Berlin 2012 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 7: Posters: Proteins

BP 7.35: Poster

Montag, 26. März 2012, 17:30–19:30, Poster A

Peptide Dynamics Simulations in Light and Heavy Water: Zooming in on Internal Friction — •Julius Christoph Friedrich Schulz Schulz¹, Lennart Schmidt¹, Joachim Dzubiella², and Roland Netz¹ — ¹Fachbereich Physik, Freie Universitaet Berlin, 14195 Berlin, Germany — ²Helmholtz Zentrum Berlin fuer Materialien und Energie, 14109 Berlin, Germany

Frictional effects due to the chain itself, rather than the solvent, may have a significant effect on protein dynamics. Experimentally, such "internal friction" has been investigated by studying folding or binding kinetics at varying solvent viscosity; however the molecular origin of these effects is hard to pinpoint. We consider the kinetics of disordered glycine-serine and alpha-helix forming alanine peptides, and a coarse-grained protein folding model in explicit-solvent molecular dynamics simulations. By varying the solvent mass over more than two orders of magnitude, we alter only the solvent viscosity and not the folding free energy. Folding dynamics at the near-vanishing solvent viscosities accessible by this approach suggest that solvent and internal friction effects are intrinsically entangled. This finding is rationalized by calculation of the polymer end-to-end distance dynamics from a Rouse model that includes internal friction. An analysis of the friction profile along different reaction coordinates suggests a connection between friction and the formation of hydrogen bonds upon folding.