Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein.

ABSTRACT: Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the

SUBMITTER: Remington JM 

PROVIDER: S-EPMC8169235 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature