Collective Motions in Protein Structures: Applications of Elastic Network Models Built from Electron Density Distributions

In this work, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM) approaches are applied to describe the dynamics of Pancreatic Trypsin Inhibitor protein graphs built from smoothed promolecular electron density (ED) distribution functions. A specific smoothing degree is selected which provides a clear partitioning of the protein structure into fragments located either on the protein backbone or side chains. A first set of analyses is carried out on results obtained from ED maxima calculated at that specific smoothing level. A second set is achieved for a protein ED network whose edges are weighted by ED overlap integral values. Results are compared with those obtained through GNM, ANM, and Normal Mode Analysis approaches, applied to the network of C atoms. © 2008 Elsevier B.V. All rights reserved.