Prediction of NMR order parameters in proteins using weighted protein contact-number model

Abstract

In the NMR experiment, the protein backbone motion can be described by the N-H order parameters. Though protein dynamics is determined by a complex network of atomic interactions, we show that the order parameter of residues can be determined using a very simple method, the weighted protein contact number model. We computed for each C alpha atom the number of neighboring C alpha atoms weighted by the inverse distance squared between them. We show that the weighted contact number of each residue is directly related to its order parameter. Despite the simplicity of this model, it performs better than the other method. Since we can compute the order parameters directly from the topological properties (such as protein contact number) of protein structures, our study underscores a very direct link between protein topological structure and its dynamics.