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 simulation, as such processes occur on long time scales. The transition path sampling method aims to sample reactive paths connecting two stable states. We used transition path sampling to investigate the mechanisms underlying the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor Photoactive Yellow Protein. This reaction is characterized by loss of alpha-helical structure and solvent exposure of the chromophore binding pocket. Advanced analysis methods predict the best model for the reaction coordinates of each step in the unfolding reactions as well as tentative transition states. We find that the unfolding of the alpha-helical region 43-51 is followed by sequential solvent exposure of Glu46 and the chromophore. Solvent exposure of the chromophore can also occur first, but is a dead-end route. Which of these two residues is exposed first, is correlated with the presence of a salt bridge that is part of the N-terminal domain.