id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-279172-d2algx16	Zheng, Kewen	Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme	2006-11-02		.txt	text/plain	6381	284	58	During the MD simulation of dimer, three interest phenomena of protomer A have been observed: (i) the distance between NE2 of His41 and SG of Cys145 averages 3.72 Å, which agrees well with the experimental observations made by X‐ray crystallography; (ii) His163 and Glu166 form the "tooth" conformational properties, resulting in the specificity for glutamine at substrate P1 site; and (iii) the substrate‐binding pocket formed by loop 140–146 and loop 184–197 is large enough to accommodate the substrate analog. In this research, by comparing the process of the MD simulation of monomer with dimer, our aim is to (i) find the structural variations and dynamics of the active site residues in SARS M pro monomer in contrast to the dimer, which result in an inactive monomer and provide useful information for receptor based drug design; (ii) investigate the detailed specific interactions involving the two monomers within the dimer and its functional roles in maintaining the activity of the dimer, which provides insights for the design of specific protease inhibitors using the interface of the dimer as a new target.	./cache/cord-279172-d2algx16.txt	./txt/cord-279172-d2algx16.txt