Open AccessEnergetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins
Author(s) -
Prashant Shingate,
Jim Warwicker,
Ramanathan Sowdhamini
Publication year - 2015
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0127716
Subject(s) - oligomer , monomer , domain (mathematical analysis) , chemistry , mechanism (biology) , biophysics , protein domain , decipher , covalent bond , protein subunit , biochemistry , bioinformatics , biology , physics , polymer , mathematical analysis , mathematics , organic chemistry , quantum mechanics , gene
Domain swapping mechanism is a specialised mode of oligomerization of proteins in which part of a protein is exchanged in a non-covalent manner between constituent subunits. This mechanism is highly affected by several physiological conditions. Here, we present a detailed analysis ofthe effect of pH on different regions of the domain swapped oligomer by considering examples which are known to be sensitive to pH in transiting from monomeric to domain-swapped dimeric form. The energetic calculations were performed using a specialized method which considers changes in pH and subsequent changes in the interactions between subunits. This analysis provides definitive hints about the pH-dependence switch from monomer to domain-swapped oligomer and the steps that may be involved in the swapping mechanism.