Regensburg 2016 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 36: Molecular Dynamics (Focus Session)

BP 36.3: Vortrag

Mittwoch, 9. März 2016, 10:15–10:30, H43

Scaling rules for vibrational energy transport in globular proteins — •Sebastian Buchenberg geb. Waltz¹, David M. Leitner², and Gerhard Stock¹ — ¹Biomolekulare Dynamik Physik Uni-Freiburg — ²Chemistry University of Nevada/Reno

Computational studies of vibrational energy flow in biomolecules have to date mapped out transport pathways on a case by case basis [1]. 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 [2]. We parameterize 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. The first for the energy transport along the protein backbone which is described by a diffusion model in which the local diffusion strongly depends on the size of the individual amino acid side chain. And the second for the energy transport between tertiary contacts which is based on a harmonic description and depends on the coupling strength of the contact and the charge of the atoms in contact. Requiring only the calculation of mean and variance of relatively few atomic distances, the approach is able to predict the pathways and timescales of vibrational energy flow in proteins.

[1] D. M. Leitner, S. Buchenberg, P. Brettl and G. Stock, J. Chem. Phys. 142, 075101 (2015) [2] S. Buchenberg, D. M. Leitner and G. Stock, submitted (2015)