title: 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 space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America; Chemistry Department, Rice University, Houston, Texas, United States of America.
authors.forename: Mary
authors.initials: M
authors.lastname: A Rohrdanz
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America; Chemistry Department, Rice University, Houston, Texas, United States of America.
authors.forename: Wenwei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America.
authors.forename: Bradley
authors.initials: B
authors.lastname: Lambeth
authors.affiliation: van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Vreede
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America; Chemistry Department, Rice University, Houston, Texas, United States of America.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Clementi
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry* / Q000502:physiology*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004058:Diffusion; D008958:Models, Molecular; D020283:Photoreceptors, Microbial / Q000737:chemistry* / Q000502:physiology*; D015398:Signal Transduction / Q000502:physiology*; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria