Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis

J Phys Chem B. 2023 Jan 26;127(3):623-633. doi: 10.1021/acs.jpcb.2c06546. Epub 2023 Jan 10.

Abstract

Allosteric signaling in proteins has been known for some half a century, yet how the signal traverses the protein remains an active area of research. Recently, the importance of electrostatics to achieve long-range signaling has become increasingly appreciated. Our laboratory has been working on developing network approaches to capture such interactions. In this study, we turn our attention to the well-studied allosteric model protein, PDZ. We study the allosteric dynamics on a per-residue basis in key constructs involving the PDZ domain, its allosteric effector, and its peptide ligand. We utilize molecular dynamics trajectories to create the networks for the constructs to explore the allosteric effect by plotting the heat kernel results onto axes defined by principal components. We introduce a new metric to quantitate the volume sampled by a residue in the latent space. We relate our findings to PDZ and the greater field of allostery.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Allosteric Regulation
  • Molecular Dynamics Simulation
  • PDZ Domains* / physiology
  • Protein Binding
  • Proteins* / chemistry
  • Signal Transduction* / physiology
  • Static Electricity

Substances

  • Proteins