Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains.

ABSTRACT: With the aim of investigating the relationship between the fast fluctuations of proteins and their allosteric behavior, we perform molecular dynamics simulations of two model PDZ domains with differential allosteric responses. We focus on protein dynamics in the THz regime (0.1-3 THz) as opposed to lower frequencies. By characterizing the dynamic modulation of the protein backbone induced by ligand binding in terms of single residue and pairwise distance fluctuations, we identify a response nucleus modulated by the ligand that is visible only at THz frequencies. The residues of this nucleus undergo a significant stiffening and an increase in mutual coordination upon binding. Additionally, we find that the dynamic modulation is significantly more intense for the side chains, where it is als

SUBMITTER: Conti Nibali V 

PROVIDER: S-EPMC6421520 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature