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Interaction Analyses on SARS-CoV-2 Spike Protein Based on Large-Scale Correlated Fragment Molecular Orbital Calculations

preprint
submitted on 11.09.2020 and posted on 11.09.2020 by Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka
At the stage of SARS-CoV-2 infection to human cell, the spike protein consisting of three chains, A, B and C, with a total of 3.3 thousand residues plays the key role, and thus its nature have attracted considerable interests. Here, we report interaction analyses on the spike protein of both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller-Plesset perturbation with singles, doubles and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. By two separate calculations for the RBD complexes with angiotensin converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that this stabilization loss of RBD was partially compensated by the binding with ACE2 or antibody.

Funding

Rikkyo SFR

AMED/BINDS (JP20am0101113)

JSPS Kakenhi (JP17H06353, JP18K03825 and JP19K12010)

History

Email Address of Submitting Author

fullmoon@rikkyo.ac.jp

Institution

Rikkyo University

Country

Japan

ORCID For Submitting Author

0000-0002-7310-5183

Declaration of Conflict of Interest

No conflict of interest

Version Notes

1st version, 2020/9/11 JST

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