Dresden 2011 – scientific programme
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BP: Fachverband Biologische Physik
BP 2: Protein Structure \& Dynamics
BP 2.6: Talk
Monday, March 14, 2011, 12:00–12:15, ZEU 260
Asymmetric folding pathways and transient misfolding in a coarse-grained model of proteins — •Katrin Wolff1, Michele Vendruscolo2, and Markus Porto3 — 1Institute for Condensed Matter and Complex Systems, University of Edinburgh, UK — 2Department of Chemistry, University of Cambridge, UK — 3Institut für Theoretische Physik, Universität zu Köln, Germany
We investigate free energy landscapes and protein folding pathways in a coarse-grained protein model. Our model’s two primary 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 which specifies the amino acids’ connectivity for any given conformation. Such an energy function, rather than favouring the formation of specific native pairwise contacts, promotes the establishment of the native connectivity for each amino acid. Specifically, we look at the free energy landscape of the villin headpiece domain (Protein Data Bank (PDB) id. 1und) and show that in its distinctive asymmetry it resembles that found in computationally much more demanding atomistic molecular dynamics studies [1]. That the asymmetry is indeed a specific feature of the villin headpiece domain is demonstrated by studying the free energy landscape of another small three-helix bundle protein (PDB id. 1dv0), for which we find an essentially symmetric free energy landscape [2].
[1] H. Lei et al., Proc. Natl. Acad. Sci. USA 104, 4925 (2007)
[2] K. Wolff et al., submitted