Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory

TL;DR

This study combines replica-exchange Monte Carlo simulations and diffusion theory to accurately predict NMR dynamical properties of a C-peptide, demonstrating good agreement with experimental data.

Contribution

It introduces a novel integration of generalized-ensemble algorithms with diffusion theory for calculating NMR dynamical properties from molecular simulations.

Findings

Good agreement between simulated and experimental NMR cross peaks

Effective evaluation of dynamical properties using combined statistical tools

Potential for routine calculation of NMR observables from simulations

Abstract

Generalized-ensemble algorithm and diffusion theory have been combined in order to compute the dynamical properties monitored by nuclear magnetic resonance experiments from efficient and reliable evaluation of statistical averages. Replica-exchange Monte Carlo simulations have been performed with a C-peptide analogue of ribonuclease A, and Smoluchowski diffusion equations have been applied. A fairly good agreement between the calculated and measured $^1$H-NOESY NMR cross peaks has been obtained. The combination of these advanced and continuously improving statistical tools allows the calculation of a wide variety of dynamical properties routinely obtained by experiments.