Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special-purpose system. Because not only the most stable structure but also meta-stable structures and intermediate structures are included in trajectories in long simulations, it becomes to be necessary to develop dynamical analysis method to automatically extract reaction coordinates that identify these structures. We have applied relaxation mode analysis (RMA) to folding simulations and several-microsecond-scale molecular dynamics simulations for investigating dynamics and kinetics of proteins. We also have developed new methods related to RMA such as PCRMA, MSRMA, and PDRMA. Here, we present RMAs and several results of protein simulations.

Dynamical analysis for protein simulations using relaxation mode analysis

ACS Spring 2022

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