Structure, dynamics and free energy studies on the effect of point mutations on SARS-CoV-2 spike protein binding with ACE2 receptor

Copyright: © 2023 Rucker et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited..

The ongoing COVID-19 pandemic continues to infect people worldwide, and the virus continues to evolve in significant ways which can pose challenges to the efficiency of available vaccines and therapeutic drugs and cause future pandemic. Therefore, it is important to investigate the binding and interaction of ACE2 with different RBD variants. A comparative study using all-atom MD simulations was conducted on ACE2 binding with 8 different RBD variants, including N501Y, E484K, P479S, T478I, S477N, N439K, K417N and N501Y-E484K-K417N on RBD. Based on the RMSD, RMSF, and DSSP results, overall the binding of RBD variants with ACE2 is stable, and the secondary structure of RBD and ACE2 are consistent after the point mutation. Besides that, a similar buried surface area, a consistent binding interface and a similar amount of hydrogen bonds formed between RBD and ACE2 although the exact residue pairs on the binding interface were modified. The change of binding free energy from point mutation was predicted using the free energy perturbation (FEP) method. It is found that N501Y, N439K, and K417N can strengthen the binding of RBD with ACE2, while E484K and P479S weaken the binding, and S477N and T478I have negligible effect on the binding. Point mutations modified the dynamic correlation of residues in RBD based on the dihedral angle covariance matrix calculation. Doing dynamic network analysis, a common intrinsic network community extending from the tail of RBD to central, then to the binding interface region was found, which could communicate the dynamics in the binding interface region to the tail thus to the other sections of S protein. The result can supply unique methodology and molecular insight on studying the molecular structure and dynamics of possible future pandemics and design novel drugs.

Media Type:

Electronic Article

Year of Publication:

2023

Publication:

2023

Contained In:

To Main Record - volume:18

Contained In:

PloS one - 18(2023), 10 vom: 05., Seite e0289432

Language:

English

Contributors:

Rucker, George [Author]
Qin, Hong [Author]
Zhang, Liqun [Author]

Links:

Volltext

Keywords:

Angiotensin-Converting Enzyme 2
EC 3.4.17.23
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Spike Glycoprotein, Coronavirus
Spike protein, SARS-CoV-2

Notes:

Date Completed 01.11.2023

Date Revised 02.11.2023

published: Electronic-eCollection

Citation Status MEDLINE

doi:

10.1371/journal.pone.0289432

funding:

Supporting institution / Project title:

PPN (Catalogue-ID):

NLM362905134