ArticleRSC advances2021
Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations.
Article in RSC advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Residue‑resolved dynamically averaged interaction analysis of direct factor Xa inhibitors by MD‑FMO combination calculations.Journal of computer-aided molecular design · 2026Article
- Advancing Medicinal Chemistry Through FMO: Sygnature's Platform.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Protein-Protein Interactions Analyzed by the Fragment Molecular Orbital Method.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses.Chemical science · 2021Article
- Fragme∩t: An Open-Source Framework for Multiscale Quantum Chemistry Based on Fragmentation.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
7 authors.
Funding
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Abstract
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 Møller-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.
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Registered trials
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