Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein.

ABSTRACT: Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the alpha-helical region 43-51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge th

SUBMITTER: Vreede J 

PROVIDER: S-EPMC2823881 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature