Berlin 2012 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 15: Proteins II
BP 15.4: Vortrag
Mittwoch, 28. März 2012, 16:00–16:15, H 1058
A coarse-grained model for protein folding based on structural profiles — •Katrin Wolff1, Michele Vendruscolo2, and Markus Porto3 — 1SUPA, School of Physics & Astronomy, University of Edinburgh, UK — 2Department of Chemistry, University of Cambridge, UK — 3Institut für Theoretische Physik, Universität Köln
We present a coarse-grained protein model based on structural profiles and apply it to the study of protein free energy landscapes and folding trajectories. Our model’s two main characteristics are a tube-like geometry to describe the self-avoidance effects of the polypeptide chain, and an energy function based on a one-dimensional structural representation [1]. The latter specifies the connectivity of a sequence in a given conformation, so that the energy function, rather than favoring the formation of specific native pairwise contacts, promotes the establishment of a specific native connectivity for each amino acid. We illustrate our approach by applying the model to the folding of the villin headpiece domain to study its folding behavior and determine heat capacities, free energy landscapes and folding trajectories in various reaction coordinates [1,2]. The results closely resemble those found in extensive molecular dynamics studies and support the idea that coarse-grained models that solely rely on the self-avoidance and the connectivity of a polypeptide chain faithfully reproduce many aspects of the folding behaviour of proteins.
[1] K. Wolff, M. Vendruscolo, M. Porto, Phys. Rev. E 84, 041934 (2011)
[2] K. Wolff, M. Vendruscolo, M. Porto, EPL 94, 48005 (2011)