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Stochastic reconstruction of protein structures from effective connectivity profiles

By Katrin Wolff, Michele Vendruscolo and Markus Porto

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 Cα-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

Topics: Research Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2666633
Provided by: PubMed Central
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    Citations

    1. (1995). Argos P: Proteins
    2. (2005). D: Science
    3. (2004). Maritan A: Proc Natl Acad Sci USA
    4. (1996). Molec Graphics
    5. (2000). Nature
    6. (2006). Nishikawa K: BMC Bioinformatics
    7. (2000). Onuchic JN:
    8. (2004). Phys Rev Lett
    9. (1978). Taketomi H: Proc Natl Acad Sci USA
    10. (2007). Tramontano A: Proteins
    11. (1987). Wolynes PG: Proc Natl Acad Sci USA

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