Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool

Abstract

We carry out an extensive statistical study of the applicability of normal modes to the prediction of mobile regions in proteins. In particular, we assess the degree to which the observed motions found in a comprehensive data set of 377 nonredundant motions can be modeled by a single normal‐mode vibration. We describe each motion in our data set by vectors connecting corresponding atoms in two crystallographically known conformations. We then measure the geometric overlap of these motion vectors with the displacement vectors of the lowest‐frequency mode, for one of the conformations. Our study suggests that the lowest mode contains useful information about the parts of a protein that move most (i.e., have the largest amplitudes) and about the direction of this movement. Based on our findings, we developed a Web tool for motion prediction (available from http://molmovdb.org/nma ) and apply it here to four representative motions—from bacteriorhodopsin, calmodulin, insulin, and T7 RNA polymerase.