Abstract
Conformational dynamics and flexibility is often essential to protein's function. Calmodulin (CaM) is a well-characterized calcium binding protein that takes functional advantage of its considerable intrinsic conformational flexibility. We investigate the allosteric open/close transition of the domains of CaM through simulations of a multiple basin, topology-based model. Our primary focus is to clarify how main chain flexibility influences the mechanism for allosteric transitions of flexible proteins. In particular, we compare the simulated transition mechanisms of the domains of CaM, which are topologically similar, but differ significantly in their conformational flexibility and dynamics. The simulated transition mechanisms are described at the residue level in terms of local structural order parameters that can be compared with predictions from a coarse grained variational model of allostery (Tripathi and Portman, J. Chem. Phys. 135 075104 (2011)).
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