Regensburg 2010 – wissenschaftliches Programm
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DY: Fachverband Dynamik und Statistische Physik
DY 5: Statistical Physics of Biological Systems II (joint session of BP + DY)
DY 5.9: Vortrag
Montag, 22. März 2010, 16:30–16:45, H45
Protein folding trajectories and free energy landscapes in a coarse-grained model — •Katrin Wolff1, Michele Vendruscolo2, and Markus Porto1 — 1Institut für Festkörperphysik, TU Darmstadt, Germany — 2Department of Chemistry, University of Cambridge, UK
We study protein free energy landscapes and folding dynamics from completely unfolded to folded structures using a coarse-grained model biased towards the native state. Proteins are modeled as a chain of uniform thickness with bending rigidity (tube model [1]) with a bias towards the native structure based on a one-dimensional representation of the structure (structure profile). This approach is conceptually very different from those relying on the assumption of minimal frustration (such as Gō-models) since it does not favour the formation of contacts between specific residues but mediates ‘connectivity’ of residues, that, much like hydrophobicity, describes a residue’s propensity to form contacts. We show that the ‘effective connectivity’ profile [2] constitutes a suitable bias towards the native structure [3] and investigate free energy landscapes, heat capacity curves and typical folding trajectories and compare our results to experimental folding behaviour and results from (much more computationally expensive) molecular dynamics simulations.
[1] T.X. Hoang et al., Proc. Natl. Acad. Sci. USA 101, 7960 (2004).
[2] U. Bastolla et al., Proteins 73, 872 (2008).
[3] K. Wolff, M. Vendruscolo, and M. Porto, PMC Biophysics 1, 5 (2008)