Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

ABSTRACT: Recently we have developed a normal-modes-based algorithm that predicts the direction of protein conformational changes given the initial state crystal structure together with a small number of pairwise distance constraints for the end state. Here we significantly extend this method to accurately model both the direction and amplitude of protein conformational changes. The new protocol implements a multisteps search in the conformational space that is driven by iteratively minimizing the error of fitting the given distance constraints and simultaneously enforcing the restraint of low elastic energy. At each step, an incremental structural displacement is computed as a linear combination of the lowest 10 normal modes derived from an elastic network model, whose eigenvectors are reorientated

SUBMITTER: Zheng W 

PROVIDER: S-EPMC1471861 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature