Deciphering collaborative sidechain motions in proteins during molecular dynamics simulations.

ABSTRACT: The dynamic structure of proteins is essential for their functions and may include large conformational transitions which can be studied by molecular dynamics (MD) simulations. However, details of these transitions are difficult to automatically track. To facilitate their analysis, we developed two scores of correlation between sidechain dihedral angles. The CIRCULAR and OMES scores are computed from, respectively, dihedral angle values and rotamer distributions. As a case study, we applied our methods to an activation-like transition of the chemokine receptor CXCR4, observed during accelerated MD simulations. The principal component analysis of the correlation matrices was consistent with the networking structure of the top ranking pairs. Both scores identify a set of residues whose "coll

SUBMITTER: Taddese B 

PROVIDER: S-EPMC7522237 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature