Explicit Models of Motion to Understand Protein Side-Chain Dynamics

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.

Automated summary

Nuclear magnetic relaxation is commonly used for studying protein dynamics, but the model-free approach falls short when it comes to describing large carbon-13 relaxation datasets in protein side chains. To overcome this limitation, molecular dynamics simulations are employed to design explicit models of motion and solve Fokker-Planck diffusion equations, resulting in improved agreement with relaxation data, mechanistic insight, and a direct linkage to configuration entropy.