Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone

PLoS Comput Biol. 2011 Sep;7(9):e1002168. doi: 10.1371/journal.pcbi.1002168. Epub 2011 Sep 29.

Abstract

Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations.

Publication types

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

MeSH terms

  • Allosteric Regulation
  • Bacterial Proteins / chemistry
  • Binding Sites
  • Calmodulin / chemistry
  • Computational Biology
  • Computer Simulation*
  • Hydrogen Bonding
  • Models, Molecular*
  • Monte Carlo Method
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Folding
  • Protein Interaction Domains and Motifs
  • Proteins / chemistry*
  • Solvents

Substances

  • Bacterial Proteins
  • Calmodulin
  • Proteins
  • Solvents
  • barstar protein, Bacillus amyloliquefaciens