Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

ABSTRACT: The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration

SUBMITTER: A Rohrdanz M 

PROVIDER: S-EPMC4214557 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature