Rigid-cluster models of conformational transitions in macromolecular machines and assemblies.

ABSTRACT: We present a rigid-body-based technique (called rigid-cluster elastic network interpolation) to generate feasible transition pathways between two distinct conformations of a macromolecular assembly. Many biological molecules and assemblies consist of domains which act more or less as rigid bodies during large conformational changes. These collective motions are thought to be strongly related with the functions of a system. This fact encourages us to simply model a macromolecule or assembly as a set of rigid bodies which are interconnected with distance constraints. In previous articles, we developed coarse-grained elastic network interpolation (ENI) in which, for example, only Calpha atoms are selected as representatives in each residue of a protein. We interpolate distance differences of

SUBMITTER: Kim MK 

PROVIDER: S-EPMC1366543 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature