A comparison of reduced coordinate sets for describing protein structure

摘要

In all-atom molecular simulation studies of proteins, each atom in the protein is represented by a point mass and interactions are defined in terms of the atomic positions. In recent years, various simplified approaches have been proposed. These approaches aim to improve computational efficiency and to provide a better physical insight. The simplified models can differ widely in their description of the geometry and the interactions inside the protein. This study explores the most fundamental choice in the simplified protein models: the choice of a coordinate set defining the protein structure. A simplified model can use fewer point masses than the all-atom model and/or eliminate some of the internal coordinates of the molecule by setting them to an average or ideal value. We look at the implications of such choices for the overall protein structure. We find that care must be taken for angular coordinates, where even very small variations can lead to significant changes in the positions of far away atoms. In particular, we show that the φ/ψ torsion angles are not a sufficient coordinate set, whereas another coordinate set with two degrees of freedom per residue, virtual C_α backbone bond, and torsion angles performs satisfactorily.