Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

被引：23

作者：

Akisawa, Kazuki ^{[1
,2
]}

Hatada, Ryo ^{[1
,2
]}

Okuwaki, Koji ^{[1
,2
]}

Mochizuki, Yuji ^{[1
,2
,3
]}

Fukuzawa, Kaori ^{[3
,4
,5
]}

Komeiji, Yuto ^{[6
]}

Tanaka, Shigenori ^{[7
]}

机构：

[1] Rikkyo Univ, Fac Sci, Dept Chem, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan

[2] Rikkyo Univ, Fac Sci, Res Ctr Smart Mol, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan

[3] Univ Tokyo, Inst Ind Sci, Meguro Ku, 4-6-1 Komaba, Tokyo 1538505, Japan

[4] Hoshi Univ, Sch Pharm & Pharmaceut Sci, Shinagawa Ku, 2-4-41 Ebara, Tokyo 1428501, Japan

[5] Tohoku Univ, Grad Sch Engn, Dept Biomol Engn, Aoba Ku, 6-6-11 Aramaki, Sendai, Miyagi 9808579, Japan

[6] AIST, Hlth & Med Res Inst, Tsukuba Cent 6, Tsukuba, Ibaraki 3058566, Japan

[7] Kobe Univ, Dept Computat Sci, Grad Sch Syst Informat, Nada Ku, 1-1 Rokkodai, Kobe, Hyogo 6578501, Japan

来源：

RSC ADVANCES | 2021年 / 11卷 / 06期

关键词：

INFLUENZA-VIRUS HEMAGGLUTININ; INTERACTION ENERGY ANALYSIS; BINDING; PREDICTION; COVID-19; RECEPTOR;

D O I：

10.1039/d0ra09555a

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

At the stage of SARS-CoV-2 infection in human cells, the spike protein consisting of three chains, A, B, and C, with a total of 3300 residues plays a key role, and thus its structural properties and the binding nature of receptor proteins to host human cells or neutralizing antibodies has attracted considerable interest. Here, we report on interaction analyses of the spike protein in 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 Moller-Plesset perturbation with singles, doubles, and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and a mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. The role of charged residues in inter-chain interactions was illuminated as well. By two separate calculations for the RBD complexes with angiotensin-converting enzyme 2 (ACE2) (; 6M0J) and B38 Fab antibody (; 7BZ5), it was found that the binding with ACE2 or antibody partially compensated for this stabilization loss of RBD.

引用

页码：3272 / 3279

页数：8

共 66 条

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