Explicit Models of Motion to Understand Protein Side-Chain Dynamics

Phys Rev Lett. 2022 Nov 11;129(20):203001. doi: 10.1103/PhysRevLett.129.203001.

Abstract

Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy.

MeSH terms

  • Diffusion
  • Entropy
  • Molecular Dynamics Simulation*
  • Motion