Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication.

ABSTRACT: A protein structure is represented as a network of residues whereby edges are determined by intramolecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino acid pair potentials. Two methodologies are utilized to calculate the average path lengths (APLs) between pairs: to minimize i), the maximum weight in the strong APL, and ii), the total weight in the weak APL. We systematically screen edges that have higher than a cutoff potential and calculate the shortest APLs in these reduced networks, while keeping chain connectivity. Therefore, perturbations introduced at a selected region of the residue network propagate to remote regions only along the nonscreened edges that retain their ability to disseminate the perturbation. T

SUBMITTER: Atilgan AR 

PROVIDER: S-EPMC1852335 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature