title: Vibrational energy flow in the villin headpiece subdomain: master equation simulations.
abstract: We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1-10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.
authors.affiliation: Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Leitner
authors.affiliation: Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Buchenberg
authors.affiliation: Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Brettel
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Stock
mesh_terms: D003198:Computer Simulation; D006801:Humans; D006860:Hydrogen Bonding; D008840:Microfilament Proteins / Q000737:chemistry*; D008958:Models, Molecular; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: D008840:Microfilament Proteins; C026615:villin; D014867:Water