Research article

Stochastic reconstruction of protein structures from effective connectivity profiles

Katrin Wolff¹, Michele Vendruscolo² and Markus Porto¹*

• * Corresponding author: Markus Porto porto@fkp.tu-darmstadt.de

Author Affiliations

¹ Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany

² Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK

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PMC Biophysics 2008, 1:5 doi:10.1186/1757-5036-1-5

Published: 26 November 2008

Abstract

We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. The structural profile is used to bias a search of the conformational space towards the target structure in a Monte Carlo scheme operating on a C_α-chain of uniform, finite thickness. Structure information thus enters the folding dynamics via the effective connectivity, but the interaction is not restricted to pairs of amino acids that form native contacts, resulting in a free energy landscape which does not rely on the assumption of minimal frustration. Moreover, effective connectivity vectors can be predicted more readily from the amino acid sequence of proteins than the corresponding contact maps, thus suggesting that the stochastic protocol presented here could be effectively combined with other current methods for predicting native structures.

PACS codes: 87.14.Ee.