Shape-Dependent Global Deformation Modes of Large Protein Structures.

ABSTRACT: Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT(Aa) proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT(Aa) biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following a

SUBMITTER: Miloshevsky GV 

PROVIDER: S-EPMC2878971 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature