title: Scaling Rules for Vibrational Energy Transport in Globular Proteins.
abstract: Computational studies of vibrational energy flow in biomolecules have to date mapped out transport pathways on a case-by-case basis. To provide a more general approach, we derive scaling rules for vibrational energy transport in a globular protein, which are identified from extensive nonequilibrium molecular dynamics simulations of vibrational energy flow in the villin headpiece subdomain HP36. We parametrize a master equation based on inter-residue, residue-solvent, and heater-residue energy-transfer rates, which closely reproduces the results of the all-atom simulations. From that fit, two scaling rules emerge, one for energy transport along the protein backbone which relies on a diffusion model and another for energy transport between tertiary contacts, which is based on a harmonic model. Requiring only the calculation of mean and variance of relatively few atomic distances, the approach holds the potential to predict the pathways and time scales of vibrational energy flow in large proteins.
authors.affiliation: Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , 79104 Freiburg, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Buchenberg
authors.affiliation: Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , 79104 Freiburg, Germany.|Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States.
authors.forename: David M
authors.initials: DM
authors.lastname: Leitner
authors.affiliation: Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , 79104 Freiburg, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Stock
mesh_terms: D004735:Energy Transfer; D008840:Microfilament Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D014732:Vibration
chemical_list: D008840:Microfilament Proteins; C026615:villin