key: cord-0849581-ewjycudf
authors: Rui, Li; Haonan, Li; Wanyi, Chen
title: Silico analysis of interaction between full-length SARS-CoV2 S protein with human Ace2 receptor: Modelling, docking, MD simulation
date: 2020-09-03
journal: Biophys Chem
DOI: 10.1016/j.bpc.2020.106472
sha: 864c2a3d090de761ce06c0b29a18aa9d88a4622d
doc_id: 849581
cord_uid: ewjycudf

Many key residues, which mediate the interaction between SARS-CoV2 spike glycoprotein (S protein) and human ACE2 receptor, have been reviewed using the SARS-CoV2 S spike protein with human ACE2 complex. The initial SARS-CoV2 S protein and ACE2 protein complex structure is formed by RBD structure of SARS-CoV2 S protein and ACE2 protein. However, the cryo-EM structure study targeting SARS-Cov S protein with human ACE2 complex has shown that there exist different binding conformations during the binding process facing ACE2 protein. It suggests the interaction between SARS-CoV2 S spike protein complex might have different binding conformations, which request full-length of SARS-CoV2 S protein complex in the structure-functional analysis. In this study, we built a full-length SARS-CoV2 S protein with human ACE2 complex by computational methods. Residues K31, H34, E35 in ACE2 protein were showed both in our full-length model and RBD structure model, which recognized as critical residues in previous studies. Surprisingly, ACE2 residues E564, R559, N556 were only found participating in the interaction of our full-length model, which suggested the full-length model has bigger binding interface. This finding was further supported by the interaction network of full-length model and RBD model. Meanwhile, the method bias was taken into consideration. Eventually, the MM-PBSA results showed the full-length model had a stronger binding free energy (almost 5-fold) than the RBD structure model of SARS-CoV2 S spike protein complex. In computational level, we present a stronger binding model containing a full-length structure of SARS-CoV2 S protein with ACE2 complex.

In early 2020, a novel coronavirus named SARS-CoV2 (COVID-19) has resulted in a global health issue with its high infectious ability and lethal consequence. It has become a continuous threat to the wellbeing of human life which has made this RNA virus to be an emergency subject [1] [2] [3] [4] . It is believed that the spike glycoprotein (S protein) on the virion surface mediates receptor recognition and host selectivity [5] .

Meanwhile, evidence has shown the SARS-Cov and SARS-CoV2 spike proteins interact with angiotensin-converting enzyme 2 (ACE2) [6, 7] . Previously, the study of cryo-EM structure has reviewed the different conformation states of SARS-Cov S protein and further confirmed that the up conformation of receptor-binding domain (RBD) is required for ACE2 binding [8] . This full-length model has shown the binding process of ACE2 protein might request full-length structure of S protein to carry on binding procedure between virus and human. In addition, only the RBD structure of SARS-COVID-2 S protein complex with human ACE2 has been solved by X-ray diffraction 2.68 Å (code: 6VW1) [9] . Based that, several structure studies have located some key residues mediating the spike protein and ACE2 protein and ACE2 residue K31, E35, M82, K353, Q24, D30, Y41, Y83, R357 are multiple showed in these studies [7, [9] [10] [11] [12] . And the binding pocket of ACE2 could be initially located. However, there still exist a need of full-length model to ensure that all the binding interfaces were under fully consideration Hence, the model containing full-length SARS-CoV2 S protein targeting human ACE2 might present the bigger binding info than RBD complex model.

With computational methods, we built a complex containing full-length SARS-CoV2 were found as well as previous studies. Meanwhile, we calculated the binding free energy of RBD structure and full-length structure of SARS-CoV2 S protein complex to find the better computational model. This study might provide further information about SARS-Cov and SARS-CoV2 targeting human ACE2.

To carry on docking and MD simulations, the SARS-Cov and ACE2 complex structure, ACE2-bound conformation 1 (code: 6ACG), was used as a template of SARS-CoV2 bound human ACE2 complex [13] . Structure of SARS-CoV2 chimeric receptor-binding domain complexed with its receptor human ACE2 (code: 6VW1) was used as a control group [8] . The SARS-CoV2 sequence used for the modelling process and binding was obtained from NCBI (NC_045512.2) [14] . The algorithm of alignment was ClustalW server (https: // www. genome. Jp /tools -bin /clustalw) and

ESPriPt sever (espript. ibcp. fr/ ESPript/ cgi-bin/ ESPript. cgi) [15] .

Homology model of SARS-CoV2 was built through server [16] . Several models were built and the quality of them was evaluated. The best model was obtained using the template 6ACG. Then, by using rosetta2019 program, the initial structure of SARS-CoV2 was refined for docking [17] .

The Rosetta program was used for docking to further locate the binding interface [18] .

The full-length S protein complexes containing SARS-CoV2 or SARS-Cov with human ACE2 complexes were carried on docking for 30 times. Docking results were evaluated by ref2015 score-function of Rosetta program. And no significant shift was observed in 30 results, thus the best model was obtained for MD simulation.

Complexes were carried on MD simulations using the GROMACS program [19, 20] .

The AMBER ff99sb force field was used in MD simulation. And all models were dissolved with TIP3P water models. All periodic boxes were set to ensure that the complex center was at least 0.5 nm away from the wall. The electroneutral system J o u r n a l P r e -p r o o f Journal Pre-proof was separately guaranteed by adding the Na + or CLseparately. After that, all systems were minimized by running the steepest descent method with step 1E-3 ps with 10,000 steps. Then, to achieve equilibration, V-rescale method and Berendsen method were used for 100 ps run. Finally, all well-prepared systems were performed under 300K and 1bar. The full-length SARS-CoV2 S protein complex was calculated for 30 ns and so did full-length SARS-Cov S protein complex. And the structure of SARS-CoV2 chimeric receptor-binding domain complexed with its receptor human ACE2 was calculated for 100 ns under the same condition. The two full-length complexes were calculated 30 ns because each system contained 471596 atoms and 472054 atoms, while the RBD structure of SARS-CoV2 S protein system contained 86388 atoms. Full-length models were almost 6-fold bigger than RBD structure complex. The most common structures were analyzed by cluster process which presented the binding state of each complex. Then, the MMPBSA.py package of AMBERTOOLS18 program was used for MM-PBSA calculation [21] . Further, we calculated the interaction network in full-length model and RBD model by using RING server, which was designed to analyze the interaction between ligands and receptor [22] . The algorithm firstly generated the network by a list of residue-residue pairs to present interaction based on distance measurements. Then the algorithm characterized contact info of input structure by using the specific type of interaction.

The sequence alignment results suggested that the sequence identity, between the full-length SARS-CoV2 S protein and the SARS-Cov S protein (code: 6ACG), was 75.12%, shown in Fig.S2-S3 . Thus, the initial model was built by using the template 6ACG. To evaluate and refine the structure, Rosetta program was used in this study.

The human ACE2 protein was docking to refined structure, firstly optimized the rigid body of complex, then optimized the ACE2 protein backbone to generate the low-resolution structure. Eventually, the side-chain rotamers were refined to generate the high-resolution structure. The top 10 docking results were listed in Table 1 Table 1 The top 10 models from evaluations of full-length SARS-CoV2 S protein with human ACE2. The total_score presented the quality of each complex. I_sc present the interface quality in each complex while pep_sc present the ACE2 quality of each complex. 

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