Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.

ABSTRACT: Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding. This is in contrast with observations made for protein-protein complexes. In terms of DNA/RNA, both base groups and phosphate groups of nuc

SUBMITTER: Peng Y 

PROVIDER: S-EPMC9843452 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature