Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin.

ABSTRACT: Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis, and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of efficiently exploring a vast conformational space in order to seek for the actual transition path for systems whose complexity is already high in the stable states. Here we report a strategy that simplifies this task attacking the complexity on several sides. We first apply a minimalist coarse-grained model to Calmodulin, based on an empirical force field with a partial structural bias, to explore the transition paths between the apo-closed state and the Ca-bound open state of the protein. We then select representative structures along the trajectory bas

SUBMITTER: Delfino F 

PROVIDER: S-EPMC6843051 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature