A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain.

ABSTRACT: Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting "dynamic MHP portraits" and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, an

SUBMITTER: Aliper ET 

PROVIDER: S-EPMC9409440 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature