matthew)
date: 2008
txt: ./txt/cord-016938-pk76snuy.txt
cache: ./cache/cord-016938-pk76snuy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121374/
doi: 10.1007/978-3-540-75409-1_8
summary:
  As atelocollagen has no telopeptides that integrate with other atelocollagen molecules, basic technology to produce intramolecular and intermolecular bonds for construction of the extracellular matrix with adequate mechanical properties required by tissue where the artificial cell-based implant is delivered is the recrosslinking method using chemical reagents or physical dynamics. Collagen can be fabricated into various forms of gel, fiber, membrane with or without pores, and it can even be grafted onto the non-viable metal, ceramic and synthetic biomaterials to introduce biological layer on surface. To produce an artificial skin, autologous dermal fibroblasts of rat were seeded into the EDC crosslinked porous collagen-laminin membrane and cultured in minimum essential medium (MEM) for 3 days to provide the cell-niche adaptation period. Although collagen based gel is favorable to fabricate cell conductive substitute, weak mechanical property is a barrier for application in the physiological stress bearing tissues, and, to resolve this problem, hybridization of collagen with polymeric biomaterials has been suggested.

abstract:
  Though transplantation of cells, tissue or organ has been regarded as an ideal approach, scarcity of donor is a practical barrier in clinics. Current progresses in cell engineering has opened a new era, providing tools for host-regeneration by implanting manipulated cells in forms of cell therapy, which includes delivery of single cells or multicellular structural support of hybridized cells, as a representative individualized treatment method. This chapter mainly concerns on the cellbased implant made of cells and collagen, the main structural protein in extracellular matrix in mammalian tissue, as it has been regarded as a promising method for manufacturing a biologically mimicked artificial tissues.


id: cord-017566-dvxrwzqw
title: Viral Proteins that Enhance Membrane Permeability
author: González, María Eugenia
date: 2005
txt: ./txt/cord-017566-dvxrwzqw.txt
cache: ./cache/cord-017566-dvxrwzqw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122156/
doi: 10.1007/0-387-28146-0_6
abstract: nan
summary:
  During the infection of cells by animal viruses, membrane permeability is modified at two different steps of the virus life cycle (Carrasco, 1995) (Figure 6 .1). The viral molecules involved are components of virions: glycoproteins when enveloped particles are analyzed or, still unidentified, domains of the structural proteins in the case of naked viruses. At late times of infection, when there is active translation of late viral mRNAs, the plasma membrane becomes permeable to small molecules and ions (Carrasco, 1978) ( Figure 6 .1). Different viral molecules may be responsible for this late enhancement of membrane permeability, including viroporins (Gonzalez and Carrasco, 2003) , glycoproteins, and even proteases (Chang et al., 1999; Blanco et al., 2003) . Entry of enveloped animal viruses leads to early membrane permeabilization, which is mediated by the formation of the two pores (fusion and TM) formed by viral fusion glycoproteins.


id: cord-020712-l9cn0n99
title: Chapter 9 Fusion of Viral Envelopes with Cellular Membranes
author: Ohnishi, Shun-Ichi
date: 2008-05-30
txt: ./txt/cord-020712-l9cn0n99.txt
cache: ./cache/cord-020712-l9cn0n99.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146812/
doi: 10.1016/s0070-2161(08)60137-9
summary:
  Residues 80-100 in El and residues 100-131 in G, which have sequence homology among the strains, may be such stretches though not strongly hydrophobic (Table 262 SHUN-ICHI OHNlSHl and the putative fusogenic segment should be able to interact with the target membrane, inducing some disturbance eventually leading to fusion (Fig. Ib) . Presence of receptors for the amino-terminal segments in target membranes has been suggested from studies on inhibition of virus replication by small peptides with amino acid sequences similar to that of the viral amino terminus (Richardson et al., 1980; Richardson and Choppin, 1983) . Why is a specific amino acid sequence of F glycoprotein required for the membrane fusion reaction between envelope of HVJ (Sendai virus) and target cell membranes? pH-Dependent membrane fusion activity of a synthetic twenty amino acid peptide with the same sequence as that of the hydrophobic segment in influenza virus hemagglutinin

abstract:
  This chapter reviews some characteristic features of membrane fusion activity for each virus and discusses the mechanisms of membrane fusion, especially low pH-induced membrane fusion. It concentrates on the interaction of the hydrophobic segment with the target cell membrane lipid bilayer and suggests the entrance of the segment into the lipid bilayer hydrophobic core as a key step in fusion. The envelope is a lipid bilayer membrane with the virus specific glycoproteins spanning it. The bilayer originates from the host cell membrane and has a lipid composition and transbilayer distribution quite similar to the host's. The viral glycoproteins have the functions of binding to the target cell surface and fusion with the cell membranes. The two functions are carried by a single glycoprotein in influenza virus (HA), vesicular stomatitis virus (VSV) G glycoprotein, and Semliki Forest virus SFV E glycoprotein. In Sendai virus (HVJ), the functions are carried by separate glycoproteins, hemagglutinin-neuraminidase (HN) for binding and fusion glycoprotein (F) for fusion. When viruses encounter target cells, they first bind to the cell surface through an interaction of the viral glycoprotein with receptors.


id: cord-020714-h1fevqcw
title: Membrane Glycoproteins of Enveloped Viruses
author: Compans, Richard W.
date: 2008-05-30
txt: ./txt/cord-020714-h1fevqcw.txt
cache: ./cache/cord-020714-h1fevqcw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146817/
doi: 10.1016/s0070-2161(08)60750-9
summary:
  Other advantages of enveloped viruses in studies of membrane structure and biogenesis include the ease of biosynthetic labeling of viruses grown in cell culture with specific radioactive precursors and the availability of mutants in defined gene products, some of which are proving to be useful in the analysis of viral membrane assembly. Apart from minor differences in carbohydrates of glycoproteins, virion proteins are indistinguishable when the virus is propagated in a variety of cells; therefore there appears to be little or no determining influence of viral proteins on the composition of the lipid bilayer. Based upon the estimated carbohydrate content (12,000 daltons) of the HA glycoprotein obtained by Laver (1971) and Schwarz and Klenk (1974) and the size estimates of the type I and I1 glycopeptides of influenza virus grown in MDBK cells, it was estimated that HA, contains a single type I glycopeptide whereas HA, possesses two type I and one or two type I1 oligosaccharide side-chains for the WSN strain (Nakamura and Com pans, 1978b) .

abstract:
  This chapter focuses on the recent information of the glycoprotein components of enveloped viruses and points out specific findings on viral envelopes. Although enveloped viruses of different major groups vary in size and shape, as well as in the molecular weight of their structural polypeptides, there are general similarities in the types of polypeptide components present in virions. The types of structural components found in viral membranes are summarized briefly in the chapter. All the enveloped viruses studied to date possess one or more glycoprotein species and lipid as a major structural component. The presence of carbohydrate covalently linked to proteins is demonstrated by the incorporation of a radioactive precursor, such as glucosamine or fucose, into viral polypeptides, which is resolved by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. Enveloped viruses share many common features in the organization of their structural components, as indicated by several approaches, including electron microscopy, surface-labeling, and proteolytic digestion experiments, and the isolation of subviral components. The chapter summarizes the detailed structure of the glycoproteins of four virus groups: (1) influenza virus glycoproteins, (2) rhabdovirus G protein, (3) togavirus glycoprotein, and (4) paramyxovirus glycoproteins The information obtained includes the size and shape of viral glycoproteins, the number of polypeptide chains in the complete glycoprotein structure, and compositional data on the polypeptide and oligosaccharide portions of the molecules.


id: cord-020788-a33vcapl
title: Signals and Mechanisms of Sorting in Epithelial Polarity
author: Gottardi, Cara J.
date: 2008-05-22
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147917/
doi: 10.1016/s1569-2558(08)60020-x
abstract:
  This chapter discusses epithelial-membrane polarity, sorting pathways in polarized cells, and the sorting-signal paradigm. Polarized epithelial cells have long captured the attention of cell biologists and cell physiologists. At the electron-microscopic level, one of the most apparent and fundamental features of this cell type is its polarized organization of intracellular organelles and its structurally and compositionally distinct lumenal (apical) and serosal (basolateral) plasma-membrane domains. The polarized epithelial phenotype is an absolute necessity for organ-system function. In the most general sense, these cells organize to form a continuous, single layer of cells, or epithelium, which serves as a semi-permeable barrier between apposing and biologically distinct compartments. Within the tubules of the nephron, these cells orchestrate complex ion-transporting processes that ultimately control the overall fluid balance of the organism. At the surface of the gastrointestinal tract, specialized versions of this cell type control the digestion, absorption, and immuno-protection of the organism.


id: cord-022504-tk7v4hoj
title: Environmental and safety issues with nanoparticles
author: nan
date: 2012-03-16
txt: ./txt/cord-022504-tk7v4hoj.txt
cache: ./cache/cord-022504-tk7v4hoj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158170/
doi: 10.1016/b978-0-444-56336-1.50007-2
abstract: nan
summary:
  During the process, large volumes of ultrapure water are consumed to clean the surface of the wafer, which generates large quantity of CMP wastewater typically having high solid content resulting from slurry abrasive particles of SiO 2 , Al 2 O 3 , or CeO 2 , depending on the nature of the CMP application. 7.2.6.2 Industrial processes with cleanrooms Cleanrooms and associated controlled environments (e.g., in the case of an ISO Class 3 cleanroom, the maximum permissible airborne particle concentration is less than 10 3 particles/m 3 for particles with the size of 0.1 m or larger, while the airborne particle concentration in ordinary indoor environments is on the order of 10 9 particles/m 3 or higher) are usually adopted to avoid particle contamination in industrial processes where precision products such as engineered nanoparticles, semiconductors, and other electronic or optical devices are fabricated because the deposition of particles onto product surfaces causes their yield reduction and quality deterioration.


id: cord-022538-1g9kmpdi
title: ENVIRONMENTAL AND SAFETY ISSUES WITH NANOPARTICLES
author: Makino, Hisao
date: 2008-05-20
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158284/
doi: 10.1016/b978-044453122-3.50010-6
abstract:
  This chapter evaluates the relationship between nanoparticles and the environment, and describes the trouble caused by nanoparticles as well as the safety issues. The relationship between nanoparticles and the environment is clarified from the viewpoint of the kind of influence nanoparticles generated either artificially or naturally have on the environment, such as in atmosphere, groundwater, wastewaters, and exhaust gases. Indoor nanoparticles originate from the several sources such as products of chemical reactions, nonvolatile residues (NVRs) of liquid droplets, printers/photocopiers, combustion, bioaerosols, and infiltration of outdoor air. The influence of nanoparticles on the indoor environment is discussed in the chapter. It describes the sources of nanoparticle generation in general industrial processes such as grinding processes, and in cleanroom or controlled environment industrial processes, such as exhaled air, ionizers, and haze by chemical reaction on solid surfaces. The chapter discusses safety issues related to nanoparticles such as possibility of dust explosion, health risks and biological effects of nanoparticle materials such as carbon nanotubes, fullerenes, nanosized metal oxides, and carbon black. The chapter also discusses methods for removing nanoparticles from gas and liquid as technology to control the influence of nanoparticles on the environment.


id: cord-023200-3caevjvh
title: Membranotropic peptides mediating viral entry
author: Falanga, Annarita
date: 2018-02-13
txt: ./txt/cord-023200-3caevjvh.txt
cache: ./cache/cord-023200-3caevjvh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167733/
doi: 10.1002/pep2.24040
summary:
  The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. [3, 4] The molecular details of the interactions at the interface of virus and cell surfaces are quite complex and highly variable, but there is a common idea that only a limited number of pathways allowing viruses to reach the sites of penetration exist, with enveloped and non-enveloped viruses presenting different and unrelated processes, but with general principles driving all fusion events. [16, 17] Viral fusion proteins undergo significant rearrangements from the pre-fusion to the post-fusion conformations which are triggered by either receptor binding, proteolytic cleavage or low endosomal pH, and eventually determine the exposure of previously sequestered hydrophobic peptides, loops, or patches, able to interact with and destabilize one or both the opposing membranes.

abstract:
  The means used by enveloped viruses to bypass cellular membranes are well characterized; however, the mechanisms used by non‐enveloped viruses to deliver their genome inside the cell remain unresolved and poorly defined. The discovery of short, membrane interacting, amphipathic or hydrophobic sequences (known as membranotropic peptides) in both enveloped and non‐enveloped viruses suggests that these small peptides are strongly involved in breaching the host membrane and in the delivery of the viral genome into the host cell. Thus, in spite of noticeable differences in entry, this short stretches of membranotropic peptides are probably associated with similar entry‐related events. This review will uncover the intrinsic features of viral membranotropic peptides involved in viral entry of both naked viruses and the ones encircled with a biological membrane with the objective to better elucidate their different functional properties and possible applications in the biomedical field.


id: cord-028738-ing07qma
author: Roy, Nimisha
date: 2020-07-08
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7340772/
doi: 10.1007/s41403-020-00148-0
title:
  Prototype of a Smart Microfluidic Platform for the Evaluation of SARS-Cov-2 Pathogenesis, Along with Estimation of the Effectiveness of Potential Drug Candidates and Antigen–Antibody Interactions in Convalescent Plasma Therapy

abstract:
  Originating in China during December 2019, the novel corona-virus, SARS-CoV-2, has created mayhem worldwide in a very short time. The outbreak has been so rapid and widespread that the only option to treat the patients was administering drugs already available in the market like chloroquine/hydroxychloroquine (an antimalarial drug) and remedesivir. A large number of patients have been cured but the attribution to survival by these drugs has been controversial. Till date, we do not have any specific drug or vaccine available for COVID-19 and the pandemic seems to be far from over. To handle the current challenges posed by the outbreak effectively, we need to employ innovative interdisciplinary approaches. Organ-on-chip (OOC), particularly lung-on-chip, is one such approach which combines the potential of microfluidics, cell culture and molecular biology into a single miniaturised platform. The device is realized to be capable of simulating in-vivo physiological responses of an organ. In the current study, an OOC, which is a multichannel 3D cell culture microfluidic device, is made via soft lithography technique, using polydimethylsiloxane-polymer and diverse polymeric porous/semipermeable membranes. Several polymer membranes i.e. PDMS, polyvinylidene fluoride (PVDF), nitrocellulose, polyester etc., integrated into the microdevices, were efficiently explored to realize their better cell-adhesion and viability property. We also propose for the application of a simple, smart and cost-effective lung-on-chip platform to study the SARS-CoV-2 pathogenesis in humans, drug toxicity testing and provide insights into antigen–antibody interactions. This platform will enable us to study multiple phenomena at a micro-level generating more reliable data and a better understanding of the underlying mechanisms of SARS-CoV-2 infection and pathogenesis.


id: cord-030961-5gzc7193
author: Wang, Jiajun
date: 2020-08-28
txt: ./txt/cord-030961-5gzc7193.txt
cache: ./cache/cord-030961-5gzc7193.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7453191/
doi: 10.1007/s42558-020-00026-3
summary:
  In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. In this work, we create a continuum model for the small-deflection adhesive contact mechanics of virus particle attachment onto the host cell membrane in terms of the principal biophysical properties of the virus, membrane, and their interaction. These results also help to retrieve conditions for lack of adhesion, pull-off force, and contact area between the virus particle and cell membrane. We now describe in outline the continuum models for adhesive contact between the virus and cell membrane, driven by adhesion and external displacement or force, and resisted by tension and elastic bending. In our models, the parameters that govern the adhesive contact mechanics are (more in Table 1 ) bending rigid κ, tension σ, adhesion free energy per receptor β, binding receptor density ρ, and the radius of the virus, R.

title:
  Adhesive contact between cylindrical (Ebola) and spherical (SARS-CoV-2) viral particles and a cell membrane

abstract:
  A critical event during the process of cell infection by a viral particle is attachment, which is driven by adhesive interactions and resisted by bending and tension. The biophysics of this process has been studied extensively, but the additional role of externally applied force or displacement has generally been neglected. In this work, we study the adhesive force-displacement response of viral particles against a cell membrane. We have built two models: one in which the viral particle is cylindrical (say, representative of a filamentous virus such as Ebola) and another in which it is spherical (such as SARS-CoV-2 and Zika). Our interest is in initial adhesion, in which case deformations are small, and the mathematical model for the system can be simplified considerably. The parameters that characterize the process combine into two dimensionless groups that represent normalized membrane bending stiffness and tension. In the limit where bending dominates, for sufficiently large values of normalized bending stiffness, there is no adhesion between viral particles and the cell membrane without applied force. (The zero external force contact width and pull-off force are both zero.) For large values of normalized membrane tension, the adhesion between virus and cell membrane is weak but stable. (The contact width at zero external force has a small value.) Our results for pull-off force and zero force contact width help to quantify conditions that could aid the development of therapies based on denying the virus entry into the cell by blocking its initial adhesion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42558-020-00026-3) contains supplementary material, which is available to authorized users.


id: cord-034898-zjfhpum2
author: Patangi, Sanjay Orathi
date: 2020-11-07
txt: ./txt/cord-034898-zjfhpum2.txt
cache: ./cache/cord-034898-zjfhpum2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647874/
doi: 10.1007/s12055-020-01051-7
summary:
  title: Veno-arterial extracorporeal membrane oxygenation: Special reference for use in ''post-cardiotomy cardiogenic shock'' — A review with an Indian perspective Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is an important modality of managing post-cardiotomy cardiogenic shock with variable outcomes which would otherwise be universally fatal. Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) has gained popularity over the years as a ''bailout'' option after conventional circulatory support methods have proved refractory in the operating room (OR)/intensive care unit (ICU). Long-term survival and major outcomes in post-cardiotomy extracorporeal membrane oxygenation for adult patients in cardiogenic shock Usefulness of cardiac biomarkers to predict cardiac recovery in patients on extracorporeal membrane oxygenation support for refractory cardiogenic shock Nosocomial infections in adult cardiogenic shock patients supported by venoarterial extracorporeal membrane oxygenation Clinical outcomes in patients after extracorporeal membrane oxygenation support for postcardiotomy cardiogenic shock: a single-centre experience of 92 cases

title:
  Veno-arterial extracorporeal membrane oxygenation: Special reference for use in ‘post-cardiotomy cardiogenic shock’ — A review with an Indian perspective

abstract:
  The ultimate goals of cardiovascular physiology are to ensure adequate end-organ perfusion to satisfy the local metabolic demand, to maintain homeostasis and achieve ‘milieu intérieur’. Cardiogenic shock is a state of pump failure which results in tissue hypoperfusion and its associated complications. There are a wide variety of causes which lead to this deranged physiology, and one such important and common scenario is the post-cardiotomy state which is encountered in cardiac surgical units. Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is an important modality of managing post-cardiotomy cardiogenic shock with variable outcomes which would otherwise be universally fatal. VA-ECMO is considered as a double-edged sword with the advantages of luxurious perfusion while providing an avenue for the failing heart to recover, but with the problems of anticoagulation, inflammatory and adverse systemic effects. Optimal outcomes after VA-ECMO are heavily reliant on a multitude of factors and require a multi-disciplinary team to handle them. This article aims to provide an insight into the pathophysiology of VA-ECMO, cannulation techniques, commonly encountered problems, monitoring, weaning strategies and ethical considerations along with a literature review of current evidence-based practices.


id: cord-035248-m5517zgn
title: Bleeding, Thromboembolism, and Clinical Outcomes in Venovenous Extracorporeal Membrane Oxygenation
author: Stokes, John W.
date: 2020-11-09
txt: ./txt/cord-035248-m5517zgn.txt
cache: ./cache/cord-035248-m5517zgn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655084/
doi: 10.1097/cce.0000000000000267
summary:
  Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. Conclusions: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. Conclusions: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. We collected the following data from the electronic health record: patient characteristics in the 24 hours prior to ECMO initiation; bleeding and thromboembolic events during venovenous ECMO as previously defined (5); and clinical outcomes, including in-hospital survival, ECMO duration, and hospital length of stay.

abstract:
  OBJECTIVES: Bleeding and thromboembolism are common during venovenous extracorporeal membrane oxygenation. The relative frequency of these complications and their impact on clinical outcomes have not been described, and no randomized trials exist to guide anticoagulation strategies in extracorporeal membrane oxygenation. Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation. DESIGN: Retrospective cohort study. SETTING: A single academic medical center. PATIENTS: Adult patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation. Eligibility criteria for this analysis were selected to emulate the population that would be recruited for a randomized trial of anticoagulation strategies during venovenous extracorporeal membrane oxygenation. Patients were excluded if they had active bleeding or thromboembolism prior to extracorporeal membrane oxygenation initiation, a history of trauma or surgery in the 7 days prior to extracorporeal membrane oxygenation initiation, an arterial extracorporeal membrane oxygenation cannula, or if they received greater than 48 hours of extracorporeal membrane oxygenation support at another institution INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Outcomes included bleeding and thromboembolic events, duration of extracorporeal membrane oxygenation support, hospital length of stay, and in-hospital survival among 55 patients receiving venovenous extracorporeal membrane oxygenation. Bleeding events occurred in 25 patients (45.5%), and thromboembolism occurred in eight patients (14.5%). Bleeding events were associated with longer duration of extracorporeal membrane oxygenation support (p = 0.007) and worse in-hospital survival (p = 0.02). Thromboembolic events did not appear to be associated with clinical outcomes. CONCLUSIONS: In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. These results highlight the need for randomized trials to evaluate the safety and efficacy of continuous IV anticoagulation among patients receiving venovenous extracorporeal membrane oxygenation.


id: cord-103739-mmkrwj8t
author: Snijder, Eric J.
date: 2020-03-24
txt: ./txt/cord-103739-mmkrwj8t.txt
cache: ./cache/cord-103739-mmkrwj8t.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.03.24.005298
doi: 10.1101/2020.03.24.005298
summary:
  Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). 106 double-membrane spherules (DMSs) 107 We first set out to analyse the ultrastructure of MERS-CoV-infected Huh7 cells under sample 108 preparation conditions favourable for autoradiography (see Materials and Methods) (Fig 1, S1 109 Video). Association of polioviral proteins of the P2 89 genomic region with the viral replication complex and virus-induced membrane synthesis as 90 visualized by electron microscopic immunocytochemistry and autoradiography

title:
  A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis

abstract:
  Zoonotic coronavirus (CoV) infections, like those responsible for the current SARS-CoV-2 epidemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). While double-membrane vesicles (DMVs) appear to be a pan-coronavirus RO element, studies to date describe an assortment of additional coronavirus-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in coronavirus infection.


id: cord-103812-ls6zgipi
title: Gap junction internalization and processing in vivo: a 3D immuno-electron microscopy study
author: Norris, Rachael P.
date: 2020-06-30
txt: ./txt/cord-103812-ls6zgipi.txt
cache: ./cache/cord-103812-ls6zgipi.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.06.29.178475
doi: 10.1101/2020.06.29.178475
summary:
  Less is understood about their internalization, which forms double membrane vesicles containing cytosol and membranes from another cell, called connexosomes or annular gap junctions. Gap junction internalization can also be considered to be a form of trogocytosis (Joly and Hudriser, 2003) in which a portion of the plasma membrane and cytosol of the neighboring cell is transferred to the engulfing cell (See Fig. 1A ). Serial sections were then imaged to obtain threedimensional information; this distinguished between internalized connexosomes and gap junctions in the process of invagination. In 7 of the 56 modified connexosomes, a patch of unlabeled outer membrane bulged outward from a labeled inner membrane ( suggesting that different types of vesicles were involved. Five serial sections through a modified connexosome containing several internal vesicles labeled with Cx43.

abstract:
  Gap junctions have well-established roles in cell-cell communication by way of forming permeable intercellular channels. Less is understood about their internalization, which forms double membrane vesicles containing cytosol and membranes from another cell, called connexosomes or annular gap junctions. Here, we systematically studied the fate of connexosomes in intact ovarian follicles. High pressure frozen, serial sectioned tissue was immunogold labeled for Connexin 43. Within a volume of electron micrographs, every labeled structure was categorized and counted. Surface area measurements indicate that large connexosomes undergo fission. Subsequent modifications are separation of inner and outer membranes, loss of Cx43 from the outer membrane, and outward budding of the modified membranes. We also documented several clear examples of organelle transfer from one cell to another by gap junction internalization. We discuss how connexosome formation and processing may be a novel means for gap junctions to mediate cell-cell communication.


id: cord-104279-choywmwd
author: nan
date: 1992-10-01
txt: ./txt/cord-104279-choywmwd.txt
cache: ./cache/cord-104279-choywmwd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2289628/
doi: nan
summary:
  First, to determine if the lumenal domain was sorted to the vacuole when expressed in the secretory pathway as a soluble protein, a gene fusion was used to create the protein ctFss-B, consisting of the NH2-terminal ER-targeting signal sequence of prepro-t~ factor fused to the lumenal domain of DPAP B at residue 49 ( Fig. 1 B) . To ad-dress the possibility that the mutant constructs analyzed in this study were mislocalized to the plasma membrane followed by rapid endocytic uptake to the vacuole, indirect immunofluorescence experiments were performed on BB-Inv, B-A-B, A20-BB, and/x22-AA-B expressed in a secl strain at 34~ As a positive control for accumulation in secretory vesicles, the localization of the fusion protein Fusl-LacZp was analyzed (Trueheart et al., 1987) .

title:
  Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment

abstract:
  The targeting signals of two yeast integral membrane dipeptidyl aminopeptidases (DPAPs), DPAP B and DPAP A, which reside in the vacuole and the Golgi apparatus, respectively, were analyzed. No single domain of DPAP B is required for delivery to the vacuolar membrane, because removal or replacement of either the cytoplasmic, transmembrane, or lumenal domain did not affect the protein's transport to the vacuole. DPAP A was localized by indirect immunofluorescence to non-vacuolar, punctate structures characteristic of the yeast Golgi apparatus. The 118-amino acid cytoplasmic domain of DPAP A is sufficient for retention of the protein in these structures, since replacement of the cytoplasmic domain of DPAP B with that of DPAP A resulted in an immunolocalization pattern indistinguishable from that of wild type DPAP A. Overproduction of DPAP A resulted in its mislocalization to the vacuole, because cells expressing high levels of DPAP A exhibited vacuolar as well as Golgi staining. Deletion of 22 residues of the DPAP A cytoplasmic domain resulted in mislocalization of the mutant protein to the vacuole. Thus, the cytoplasmic domain of DPAP A is both necessary and sufficient for Golgi retention, and removal of the retention signal, or saturation of the retention apparatus by overproducing DPAP A, resulted in transport to the vacuole. Like wild type DPAP B, the delivery of mutant membrane proteins to the vacuole was unaffected in the secretory vesicle-blocked sec1 mutant; thus, transport to the vacuole was not via the plasma membrane followed by endocytosis. These data are consistent with a model in which membrane proteins are delivered to the vacuole along a default pathway.


id: cord-253366-03cg831z
author: Chakraborty, Hirak
date: 2020-07-22
txt: ./txt/cord-253366-03cg831z.txt
cache: ./cache/cord-253366-03cg831z.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0301462220301460
doi: 10.1016/j.bpc.2020.106438
summary:
  In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. An efficient membrane fusion mechanism between SARS-CoV-2 and host cell could also be responsible for the high level of infection. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides Identification of the membraneactive regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes

title:
  Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics

abstract:
  The emerging and re-emerging viral diseases are continuous threats to the wellbeing of human life. Previous outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS had evidenced potential threats of coronaviruses in human health. The recent pandemic due to SARS-CoV-2 is overwhelming and has been going beyond control. Vaccines and antiviral drugs are ungently required to mitigate the pandemic. Therefore, it is important to comprehend the mechanistic details of viral infection process. The fusion between host cell and virus being the first step of infection, understanding the fusion mechanism could provide crucial information to intervene the infection process. Interestingly, all enveloped viruses contain fusion protein on their envelope that acts as fusion machine. For coronaviruses, the spike or S glycoprotein mediates successful infection through receptor binding and cell fusion. The cell fusion process requires merging of virus and host cell membranes, and that is essentially performed by the S2 domain of the S glycoprotein. In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. We have further discussed about the cell fusion of SARS-CoV-2 in the context of present pandemic situation.


id: cord-257754-pqxkyg8z
title: Membrane Origin for Autophagy
author: Reggiori, Fulvio
date: 2006-07-21
txt: ./txt/cord-257754-pqxkyg8z.txt
cache: ./cache/cord-257754-pqxkyg8z.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0070215306740017
doi: 10.1016/s0070-2153(06)74001-7
summary:
  In addition, a study analyzing conditional knock-out mice defective for autophagy has revealed that the mutant animal accumulates numerous ubiquitinated aggregates in the cytosol, suggesting that this covalent protein modification could serve to specifically target to autophagosomes large structures that have to be eliminated (Komatsu et al., 2005) . In contrast to mammalian cells where several isolation membranes can be simultaneously activated, a single perivacuolar site of organization for double-membrane vesicle formation (named the pre-autophagosomal structure, PAS) is observed in the yeast S. Because the three mammalian Atg8 homologs are diVerently expressed in various tissues (Tanida et al., 2004) , another intriguing option is that these proteins are involved in supplying the autophagosome with membranes derived from diVerent compartments depending on the cell type; for example, GATE-16 from the Golgi complex and GABARAP from the same organelle as well as the synaptic cisternae (Kittler et al., 2001; Kneussel et al., 2000; Sagiv et al., 2000) .

abstract:
  Autophagy is a degradative transport route conserved among all eukaryotic organisms. During starvation, cytoplasmic components are randomly sequestered into large double‐membrane vesicles called autophagosomes and delivered into the lysosome/vacuole where they are destroyed. Cells are able to modulate autophagy in response to their needs, and under certain circumstances, cargoes, such as aberrant protein aggregates, organelles, and bacteria can be selectively and exclusively incorporated into autophagosomes. As a result, this pathway plays an active role in many physiological processes, and it is induced in numerous pathological situations because of its ability to rapidly eliminate unwanted structures. Despite the advances in understanding the functions of autophagy and the identification of several factors, named Atg proteins that mediate it, the mechanism that leads to autophagosome formation is still a mystery. A major challenge in unveiling this process arises from the fact that the origin and the transport mode of the lipids employed to compose these structures is unknown. This compendium will review and analyze the current data about the possible membrane source(s) with a particular emphasis on the yeast Saccharomyces cerevisiae, the leading model organism for the study of autophagosome biogenesis, and on mammalian cells. The information acquired investigating the pathogens that subvert autophagy in order to replicate in the host cells will also be discussed because it could provide important hints for solving this mystery.


id: cord-264996-og3sg0qw
title: Cell Biology of Membrane Trafficking in Human Disease
author: Howell, Gareth J.
date: 2006-09-17
txt: ./txt/cord-264996-og3sg0qw.txt
cache: ./cache/cord-264996-og3sg0qw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16984815/
doi: 10.1016/s0074-7696(06)52005-4
summary:
  Many of these transport intermediates or vesicles, whether derived from the ER, other internal organelles, or the plasma membrane, are ''''coated'''' with unique protein complexes, tethering factors, and regulatory factors that ensure correct targeting to an acceptor compartment. Breast cancer Caveolin-1 Deletion or dominant negative mutation of caveolin-1 promotes tumor progression Breast cancer (Bouras et al., 2004; Williams and Lisanti, 2005) (Hayasaka et al., 1993; Matsuyama et al., 2002) Chediak-Higashi syndrome (CHS) CHS1/Lyst Lyst involved in regulation of protein secretion from lysosomes -enlarged lysosomes Partial albinism, recurrent bacterial infections, impaired chemotaxis and abnormal natural killer cell function (Shiflett et al., 2002; Ward et al., 2003) 214500 Choroideremia (CHM) Rab Escort Protein 1 (REP1) RAB27a remains cytosolic due to defective geranylgeranyl modification in CHM lymphoblasts X-linked form of retinal degeneration 303100 Various mechanisms control the traYcking of proteins from the TGN by the formation and delivery of membrane-derived transport vesicles to the plasma membrane, endosomes, or lysosomal structures (Ponnambalam and Baldwin, 2003) .

abstract:
  Understanding the molecular and cellular mechanisms underlying membrane traffic pathways is crucial to the treatment and cure of human disease. Various human diseases caused by changes in cellular homeostasis arise through a single gene mutation(s) resulting in compromised membrane trafficking. Many pathogenic agents such as viruses, bacteria, or parasites have evolved mechanisms to subvert the host cell response to infection, or have hijacked cellular mechanisms to proliferate and ensure pathogen survival. Understanding the consequence of genetic mutations or pathogenic infection on membrane traffic has also enabled greater understanding of the interactions between organisms and the surrounding environment. This review focuses on human genetic defects and molecular mechanisms that underlie eukaryote exocytosis and endocytosis and current and future prospects for alleviation of a variety of human diseases.


id: cord-265887-g5zhoyo9
author: Mukherjee, Shruti
date: 2020-08-11
txt: ./txt/cord-265887-g5zhoyo9.txt
cache: ./cache/cord-265887-g5zhoyo9.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0301462220301605
doi: 10.1016/j.bpc.2020.106452
summary:
  (56) Apart from these highly conserved sequences throughout the genus, there are distinct potent glycosylation sites along the stretch that can serve as chaperone interacting motifs to help in the protein folding and/or aid in J o u r n a l P r e -p r o o f Journal Pre-proof trafficking along with the cellular machinery.(57) Glycosylation of particular asparagine residues (Asn 45, Asn 48, Asn 64, and Asn 68) in the SARS-CoV has been shown to be crucial in maintaining the proteinoligomerization events associated with the host membranes. (41) The formation of a disulfide bond may also play a crucial role in the oligomerization of the E protein, forming stable dimers, trimers, and pentamers depending on its functional requirement.(105) Thus even though the TMD spans the lipid bilayer, the CxxC motif could serve as an essential key to defining the membrane-associated oligomerization events-providing newer targets for preemptive therapeutic intervention.

title:
  Host-membrane interacting interface of the SARS coronavirus envelope protein: Immense functional potential of C-terminal domain

abstract:
  The Envelope (E) protein in SARS Coronavirus (CoV) is a small structural protein, incorporated as part of the envelope. A major fraction of the protein has been known to be associated with the host membranes, particularly organelles related to intracellular trafficking, prompting CoV packaging and propagation. Studies have elucidated the central hydrophobic transmembrane domain of the E protein being responsible for much of the viroporin activity in favor of the virus. However, newer insights into the organizational principles at the membranous compartments within the host cells suggest further complexity of the system. The lesser hydrophobic Carboxylic-terminal of the protein harbors interesting amino acid sequences- suggesting at the prevalence of membrane-directed amyloidogenic properties that remains mostly elusive. These highly conserved segments indicate at several potential membrane-associated functional roles that can redefine our comprehensive understanding of the protein. This should prompt further studies in designing and characterizing of effective targeted therapeutic measures.


id: cord-269756-tid8a464
title: SARS-CoV fusion peptides induce membrane surface ordering and curvature
author: Basso, Luis G. M.
date: 2016-11-28
url: https://doi.org/10.1038/srep37131
doi: 10.1038/srep37131
abstract:
  Viral membrane fusion is an orchestrated process triggered by membrane-anchored viral fusion glycoproteins. The S2 subunit of the spike glycoprotein from severe acute respiratory syndrome (SARS) coronavirus (CoV) contains internal domains called fusion peptides (FP) that play essential roles in virus entry. Although membrane fusion has been broadly studied, there are still major gaps in the molecular details of lipid rearrangements in the bilayer during fusion peptide-membrane interactions. Here we employed differential scanning calorimetry (DSC) and electron spin resonance (ESR) to gather information on the membrane fusion mechanism promoted by two putative SARS FPs. DSC data showed the peptides strongly perturb the structural integrity of anionic vesicles and support the hypothesis that the peptides generate opposing curvature stresses on phosphatidylethanolamine membranes. ESR showed that both FPs increase lipid packing and head group ordering as well as reduce the intramembrane water content for anionic membranes. Therefore, bending moment in the bilayer could be generated, promoting negative curvature. The significance of the ordering effect, membrane dehydration, changes in the curvature properties and the possible role of negatively charged phospholipids in helping to overcome the high kinetic barrier involved in the different stages of the SARS-CoV-mediated membrane fusion are discussed.


id: cord-272666-3uidpr79
title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing
author: Doyle, Nicole
date: 2018-09-06
txt: ./txt/cord-272666-3uidpr79.txt
cache: ./cache/cord-272666-3uidpr79.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v10090477
doi: 10.3390/v10090477
summary:
  In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. In a subsequent study by others, it was shown that expression of only nsp3 and 4 from either MERS-CoV or SARS-CoV was able to induce DMV formation, and furthermore, addition of nsp6 made no difference to their shape or size, and did not induce the spherule-like structures seen following infection with whole virus [26] .

abstract:
  Positive-strand RNA viruses, such as coronaviruses, induce cellular membrane rearrangements during replication to form replication organelles allowing for efficient viral RNA synthesis. Infectious bronchitis virus (IBV), a pathogenic avian Gammacoronavirus of significant importance to the global poultry industry, has been shown to induce the formation of double membrane vesicles (DMVs), zippered endoplasmic reticulum (zER) and tethered vesicles, known as spherules. These membrane rearrangements are virally induced; however, it remains unclear which viral proteins are responsible. In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. Three non-structural transmembrane proteins, nsp3, nsp4, and nsp6, were expressed in cells singularly or in combination and the effects on cellular membranes investigated using electron microscopy and electron tomography. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. This study highlights further differences in the mechanism of membrane rearrangements between members of the coronavirus family.


id: cord-274101-vm9nh8lc
author: Perez Espitia, Paula Judith
date: 2012-02-29
url: https://www.ncbi.nlm.nih.gov/pubmed/32368201/
doi: 10.1111/j.1541-4337.2011.00179.x
title:
  Bioactive Peptides: Synthesis, Properties, and Applications in the Packaging and Preservation of Food

abstract:
  Abstract: Bioactive peptides are protein fragments which have a positive impact on the functions and conditions of living beings. Peptides have shown several useful properties for human health, including antimicrobial, antifungal, antiviral, and antitumor activities. These compounds are produced by almost all species of life. However, they are produced in limited quantities in nature. As a result, researchers have tried to synthesize bioactive peptides to study their properties and applications in various areas. Among their applications in food preservation, peptides have been incorporated into packaging materials. This review begins with a brief description of the methods used for the synthesis, purification, and characterization of peptides. Also, the main bioproperties and mechanisms of action of peptides are discussed. Finally, some applications of peptides are presented, especially their use in active packaging, their effects on the polymeric matrix, and peptide migration.


id: cord-276456-oa6hh7ky
title: 5.14 The Biophysics of Membrane Fusion
author: Collins, R.N.
date: 2012-05-03
url: https://api.elsevier.com/content/article/pii/B9780123749208005233
doi: 10.1016/b978-0-12-374920-8.00523-3
abstract:
  A crucial interplay between protein conformations and lipid membrane energetics emerges as the guiding principle for the regulation and mechanism of membrane fusion in biological systems. As some of the basics of fusion become clear, a myriad of compelling questions come to the fore. Is the interior of the fusion pore protein or lipid? Why is synaptic release so fast? Why is PIP(2) needed for exocytosis? How does fusion peptide insertion lead to fusion of viruses to cell membranes? What role does the TMD play? How can studies on membrane fission contribute to our understanding of membrane fusion? What exactly are SNARE proteins doing?


id: cord-279463-bli8hwda
author: Lipp, Joachim
date: 1986-09-26
txt: ./txt/cord-279463-bli8hwda.txt
cache: ./cache/cord-279463-bli8hwda.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/3530500/
doi: 10.1016/0092-8674(86)90710-5
summary:
  As type II membrane proteins contain only a single stretch of hydrophobic amino acid residues, this might function as a signal for membrane insertion as well as a membrane anchor (Markoff et al., 1984; Spiess and Lodish, 1986) . plycat is an in-frame fusion between the 5'' region of ly encoding the cytoplas, mic, membrane-spanning segment plus 12 amino acids of the exoplasmic portion of ly and the gene encoding the cytoplasmic protein chloramphenicol acetyltransferase (CAT). After protease digestion in the presence of microsomal membranes, lyCAT* is reduced in molecular weight by about 2 kd, suggesting that it exposes 20-30 amino acid residues on the cytoplasmic side ( Figure 3 , lanes 2 and 3). This signal sequence is located in the amino-terminal half of the membrane-spanning segment, and it is cleaved when the preceding cytoplasmic domain is removed.

title:
  The membrane-spanning segment of invariant chain (Iγ) contains a potentially cleavable signal sequence

abstract:
  Abstract The human invariant chain (Iγ) of class II histocompatibility antigens spans the membrane of the endoplasmic reticulum once. It exposes a small amino-terminal domain on the cytoplasmic side and a carboxyterminal, glycosylated domain on the exoplasmic side of the membrane. When the exoplasmic domain of Iγ is replaced by the cytoplasmic protein chloramphenicol acetyltransferase (CAT), CAT becomes the exoplasmic, glycosylated domain of the resulting membrane protein IγCAT∗. Deletion of the hydrophilic cytoplasmic domain from IγCAT gives rise to a secreted protein from which an amino-terminal segment is cleaved, most likely by signal peptidase. We conclude that the membrane-spanning region of Iγ contains a signal sequence in its amino-terminal half and that hydrophilic residues at the amino-terminal end of a signal sequence can determine cleavage by signal peptidase.


id: cord-284690-ogu1gmcb
author: da Cunha, Nicolau B.
date: 2016-11-23
txt: ./txt/cord-284690-ogu1gmcb.txt
cache: ./cache/cord-284690-ogu1gmcb.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1359644616304135
doi: 10.1016/j.drudis.2016.10.017
summary:
  The use of viral vectors based on the tobacco mosaic virus (TMV) and potato virus X (PVX) for cloning and massively expressing AMP genes in Nicotiana benthamiana appears to be an interesting new approach to considerably enhance recombinant peptide production before structural and functional characterization. However, frequent gene silencing at the transcriptional level and instability of genes cloned in vectors for stable or transient expression remain major challenges limiting the efficient production of AMPs. Another persistent issue is the poor quality of the peptides endogenously synthesized in bacteria, yeast, and plants, particularly resulting from undesirable post-translational modifications [2, 33] . Some drawbacks presented by plant expression systems are solved by the CRISPR system, a revolutionary genome-editing technology that presents myriad possibilities for genetic manipulation at the genomic level and provides unprecedented tools (CRISPRi and CRISPRa) to precisely control gene expression and the structural modification of AMPs. Despite its current minor limitations (e.g. off-target effects), CRISPR could have a key role in the future development of clinical drugs as biotechnological antiinfective agents, including the rational biosynthesis of next-generation antimicrobials.

title:
  The next generation of antimicrobial peptides (AMPs) as molecular therapeutic tools for the treatment of diseases with social and economic impacts

abstract:
  Anti-infective drugs have had a key role in the contemporary world, contributing to dramatically decrease mortality rates caused by infectious diseases worldwide. Antimicrobial peptides (AMPs) are multifunctional effectors of the innate immune system of mucosal surfaces and present antimicrobial activity against a range of pathogenic viruses, bacteria, and fungi. However, the discovery and development of new antibacterial drugs is a crucial step to overcome the great challenge posed by the emergence of antibiotic resistance. In this review, we outline recent advances in the development of novel AMPs with improved antimicrobial activities that were achieved through characteristic structural design. In addition, we describe recent progress made to overcome some of the major limitations that have hindered peptide biosynthesis.


id: cord-285620-oawrnmhy
title: Efficient removal of water bacteria and viruses using electrospun nanofibers
author: Fahimirad, Shohreh
date: 2020-08-16
txt: ./txt/cord-285620-oawrnmhy.txt
cache: ./cache/cord-285620-oawrnmhy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32866832/
doi: 10.1016/j.scitotenv.2020.141673
summary:
  This review intends to provide a detailed summary of the recent advances in the fabrication of antibacterial and antiviral electrospun nanofibers and discuss their application efficiency as a water filtration membrane. The present work reviews previous studies on the production and application of electrospun nanofibers as antimicrobial water filtration membranes. The objectives of this review were to: (i) introduce the different procedures, which have been applied for incorporation of the various antimicrobial agents into electrospun nanofibers (ii) discuss the different antimicrobial tests used for proving antimicrobial activity of the fabricated electrospun water filters (iii) study the efficiency of the produced antimicrobial electrospun application in the water treatment industry. Based on the majority of researches studied in this review, blending and post-modification strategies are two commonly used techniques to incorporate biocide agents into nanofibers aiming for water disinfection application (Shalaby et al., 2018; He et al., 2018; Makaremi et al., 2016) .

abstract:
  Abstract Pathogenic contamination has been considered as a significant worldwide water quality concern. Due to providing promising opportunities for the production of nanocomposite membranes with tailored porosity, adjustable pore size, and scaled-up ability of biomolecules incorporation, electrospinning has become the center of attention. This review intends to provide a detailed summary of the recent advances in the fabrication of antibacterial and antiviral electrospun nanofibers and discuss their application efficiency as a water filtration membrane. The current review attempts to give a functionalist perspective of the fundamental progress in construction strategies of antibacterial and antiviral electrospun nanofibers. The review provides a list of antibacterial and antiviral agents commonly used as water membrane filters and discusses the challenges in the incorporation process. We have thoroughly studied the recent application of functionalized electrospun nanofibers in the water disinfection process, with an emphasis on their efficiency. Moreover, different antibacterial and antiviral assay techniques for membranes are discussed, the gaps and limitations are highlighted and promising strategies to overcome barriers are studies.


id: cord-287093-9mertwj7
title: Virus factories, double membrane vesicles and viroplasm generated in animal cells
author: Netherton, Christopher L
date: 2011-10-12
txt: ./txt/cord-287093-9mertwj7.txt
cache: ./cache/cord-287093-9mertwj7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22440839/
doi: 10.1016/j.coviro.2011.09.008
summary:
  In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. In this review, we discuss how three supergroups of (+)strand RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses (NCLDV). The RNA-dependent RNA polymerases (RdRp) of the (+)strand RNA viruses are targeted to the cytoplasmic face of membrane-bound organelles and subsequent assembly of the replicase complex induces membrane curvature and the formation of densely packed membrane vesicles (reviewed in [1, 2] ) ( Figure 1 ). This suggests that replication may take place on CM and that genomes are transferred to vesicular packets for envelopment and budding, while excess viral RNA may be stored in DMVs. Picornaviruses generate densely packed DMVs between 200 and 400 nm in diameter, a series of single membraned vesicles resulting from fragmentation of the Golgi, and autophagosomes possibly generated as a bystander response to infection [11 ,12-16] .

abstract:
  Many viruses reorganise cellular membrane compartments and the cytoskeleton to generate subcellular microenvironments called virus factories or ‘viroplasm’. These create a platform to concentrate replicase proteins, virus genomes and host proteins required for replication and also protect against antiviral defences. There is growing interest in understanding how viruses induce such large changes in cellular organisation, and recent studies are beginning to reveal the relationship between virus factories and viroplasm and the cellular structures that house them. In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses.


id: cord-289541-y7lewk1t
author: Zhang, Li-Zhi
date: 2006-05-01
txt: ./txt/cord-289541-y7lewk1t.txt
cache: ./cache/cord-289541-y7lewk1t.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.memsci.2005.09.035
doi: 10.1016/j.memsci.2005.09.035
summary:
  The membrane is composed of three layers: two hydrophobic protective layers and a sandwiched hydrophilic support layer in which LiCl solution is immobilized to facilitate water vapor transfer. Further, the supported liquid layer only accounts for 12% of the total moisture transfer resistance in the cell, indicating that there is much potential for further performance improvement. The core material of an MTHR ventilator are vapor-permeable membranes, therefore both heat and moisture are transferred between these two air streams when they flow through the unit. However, moisture diffusion coefficients in such polymer membranes are usually very low, in the order of 10 −12 to 10 −13 m 2 s −1 [11, 18] , while MTHR ventilators only have limited transmembrane vapor partial pressure difference, consequently performances are quite limited currently. To improve the performances of MTHR ventilators, in this study, a novel membrane, a composite SLM, which employs LiCl liquid solution immobilized in a porous support membrane to facilitate the transport of moisture, is prepared.

title:
  Fabrication of a lithium chloride solution based composite supported liquid membrane and its moisture permeation analysis

abstract:
  A novel composite supported liquid membrane has been prepared for ventilation air moisture recovery. The membrane is composed of three layers: two hydrophobic protective layers and a sandwiched hydrophilic support layer in which LiCl solution is immobilized to facilitate water vapor transfer. A test is conducted to measure the moisture permeation rate through the composite membrane. Various resistances in the cell and in the composite membrane are clarified. Linear equilibrium relations between humidity, temperature, and LiCl concentration in the liquid solution layer are obtained to aid in the model set-up. It has been found that the mean moisture permeation rate through the composite membrane is around 1.14 × 10(−4) kg m(−2) s(−1), almost two times higher than that through a solid hydrophilic cellulose acetate membrane with comparative thickness. Further, the supported liquid layer only accounts for 12% of the total moisture transfer resistance in the cell, indicating that there is much potential for further performance improvement.


id: cord-294842-aesiff1f
title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses
author: Romero-Brey, Inés
date: 2014-07-22
txt: ./txt/cord-294842-aesiff1f.txt
cache: ./cache/cord-294842-aesiff1f.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v6072826
doi: 10.3390/v6072826
summary:
  Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein

abstract:
  In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments.


id: cord-298019-gf2asni1
title: gH625: A milestone in understanding the many roles of membranotropic peptides
author: Galdiero, Stefania
date: 2014-10-12
txt: ./txt/cord-298019-gf2asni1.txt
cache: ./cache/cord-298019-gf2asni1.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0005273614003411
doi: 10.1016/j.bbamem.2014.10.006
summary:
  While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. Peptides with a propensity for membrane binding can also interfere with enveloped virus entry by direct physical interaction with the hydrophobic surfaces present on cell membranes and/or fusion proteins. Since not all membranotropic peptides are able to cross the membrane bilayer, it is essential to identify structural characteristics of hydrophobic peptides know to enter the cell membrane to highlight any feature that is involved in the penetration which may help in the design of novel delivery tools. Dendrimer functionalization with a membrane-interacting domain of herpes simplex virus type 1: towards intracellular delivery

abstract:
  Here, we review the current knowledge about viral derived membranotropic peptides, and we discuss how they may be used for many therapeutic applications. While they have been initially discovered in viral fusion proteins and have been involved in the mechanism of viral entry, it is now clear that their features and their mode of interaction with membrane bilayers can be exploited to design viral inhibitors as well as to favor delivery of cargos across the cell membrane and across the blood–brain barrier. The peptide gH625 has been extensively used for all these purposes and provides a significant contribution to the field. We describe the roles of this sequence in order to close the gap between the many functions that are now emerging for membranotropic peptides.


id: cord-299270-fwbz3t25
title: Structure and function of proteins in membranes and nanodiscs
author: Lemieux, M. Joanne
date: 2020-08-22
txt: ./txt/cord-299270-fwbz3t25.txt
cache: ./cache/cord-299270-fwbz3t25.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0005273620302881
doi: 10.1016/j.bbamem.2020.183445
summary:
  Abstract The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. Comparisons with the performance of conventional detergents suggests that the development of neutral or basic copolymers related to SMA could offer advantages, providing avenues for solubilization and analysis of a broader array of biological membrane:protein assemblies (memteins). The individual components of erythrocyte membranes including Rh proteins are well known, but their multimeric lipid complexes are dissociated in detergent-based preparations and hence no longer recognizable or extractable using conformation-specific antibodies. A set of ABCG2 protein constructs were designed with N-terminal GFP or SNAP and His 6 tags and solubilized from HEK cells using SMA(2:1) copolymer, as were CD28 and CD86 Antibiotics include lipid-specific peptides that self-associate into pores, which permeabilize bacterial membranes.

abstract:
  Abstract The field of membrane structural biology represents a fast-moving field with exciting developments including native nanodiscs that allow preparation of complexes of post-translationally modified proteins bound to biological lipids. This has led to conceptual advances including biological membrane:protein assemblies or “memteins” as the fundamental functional units of biological membranes. Tools including cryo-electron microscopy and X-ray crystallography are maturing such that it is becoming increasingly feasible to solve structures of large, multicomponent complexes, while complementary methods including nuclear magnetic resonance spectroscopy yield unique insights into interactions and dynamics. Challenges remain, including elucidating exactly how lipids and ligands are recognized at atomic resolution and transduce signals across asymmetric bilayers. In this special volume some of the latest thinking and methods are gathered through the analysis of a range of transmembrane targets. Ongoing work on areas including polymer design, protein labelling and microfluidic technologies will ensure continued progress on improving resolution and throughput, providing deeper understanding of this most important group of targets.


id: cord-300429-b0zev8zb
title: Protein Palmitoylation and Its Role in Bacterial and Viral Infections
author: Sobocińska, Justyna
date: 2018-01-19
url: https://www.ncbi.nlm.nih.gov/pubmed/29403483/
doi: 10.3389/fimmu.2017.02003
abstract:
  S-palmitoylation is a reversible, enzymatic posttranslational modification of proteins in which palmitoyl chain is attached to a cysteine residue via a thioester linkage. S-palmitoylation determines the functioning of proteins by affecting their association with membranes, compartmentalization in membrane domains, trafficking, and stability. In this review, we focus on S-palmitoylation of proteins, which are crucial for the interactions of pathogenic bacteria and viruses with the host. We discuss the role of palmitoylated proteins in the invasion of host cells by bacteria and viruses, and those involved in the host responses to the infection. We highlight recent data on protein S-palmitoylation in pathogens and their hosts obtained owing to the development of methods based on click chemistry and acyl-biotin exchange allowing proteomic analysis of protein lipidation. The role of the palmitoyl moiety present in bacterial lipopolysaccharide and lipoproteins, contributing to infectivity and affecting recognition of bacteria by innate immune receptors, is also discussed.


id: cord-303238-us3dybue
title: Membrane Topology of Murine Coronavirus Replicase Nonstructural Protein 3
author: Kanjanahaluethai, Amornrat
date: 2007-05-01
txt: ./txt/cord-303238-us3dybue.txt
cache: ./cache/cord-303238-us3dybue.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17222884/
doi: 10.1016/j.virol.2006.12.009
summary:
  The papain-like protease (PLpro) encoded by the coronavirus that causes severe acute respiratory syndrome (SARS-CoV) processes three sites in the replicase polyprotein (Harcourt et al., 2004) , and has recently been shown to have de-ubiquitinating activity (Barretto et al., 2005; Lindner et al., 2005) . To extend these studies of membrane association of coronavirus replicase products, we analyzed the amino acid sequence of MHV-JHM nsp3 (from glycine-833 to glycine-2840) for probability of transmembrane helices using the five different programs designed to search for putative membrane-spanning sequences: Phobius, TMHMM, HMMTOP, SOSUI and TMpred (Fig. 2) . In contrast, when CMMs were added to the mixture, protein products that included all or part of nsp3-TM (PLP2-2485, -2390 and -2258) were detected predominantly in the pelleted fraction, consistent with membrane association (Fig. 3B ).

abstract:
  Mouse hepatitis virus (MHV) is a member of the family Coronaviridae. These positive strand RNA viruses encode a replicase polyprotein that is processed into 16 nonstructural proteins (nsps). The nsps assemble with membranes to generate double membrane vesicles, which are the sites of viral RNA synthesis. MHV nsp3 contains multiple domains including two papain-like protease domains, PLP1 and PLP2, and a predicted transmembrane (TM) domain. In this study, we determined the membrane topology of nsp3-TM and showed that TM-mediated tethering of PLP2 is important for processing at cleavage site 3. Biochemical analysis revealed that nsp3 is an integral membrane protein that is inserted into endoplasmic reticulum (ER) membranes co-translationally and glycosylated at asparagine-2357. Proteinase K digestion experiments indicate that the TM domain of nsp3 has 4 membrane-spanning helices. We show that nsp3-TM is sufficient to mediate ER membrane association of a cytosolic protein. This study is the first detailed analysis of the topology and function of the coronavirus nsp3 TM domain.


id: cord-309384-vlk8cebh
title: Ganglioside Biochemistry
author: Kolter, Thomas
date: 2012-12-19
txt: ./txt/cord-309384-vlk8cebh.txt
cache: ./cache/cord-309384-vlk8cebh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25969757/
doi: 10.5402/2012/506160
summary:
  A principal difference between ganglioside biosynthesis in the Golgi apparatus and degradation in the endolysosomal compartment is that during GSL formation, membranebound glycosyltransferases interact with their membranebound glycolipid substrates by diffusion within the twodimensional plane of the lipid bilayer. As glycosidase substrates, GSLs with four carbohydrate residues or less require the additional presence of small lipid binding glycoproteins, either the GM2 activator protein or one of the four saposins A-D. In vitro, in addition to enzymes and activator proteins, also an appropriate membrane-lipid composition of the ganglioside-containing membrane is required for degradation [222] . Due to the deficiency of two enzyme activities, β-hexosaminidases A and B, storage of negatively charged glycolipids characteristic for Tay-Sachs disease and, in addition, of uncharged substrates such as GA2 in the brain and globoside in visceral organs (Figure 16 ) is observed.

abstract:
  Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized.


id: cord-313599-5j19stye
author: Wang, Xianfeng
date: 2013-05-26
txt: ./txt/cord-313599-5j19stye.txt
cache: ./cache/cord-313599-5j19stye.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32287484/
doi: 10.1016/j.pmatsci.2013.05.001
summary:
  NFN possess the general properties and functions of conventional electrospun nanofibers and other 1D nanostructures fabricated using different techniques, as well as the impressive feature characters (e.g. extremely small diameter, high porosity, Steiner tree network geometry, controllable coverage rate) that distinguish themselves from their counterparts, the properties donated by the polymer phase, and the 2D net-like geometry. Therefore, strongly interconnected thin MPEG spider-web-like nano-nets with thick PA-6 nanofibers are responsible to increase mechanical strength and hydrophilic nature of PA-6 fibrous membranes, which make composite MPEG/PA-6 NFN membranes great potential in air filtration and different biomedical application. More recently, our group has presented continuous efforts toward the aim of generating PANI-based nanostructured materials and for the first time fabricated composite PANI/PA-6 NFN membranes (Fig. 20a) , which were used as a platform for efficient sensing reaction by providing high specific surface area and porosity.

title:
  Electro-spinning/netting: A strategy for the fabrication of three-dimensional polymer nano-fiber/nets

abstract:
  Since 2006, a rapid development has been achieved in a subject area, so called electro-spinning/netting (ESN), which comprises the conventional electrospinning process and a unique electro-netting process. Electro-netting overcomes the bottleneck problem of electrospinning technique and provides a versatile method for generating spider-web-like nano-nets with ultrafine fiber diameter less than 20 nm. Nano-nets, supported by the conventional electrospun nanofibers in the nano-fiber/nets (NFN) membranes, exhibit numerious attractive characteristics such as extremely small diameter, high porosity, and Steiner tree network geometry, which make NFN membranes optimal candidates for many significant applications. The progress made during the last few years in the field of ESN is highlighted in this review, with particular emphasis on results obtained in the author’s research units. After a brief description of the development of the electrospinning and ESN techniques, several fundamental properties of NFN nanomaterials are addressed. Subsequently, the used polymers and the state-of-the-art strategies for the controllable fabrication of NFN membranes are highlighted in terms of the ESN process. Additionally, we highlight some potential applications associated with the remarkable features of NFN nanostructure. Our discussion is concluded with some personal perspectives on the future development in which this wonderful technique could be pursued.


id: cord-314402-kjzkk51t
title: EML webinar overview: Simulation-assisted discovery of membrane targeting nanomedicine
author: Zou, Guijin
date: 2020-06-08
url: https://www.ncbi.nlm.nih.gov/pubmed/32537481/
doi: 10.1016/j.eml.2020.100817
abstract:
  The COVID-19 pandemic has brought infectious diseases again to the forefront of global public health concerns. In this EML webinar (Gao, 2020), we discuss some recent work on simulation-assisted discovery of membrane targeting nanomedicine to counter increasing antimicrobial resistance and potential application of similar ideas to the current pandemic. A recent report led by the world health organization (WHO) warned that 10 million people worldwide could die of bacterial infections each year by 2050. To avert the crisis, membrane targeting antibiotics are drawing increasing attention due to their intrinsic advantage of low resistance development. In collaboration with a number of experimental groups, we show examples of simulation-assisted discovery of molecular agents capable of selectively penetrating and aggregating in bacterial lipid membranes, causing membrane permeability/rupture. Through systematic all-atom molecular dynamics simulations and free energy analysis, we demonstrate that the membrane activity of the molecular agents correlates with their ability to enter, perturb and permeabilize the lipid bilayers. Further study on different cell membranes demonstrates that the selectivity results from the presence of cholesterol in mammalian but not in bacterial membranes, as the cholesterol can condense the hydrophobic region of membrane, preventing the penetration of the molecular agents. Following the molecular penetration, we establish a continuum theory and derive the energetic driving force for the domain aggregation and pore growth on lipid membrane. We show that the energy barrier to membrane pore formation can be significantly lowered through molecular aggregation on a large domain with intrinsic curvature and a sharp interface. The theory is consistent with experimental observations and validated with coarse-grained molecular dynamics simulations of molecular domain aggregation leading to pore formation in a lipid membrane. The mechanistic modelling and simulation provide some fundamental principles on how molecular antimicrobials interact with bacterial membranes and damage them through domain aggregation and pore formation. For treating viral infections and cancer therapy, we discuss potential size- and lipid-type-based selectivity principles for developing membrane active nanomedicine. These studies suggest a general simulation-assisted platform to accelerate discovery and innovation in nanomedicine against infectious diseases. EML Webinar speakers are updated at https://imechanica.org/node/24132


id: cord-314604-w61sqy17
title: Modulation of Coiled-Coil Binding Strength and Fusogenicity through Peptide Stapling
author: Crone, Niek S. A.
date: 2020-02-14
url: https://www.ncbi.nlm.nih.gov/pubmed/32058706/
doi: 10.1021/acs.bioconjchem.0c00009
abstract:
  [Image: see text] Peptide stapling is a technique which has been widely employed to constrain the conformation of peptides. One of the effects of such a constraint can be to modulate the interaction of the peptide with a binding partner. Here, a cysteine bis-alkylation stapling technique was applied to generate structurally isomeric peptide variants of a heterodimeric coiled-coil forming peptide. These stapled variants differed in the position and size of the formed macrocycle. C-terminal stapling showed the most significant changes in peptide structure and stability, with calorimetric binding analysis showing a significant reduction of binding entropy for stapled variants. This entropy reduction was dependent on cross-linker size and was accompanied by a change in binding enthalpy, illustrating the effects of preorganization. The stapled peptide, along with its binding partner, were subsequently employed as fusogens in a liposome model system. An increase in both lipid- and content-mixing was observed for one of the stapled peptide variants: this increased fusogenicity was attributed to increased coiled-coil binding but not to membrane affinity, an interaction theorized to be a primary driving force in this fusion system.


id: cord-317430-uvx8si42
title: Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions
author: Chen, Yaping
date: 2020-08-26
txt: ./txt/cord-317430-uvx8si42.txt
cache: ./cache/cord-317430-uvx8si42.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32844502/
doi: 10.1002/adma.202001668
summary:
  [6] In particular, SiNW arrays demonstrated high efficiency (>90%) in transfecting exogenous genetic materials into primary immune cells-which are notoriously hard to transfect-while maintaining high viability and immunological competence; [27, 28, 36] siRNAs were transfected via SiNWs into primary B cells and CD4 + T cells to knock down predicted target genes, facilitating discovery of essential signaling pathways and genetic regulatory circuits for immune cell activation and differentiation; [27, 28] SiNWs were used to administer a small-molecule inhibitor of the enzyme Polo-like kinase (Plk) into bone-marrow derived dendritic cells (BMDCs), confirming the essential role of Plk2 and Plk4 in regulating antiviral gene expression in these cell; [37] by using vertical carbon nanosyringe arrays (CNSAs) under applied centrifugal g-force, pEGFP plasmids were transfected www.advmat.de www.advancedsciencenews.com into primary lymphocytes with significantly higher efficiency than conventional Lipofectamine 2000-mediated method.

abstract:
  Engineered nano–bio cellular interfaces driven by 1D vertical nanostructures (1D‐VNS) are set to prompt radical progress in modulating cellular processes at the nanoscale. Here, tuneable cell–VNS interfacial interactions are probed and assessed, highlighting the use of 1D‐VNS in immunomodulation, and intracellular delivery into immune cells—both crucial in fundamental and translational biomedical research. With programmable topography and adaptable surface functionalization, 1D‐VNS provide unique biophysical and biochemical cues to orchestrate innate and adaptive immunity, both ex vivo and in vivo. The intimate nanoscale cell–VNS interface leads to membrane penetration and cellular deformation, facilitating efficient intracellular delivery of diverse bioactive cargoes into hard‐to‐transfect immune cells. The unsettled interfacial mechanisms reported to be involved in VNS‐mediated intracellular delivery are discussed. By identifying up‐to‐date progress and fundamental challenges of current 1D‐VNS technology in immune‐cell manipulation, it is hoped that this report gives timely insights for further advances in developing 1D‐VNS as a safe, universal, and highly scalable platform for cell engineering and enrichment in advanced cancer immunotherapy such as chimeric antigen receptor‐T therapy.


id: cord-319754-5isw53wl
title: Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update
author: Balgoma, David
date: 2020-08-31
url: https://www.ncbi.nlm.nih.gov/pubmed/32878290/
doi: 10.3390/metabo10090356
abstract:
  The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection.


id: cord-323319-u5hfkjv8
author: Xu, Mengchang
date: 2020-10-22
url: https://doi.org/10.1016/j.chemosphere.2020.128716
doi: 10.1016/j.chemosphere.2020.128716
title:
  Analysis of the biodegradation performance and biofouling in a halophilic MBBR-MBR to improve the treatment of disinfected saline wastewater

abstract:
  Disinfectant-containing wastewaters have been generated from many places, including marine industries. The synthetic NaClO-containing wastewaters have been effectively treated in a saline MBBR-MBR (moving bed biofilm reactor & membrane bioreactor) system containing marine microorganisms. A low concentration of NaCl (below 100 mg/L) is not enough to kill the microorganisms, but can affect their bioactivity and induce membrane biofouling. A linear relationship has been obtained for the half-life of membrane biofouling as a function of the NaClO concentration (10-100 mg/L): [half-life] = 25－0.12×[NaClO concentration]. The COD and NH(3)-N removals are the highest at a salinity of 30 g/L for the marine bioreactors. The behaviour of the typical biofoulants, measured real-timely by fluorescence spectroscopy, can indicate the levels of membrane biofouling and microbial activity, responding to the NaClO and NaCl influences. Based on the behavior of biofoulants, this work has also proposed a novel strategy of biofoulants monitoring for membrane antifouling, where antifouling responses can be carried out when the concentration of biofoulants significantly increases.


id: cord-325712-9kbnyqt3
author: Nathan, Lakshmi
date: 2019-07-18
url: https://www.ncbi.nlm.nih.gov/pubmed/31317494/
doi: 10.1007/978-3-030-14741-9_2
title:
  Single Virion Tracking Microscopy for the Study of Virus Entry Processes in Live Cells and Biomimetic Platforms

abstract:
  The most widely-used assays for studying viral entry, including infectivity, cofloatation, and cell-cell fusion assays, yield functional information but provide low resolution of individual entry steps. Structural characterization provides high-resolution conformational information, but on its own is unable to address the functional significance of these conformations. Single virion tracking microscopy techniques provide more detail on the intermediate entry steps than infection assays and more functional information than structural methods, bridging the gap between these methods. In addition, single virion approaches also provide dynamic information about the kinetics of entry processes. This chapter reviews single virion tracking techniques and describes how they can be applied to study specific virus entry steps. These techniques provide information complementary to traditional ensemble approaches. Single virion techniques may either probe virion behavior in live cells or in biomimetic platforms. Synthesizing information from ensemble, structural, and single virion techniques ultimately yields a more complete understanding of the viral entry process than can be achieved by any single method alone.


id: cord-325915-dw989txm
title: Downstream processing of cell culture-derived virus particles
author: Wolf, Michael W
date: 2014-01-09
url: https://doi.org/10.1586/erv.11.111
doi: 10.1586/erv.11.111
abstract:
  Manufacturing of cell culture-derived virus particles for vaccination and gene therapy is a rapidly growing field in the biopharmaceutical industry. The process involves a number of complex tasks and unit operations ranging from selection of host cells and virus strains for the cultivation in bioreactors to the purification and formulation of the final product. For the majority of cell culture-derived products, efforts focused on maximization of bioreactor yields, whereas design and optimization of downstream processes were often neglected. Owing to this biased focus, downstream procedures today often constitute a bottleneck in various manufacturing processes and account for the majority of the overall production costs. For efficient production methods, particularly in sight of constantly increasing economic pressure within human healthcare systems, highly productive downstream schemes have to be developed. Here, we discuss unit operations and downstream trains to purify virus particles for use as vaccines and vectors for gene therapy.


id: cord-327765-qdbgkm53
title: Lateral Heterogeneity and Domain Formation in Cellular Membranes
author: Kinnun, Jacob J.
date: 2020-09-15
txt: ./txt/cord-327765-qdbgkm53.txt
cache: ./cache/cord-327765-qdbgkm53.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0009308420301079
doi: 10.1016/j.chemphyslip.2020.104976
summary:
  where a 0 is the area per molecule, R is the domain radius, ε is the dielectric constant of the interfacial water, ε 0 is the permittivity of free space, e is Euler''s number, and δ is the molecular cut-off distance ∼ 0.5nm 26 Lipids and membrane proteins have varying intrinsic hydrophobic thicknesses. In terms of specific theoretical energetics, this contribution to line tension is less 6 J o u r n a l P r e -p r o o f Figure 2 : (a) The registration of domains across membrane leaflets maximizes dynamics, is entropically favorable, and is one mechanism for domain coalescence (adapted from Haataja et al. In other words, the simple phenomenological free energy approach presented here provides a conceptual framework for understanding the scattering data and interpreting the wide range of phase behaviors observed for lateral lipid organization in cell membranes. Lipid lateral diffusion in bilayers with phosphatidylcholine, sphingomyelin and cholesterol: An NMR study of dynamics and lateral phase separation

abstract:
  As early as the development of the fluid mosaic model for cellular membranes, researchers began observing the telltale signs of lateral heterogeneity. Over the decades this has led to the development of the lipid raft hypothesis and the ensuing controversy that has unfolded. Here, we review the physical concepts behind domain formation in lipid membranes, both of their structural and dynamic origins. This, then leads into a discussion of coarse-grained, phenomenological approaches that describe the wide range of phases associated with lipid lateral heterogeneity. We use these physical concepts to describe the interaction between raft-lipid species, such as long-chain saturated lipids, sphingomyelin, and cholesterol with non-raft forming lipids, such as those with short acyl chains or unsaturated fatty acids. While debate has persisted on the biological relevance of lipid domains, recent research, described here, continues to identify biological roles for rafts and new experimental approaches have revealed the existence of lipid domains in living systems. Given the recent progress on both the biological and structural aspects of raft formation, the research area of membrane lateral heterogeneity will not only expand, but will continue to produce exciting results.


id: cord-329448-kxxy60x9
title: Endocytosis unplugged: multiple ways to enter the cell
author: Kumari, Sudha
date: 2010-02-02
txt: ./txt/cord-329448-kxxy60x9.txt
cache: ./cache/cord-329448-kxxy60x9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20125123/
doi: 10.1038/cr.2010.19
summary:
  These factors include one or more underlying principle in cargo enrichment, necessitating specific coat and coat-associated protein assembly, a scission mechanism, and a means to integrate these steps; several molecules and membrane parameters can influence and diversify an endocytic process. CtBP1/BARS (C-terminal-binding protein-1/brefeldin A ribosylation substrate) proteins were originally demonstrated to regulate dynamin-independent fluid uptake in a variety of cell lines, and were later reported to localize to the site of and affect macropinosome membrane closure in a phosphorylation-dependent manner [36] . Overexpression of dominant negative, GTP-binding mutants of dynamin also blocked receptor-mediated endocytosis in various cells, suggesting a role for the GTPase activity of dynamin in the clathrin-dependent endocytic process outside the nervous system. The identification of an endocytic pathway as distinct has been primarily based on associated cargo proteins or lipids, and molecular regulators; the contribution of kinetics and detailed physical mechanism to such categorization is not generally available except in some wellcharacterized situations, namely clathrin-pit endocytosis or endocytosis by actin-dependent forces in yeast.

abstract:
  Endocytosis occurs at the cell surface and involves internalization of the plasma membrane (PM) along with its constituent membrane proteins and lipids. Endocytosis is involved in sampling of the extracellular milieu and also serves to regulate various processes initiated at the cell surface. These include nutrient uptake, signaling from cell-surface receptors, and many other processes essential for cell and tissue functioning in metazoans. It is also central to the maintenance of PM lipid and protein homeostasis. There are multiple means of internalization that operate concurrently, at the cell surface. With advancement in high-resolution visualization techniques, it is now possible to track multiple endocytic cargo at the same time, revealing a remarkable diversity of endocytic processes in a single cell. A combination of live cell imaging and efficient genetic manipulations has also aided in understanding the functional hierarchy of molecular players in these mechanisms of internalization. Here we provide an account of various endocytic routes, their mechanisms of operation and occurrence across phyla.


id: cord-330110-pamxy4av
title: Mechanism of Inhibition of Enveloped Virus Membrane Fusion by the Antiviral Drug Arbidol
author: Teissier, Elodie
date: 2011-01-25
url: https://doi.org/10.1371/journal.pone.0015874
doi: 10.1371/journal.pone.0015874
abstract:
  The broad-spectrum antiviral arbidol (Arb) inhibits cell entry of enveloped viruses by blocking viral fusion with host cell membrane. To better understand Arb mechanism of action, we investigated its interactions with phospholipids and membrane peptides. We demonstrate that Arb associates with phospholipids in the micromolar range. NMR reveals that Arb interacts with the polar head-group of phospholipid at the membrane interface. Fluorescence studies of interactions between Arb and either tryptophan derivatives or membrane peptides reconstituted into liposomes show that Arb interacts with tryptophan in the micromolar range. Interestingly, apparent binding affinities between lipids and tryptophan residues are comparable with those of Arb IC50 of the hepatitis C virus (HCV) membrane fusion. Since tryptophan residues of membrane proteins are known to bind preferentially at the membrane interface, these data suggest that Arb could increase the strength of virus glycoprotein's interactions with the membrane, due to a dual binding mode involving aromatic residues and phospholipids. The resulting complexation would inhibit the expected viral glycoprotein conformational changes required during the fusion process. Our findings pave the way towards the design of new drugs exhibiting Arb-like interfacial membrane binding properties to inhibit early steps of virus entry, i.e., attractive targets to combat viral infection.


id: cord-333757-h12aozg2
title: Class II Fusion Proteins
author: Modis, Yorgo
date: 2013-07-10
url: https://www.ncbi.nlm.nih.gov/pubmed/23884590/
doi: 10.1007/978-1-4614-7651-1_8
abstract:
  Enveloped viruses rely on fusion proteins in their envelope to fuse the viral membrane to the host-cell membrane. This key step in viral entry delivers the viral genome into the cytoplasm for replication. Although class II fusion proteins are genetically and structurally unrelated to class I fusion proteins, they use the same physical principles and topology as other fusion proteins to drive membrane fusion. Exposure of a fusion loop first allows it to insert into the host-cell membrane. Conserved hydrophobic residues in the fusion loop act as an anchor, which penetrates only partway into the outer bilayer leaflet of the host-cell membrane. Subsequent folding back of the fusion protein on itself directs the C-terminal viral transmembrane anchor towards the fusion loop. This fold-back forces the host-cell membrane (held by the fusion loop) and the viral membrane (held by the C-terminal transmembrane anchor) against each other, resulting in membrane fusion. In class II fusion proteins, the fold-back is triggered by the reduced pH of an endosome, and is accompanied by the assembly of fusion protein monomers into trimers. The fold-back occurs by domain rearrangement rather than by an extensive refolding of secondary structure, but this domain rearrangement and the assembly of monomers into trimers together bury a large surface area. The energy that is thus released exerts a bending force on the apposed viral and cellular membranes, causing them to bend towards each other and, eventually, to fuse.


id: cord-336929-2rnkotqy
title: Host‐cell lipid rafts: a safe door for micro‐organisms?
author: Vieira, Flávia Sarmento
date: 2012-01-03
txt: ./txt/cord-336929-2rnkotqy.txt
cache: ./cache/cord-336929-2rnkotqy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1042/bc20090138
doi: 10.1042/bc20090138
summary:
  In addition to the lipid components, a variety of cell receptors and signalling proteins are known to be associated with membrane rafts. Many animal viruses exploit the endocytic machinery of their host cell for infection, and lipid rafts are often a site for entry, assembly and budding of microbial pathogens, as confirmed by biochemical approaches and microscopy evidence (Kovbasnjuk et al., 2001; Suomalainen, 2002; Lu et al., 2008) . Interestingly, it had already been demonstrated that Brucella abortus infection is related with PrP C (cellular PrP), one of the lipid raft-associated molecules on the plasma membrane of different cell types. In the macrophage-like cell line RAW 264.7, for example, LPS stimulation induces translocation of CD14, ERK-2 (extracellular-signalregulated kinase 2) and p38 to lipid rafts, but other proteins also involved in the LPS signalling response do not migrate within these microdomains (Triantafilou et al., 2007; Olsson and Sundler, 2006) .

abstract:
  The lipid raft hypothesis proposed that these microdomains are small (10–200 nM), highly dynamic and enriched in cholesterol, glycosphingolipids and signalling phospholipids, which compartmentalize cellular processes. These membrane regions play crucial roles in signal transduction, phagocytosis and secretion, as well as pathogen adhesion/interaction. Throughout evolution, many pathogens have developed mechanisms to escape from the host immune system, some of which are based on the host membrane microdomain machinery. Thus lipid rafts might be exploited by pathogens as signalling and entry platforms. In this review, we summarize the role of lipid rafts as players in the overall invasion process used by different pathogens to escape from the host immune system.


id: cord-338827-1moy43hr
title: Membrane Transport
author: Stillwell, William
date: 2016-07-15
url: https://www.sciencedirect.com/science/article/pii/B9780444637727000191
doi: 10.1016/b978-0-444-63772-7.00019-1
abstract:
  Life depends on a membrane's ability to precisely control the level of solutes in the aqueous compartments, inside and outside, bathing the membrane. The membrane determines what solutes enter and leave a cell. Transmembrane transport is controlled by complex interactions between membrane lipids, proteins, and carbohydrates. How the membrane accomplishes these tasks is the topic of this chapter.


id: cord-339172-210dwhgj
author: Knoops, Kèvin
date: 2008-09-16
url: https://www.ncbi.nlm.nih.gov/pubmed/18798692/
doi: 10.1371/journal.pbio.0060226
title:
  SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum

abstract:
  Positive-strand RNA viruses, a large group including human pathogens such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of infected host cells. Their replication complexes are commonly associated with modified host cell membranes. Membrane structures supporting viral RNA synthesis range from distinct spherular membrane invaginations to more elaborate webs of packed membranes and vesicles. Generally, their ultrastructure, morphogenesis, and exact role in viral replication remain to be defined. Poorly characterized double-membrane vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis. We have now applied electron tomography of cryofixed infected cells for the three-dimensional imaging of coronavirus-induced membrane alterations at high resolution. Our analysis defines a unique reticulovesicular network of modified endoplasmic reticulum that integrates convoluted membranes, numerous interconnected DMVs (diameter 200–300 nm), and “vesicle packets” apparently arising from DMV merger. The convoluted membranes were most abundantly immunolabeled for viral replicase subunits. However, double-stranded RNA, presumably revealing the site of viral RNA synthesis, mainly localized to the DMV interior. Since we could not discern a connection between DMV interior and cytosol, our analysis raises several questions about the mechanism of DMV formation and the actual site of SARS-CoV RNA synthesis. Our data document the extensive virus-induced reorganization of host cell membranes into a network that is used to organize viral replication and possibly hide replicating RNA from antiviral defense mechanisms. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of this “replication network” will aid to further dissect the early stages of the coronavirus life cycle and its virus-host interactions.


id: cord-341129-eo0vjcmk
title: Virus membrane-fusion proteins: more than one way to make a hairpin
author: Kielian, Margaret
date: 2006
url: https://www.ncbi.nlm.nih.gov/pubmed/16357862/
doi: 10.1038/nrmicro1326
abstract:
  Structure–function studies have defined two classes of viral membrane-fusion proteins that have radically different architectures but adopt a similar overall 'hairpin' conformation to induce fusion of the viral and cellular membranes and therefore initiate infection. In both classes, the hairpin conformation is achieved after a conformational change is triggered by interaction with the target cell. This review will focus in particular on the properties of the more recently described class II proteins.


id: cord-341378-pw60qx7c
author: Armstrong, John
date: 1984
url: https://www.ncbi.nlm.nih.gov/pubmed/6325918/
doi: 10.1038/308751a0
title:
  Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus

abstract:
  In the eukaryotic cell, both secreted and plasma membrane proteins are synthesized at the endoplasmic reticulum, then transported, via the Golgi complex, to the cell surface(1–4). Each of the compartments of this transport pathway carries out particular metabolic functions(5–8), and therefore presumably contains a distinct complement of membrane proteins. Thus, mechanisms must exist for localizing such proteins to their respective destinations. However, a major obstacle to the study of such mechanisms is that the isolation and detailed analysis of such internal membrane proteins pose formidable technical problems. We have therefore used the E1 glycoprotein from coronavirus MHV-A59 as a viral model for this class of protein. Here we present the primary structure of the protein, determined by analysis of cDNA clones prepared from viral mRNA. In combination with a previous study of its assembly into the endoplasmic reticulum membrane(9), the sequence reveals several unusual features of the protein which may be related to its intracellular localization.


id: cord-346446-i7gpxcyo
title: Biosynthetic Polymalic Acid as a Delivery Nanoplatform for Translational Cancer Medicine
author: Zhang, Jianguo
date: 2020-10-22
txt: ./txt/cord-346446-i7gpxcyo.txt
cache: ./cache/cord-346446-i7gpxcyo.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0968000420302449
doi: 10.1016/j.tibs.2020.09.008
summary:
  pullulan, the addition of exogenous carbonates augments CO 2 fixation and pyruvate carboxylation into oxaloacetate by pyruvate carboxylase in the cytoplasm, abolishing the intramitochondrial pathways for L-malate production and ensuing PMLA synthesis ( Figure 2 ) [23, 30] . At pH 7.4, the terminal α-carboxylic acid in the side chain is deprotonated and ionized; this would be repelled from the cell membrane, but, because of strong hydrophobic interactions, indole in the side chain can attract and intercalate into phospholipids, generating PMLA tritryptophan-lipid complexes and releasing binding energy to stabilize the structure. To increase the interaction between the biopolymer and the plasma membrane, methylation of carboxylic acid groups with different levels of diazomethane was used to generate a PMLA-Me x H 100−x copolymer (where x is the percentage of methyl units) [77, 78] . Analysis of the L-malate biosynthesis pathway involved in poly(beta-L-malic acid) production in Aureobasidium melanogenum GXZ-6 by addition of metabolic intermediates and inhibitors

abstract:
  Poly(β-L-malic acid) (PMLA) is a natural polyester produced by numerous microorganisms. Regarding its biosynthetic machinery, a nonribosomal peptide synthetase (NRPS) is proposed to direct polymerization of L-malic acid in vivo. Chemically versatile and biologically compatible, PMLA can be used as an ideal carrier for several molecules, including nucleotides, proteins, chemotherapeutic drugs, and imaging agents, and can deliver multimodal theranostics through biological barriers such as the blood–brain barrier. We focus on PMLA biosynthesis in microorganisms, summarize the physicochemical and physiochemical characteristics of PMLA as a naturally derived polymeric delivery platform at nanoscale, and highlight the attachment of functional groups to enhance cancer detection and treatment.


id: cord-349341-ap5n6ijl
author: Kopek, Benjamin G
date: 2007-08-14
url: https://www.ncbi.nlm.nih.gov/pubmed/17696647/
doi: 10.1371/journal.pbio.0050220
title:
  Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle

abstract:
  Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)–infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5'-triphosphate incorporation localized between inner and outer mitochondrial membranes inside ∼50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of ∼10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of ∼100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions.


id: cord-353815-w35spqqt
author: Huan, Yuchen
date: 2020-10-16
txt: ./txt/cord-353815-w35spqqt.txt
cache: ./cache/cord-353815-w35spqqt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33178164/
doi: 10.3389/fmicb.2020.582779
summary:
  This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane''s abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) .

title:
  Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields

abstract:
  Antimicrobial peptides (AMPs) are a class of small peptides that widely exist in nature and they are an important part of the innate immune system of different organisms. AMPs have a wide range of inhibitory effects against bacteria, fungi, parasites and viruses. The emergence of antibiotic-resistant microorganisms and the increasing of concerns about the use of antibiotics resulted in the development of AMPs, which have a good application prospect in medicine, food, animal husbandry, agriculture and aquaculture. This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. The research progress on antivirus peptides, especially anti-coronavirus (COVID-19) peptides, has been introduced given the COVID-19 pandemic worldwide in 2020.


id: cord-356090-oj3d9ail
title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane
author: Gorgun, D.
date: 2020-10-27
url: https://doi.org/10.1101/2020.10.27.357350
doi: 10.1101/2020.10.27.357350
abstract:
  Infection of human cells by the SARS-CoV2 relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas. In 60% of the simulations, the FP reaches a stable, membrane-bound configuration where the peptide deeply penetrated into the membrane. Clustering of the results reveals two major membrane binding modes, the helix-binding mode and the loop-binding mode. Taken into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, we propose that the helix-binding mode represents more closely the biologically relevant form. In the helix-binding mode, the helix is stabilized in an oblique angle with respect to the membrane with its N-terminus tilted towards the membrane core. Analysis of the FP-lipid interactions shows the involvement of specific residues of the helix in membrane binding previously described as the fusion active core residues. Taken together, the results shed light on a key step involved in SARS-CoV2 infection with potential implications in designing novel inhibitors. SIGNIFICANCE A key step in cellular infection by the SARS-CoV2 virus is its attachment to and penetration into the plasma membrane of human cells. These processes hinge upon the membrane interaction of the viral fusion peptide, a segment exposed by the spike protein upon its conformational changes after encountering the host cell. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of the bound state.


