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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, 06:07 and posted on 11.09.2020, 13:10 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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