A Retrospective on the Development of Methods for the Analysis of Protein Conformational Ensembles

Abstract

Analysing protein conformational ensembles whether from molecular dynamics (MD) simulation or other sources for functionally relevant conformational changes can be very challenging. In the nineteen nineties dimensional reduction methods were developed primarily for analysing MD trajectories to determine dominant motions with the aim of understanding their relationship to function. Coarse-graining methods were also developed so the conformational change between two structures could be described in terms of the relative motion of a small number of quasi-rigid regions rather than in terms of a large number of atoms. When these methods are combined, they can characterize the large-scale motions inherent in a conformational ensemble providing insight into possible functional mechanism. The dimensional reduction methods first applied to protein conformational ensembles were referred to as Quasi-Harmonic Analysis, Principal Component Analysis and Essential Dynamics Analysis. A retrospective on the origin of these methods is presented, the relationships between them explained, and more recent developments reviewed.