Hydrogen bonds vs RMSD: Geometric reaction coordinates for protein folding.

Abstract

Reaction coordinates are a useful tool that allows the complex dynamics of a protein in high-dimensional phase space to be projected onto a much simpler model with only a few degrees of freedom, while preserving the essential aspects of that dynamics. In this way, reaction coordinates could provide an intuitive, albeit simplified, understanding of the complex dynamics of proteins. Together with molecular dynamics (MD) simulations, reaction coordinates can also be used to sample the phase space very efficiently and to calculate transition rates and paths between different metastable states. Unfortunately, ideal reaction coordinates for a system capable of these performances are not known a priori, and an efficient calculation in the course of an MD simulation is currently an active field of research. An alternative is to use geometric reaction coordinates, which, although generally unable to provide quantitative accuracy, are useful for simplified mechanistic models of protein dynamics and can thus help gain insights into the fundamental aspects of these dynamics. In this study, five such geometric reaction coordinates, such as the end-to-end distance, the radius of gyration, the solvent accessible surface area, the root-mean-square distance (RMSD), and the mean native hydrogen bond length, are compared. For this purpose, extensive molecular dynamics simulations were carried out for two peptides and a small protein in order to calculate and compare free energy profiles with the aid of the reaction coordinates mentioned. While none of the investigated geometrical reaction coordinates could be demonstrated to be an optimal reaction coordinate, the RMSD and the mean native hydrogen bond length appeared to perform more effectively than the other three reaction coordinates.