Detection of Functional Modes in Protein Dynamics

Abstract

Proteins frequently accomplish their biological function by collective atomic motions. Yet the identification of a collective motions related to a specific protein function from, e.g. a molecular dynamics trajectory or an NMR ensemble, is often non-trivial. Here, we propose a novel technique termed ‘functional mode analysis’ that aims to detect the collective motion that is directly related to a particular protein function. Based on an ensemble of structures, together with an arbitrary ‘functional quantity’ that quantifies the functional state of the protein, the method detects the collective motion that is maximally correlated to the functional quantity.