Conformational and Stability Analysis of SARS-CoV-2 Spike Protein Variants by Molecular Simulation.

ABSTRACT: We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of each variant were characterized by analyzing their distributions within a selected space of collective variables (CVs), such as inter-domain distances between the receptor-binding domain (RBD) and the N-terminal domain (NTD). Our primary focus was to identify conformational states relevant to potential structural transitions and to determine the set of native contacts (NCs) that stabilize these conformations. The results reveal that genetically more distant variants, such as

SUBMITTER: Olivos-Ramirez GE 

PROVIDER: S-EPMC11945020 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature