End-point targeted molecular dynamics: large-scale conformational changes in potassium channels.

ABSTRACT: Large-scale conformational changes in proteins that happen often on biological time scales may be relatively rare events on the molecular dynamics time scale. We have implemented an approach to targeted molecular dynamics called end-point targeted molecular dynamics that transforms proteins between two specified conformational states through the use of nonharmonic "soft" restraints. A key feature of the method is that the protein is free to discover its own conformational pathway through the plethora of possible intermediate states. The method is applied to the Shaker K(v)1.2 potassium channel in implicit solvent. The rate of cycling between the open and closed states was varied to explore how slow the cycling rate needed to be to ensure that microscopic reversibility along the transition

SUBMITTER: Mashl RJ 

PROVIDER: S-EPMC2480670 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature