Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses.

ABSTRACT:

Motivation

Evolution couples differences in ambient pH to biological function through protonatable groups, in particular, those that switch from buried to exposed and alter protonation state in doing so. We present a tool focusing on structure-based discovery and display of these groups.

Results

Since prediction of buried group pKas is computationally intensive, solvent accessibility of ionizable groups is displayed, from which the user can iteratively select pKa calculation centers. Results are color-coded, with emphasis on buried groups. Utility is demonstrated with benchmarking against known pH sensing sites in influenza virus hemagglutinin and in variants of murine hepatitis virus, a coronavirus. A pair of histidine residues, which are conserved in coronavirus spike prot

SUBMITTER: Hebditch M 

PROVIDER: S-EPMC7454282 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature