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Atomistic modeling of peptides bound to a chemically active surface: conformational implications

Authors

  • David Curcó,

    1. Department d'Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí Franques 1, Barcelona E-08028, Spain
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  • Guillem Revilla-López,

    1. Departament d'Enginyeria Química, E. T. S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
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  • Carlos Alemán,

    Corresponding author
    1. Departament d'Enginyeria Química, E. T. S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
    2. Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
    • Departament d'Enginyeria Química, E. T. S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.
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  • David Zanuy

    Corresponding author
    1. Departament d'Enginyeria Química, E. T. S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
    • Departament d'Enginyeria Química, E. T. S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.
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  • Special issue devoted to contributions presented at the E-MRS Symposium C “Peptide-based materials: from nanostructures to applications”, 7–11 June 2010, Strasbourg, France.

Abstract

This work presents a computational strategy to model flexible molecules tethered to a metallic rigid surface. The method is based on a previously developed procedure for inert surfaces, in which peptide–surface interactions were not considered. This procedure is able to generate uncorrelated relaxed microstructures at the atomistic level of systems containing relatively high densities of peptides tethered to the surface. The reliability of the strategy has been tested by simulating CREKA (Cys-Arg-Glu-Lys-Ala), a short linear pentapeptide that recognizes clotted plasma proteins and selectively homes to tumors, covalently tethered to a gold surface, results being compared with those obtained when the surface was represented as inert. The results indicate that the whole conformational profile of CREKA presents some correlation with the chemical activity of the surface, even though the bioactive conformation was found as the most favored in all cases. Specifically, simulations reflect that consideration of the peptide-surface interactions affect the geometrical orientation of the side chains, whereas the main chain conformation does not undergo significant modifications. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.

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