501Y.V2 spike protein resists the neutralizing antibody in atomistic simulations. (April 2022)

• Record Type: Journal Article
• Authors: Ngo, Son Tung
• Is Part Of: Computational biology and chemistry. Volume 97(2022)
• Publication Date: 2022-04
• Subjects: SARS-CoV-2 -- Spike protein -- 501Y.V2 -- B.1.351 -- SMD simulations -- Neutralizing antibody; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2022.107636
• Languages: English
• ISSNs: 1476-9271

Abstract

Abstract: SARS-CoV-2 outbreaks worldwide caused COVID-19 pandemic, which is related to several million deaths. In particular, SARS-CoV-2 Spike (S) protein is a major biological target for COVID-19 vaccine design. Unfortunately, recent reports indicated that Spike (S) protein mutations can lead to antibody resistance. However, understanding the process is limited, especially at the atomic scale. The structural change of S protein and neutralizing antibody fragment (FAb) complexes was thus probed using molecular dynamics (MD) simulations. In particular, the backbone RMSD of the 501Y.V2 complex was significantly larger than that of the wild-type one implying a large structural change of the mutation system. Moreover, the mean of R g, CCS, and SASA are almost the same when compared two complexes, but the distributions of these values are absolutely different. Furthermore, the free energy landscape of the complexes was significantly changed when the 501Y.V2 variant was induced. The binding pose between S protein and FAb was thus altered. The FAb-binding affinity to S protein was thus reduced due to revealing over steered-MD (SMD) simulations. The observation is in good agreement with the respective experiment that the 501Y.V2 SARS-CoV-2 variant can escape from neutralizing antibody (NAb). Graphical Abstract: ga1 Highlights: 501Y.V2 spike protein resists the neutralizing antibody. Free energy landscape was significantly changed when the 501Y.V2 variant was induced. The 501Y.V2 S protein + FAb structure is more flexible than the wild-type system.