Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.

ABSTRACT: By representing the high-resolution crystal structures of a number of enzymes using the elastic network model, it has been shown that only a few low-frequency normal modes are needed to describe the large-scale domain movements that are triggered by ligand binding. Here we explore a link between the nearly invariant nature of the modes that describe functional dynamics at the mesoscopic level and the large evolutionary sequence variations at the residue level. By using a structural perturbation method (SPM), which probes the residue-specific response to perturbations (or mutations), we identify a sparse network of strongly conserved residues that transmit allosteric signals in three structurally unrelated biological nanomachines, namely, DNA polymerase, myosin motor, and the Escherichia co

SUBMITTER: Zheng W 

PROVIDER: S-EPMC1472502 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature