title: Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System.
abstract: Coarse-grained molecular dynamics (CG-MD) may be applied as part of a multiscale modeling approach to protein-protein interactions. The cohesin-dockerin interaction provides a valuable test system for evaluation of the use of CG-MD, as structural (X-ray) data indicate a dual binding mode for the cohesin-dockerin pair. CG-MD simulations (of 5 μs duration) of the association of cohesin and dockerin identify two distinct binding modes, which resemble those observed in X-ray structures. For each binding mode, ca. 80% of interfacial residues are predicted correctly. Furthermore, each of the binding modes identified by CG-MD is conformationally stable when converted to an atomistic model and used as the basis of a conventional atomistic MD simulation of duration 20 ns.
authors.affiliation: Department of Biochemistry & Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Hall
authors.affiliation: Department of Biochemistry & Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom