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Coarse-grained representation of beta-helical protein building blocks

  1. Author:
    Curco, D.
    Nussinov, R.
    Aleman, C.
  2. Author Address

    Univ Barcelona, Fac Quim, Dept Engn Quim, E-08028 Barcelona, Spain. NCI, Basic Res Program, SAIC Frederick Inc, Ctr Canc Res Nanobiol Program, Frederick, MD 21702 USA. Tel Aviv Univ, Sackler Sch Med, Dept Human Genet, IL-69978 Tel Aviv, Israel. Univ Politecn Catalunya, ETS Engn Ind Barcelona, Dept Engn Quim, E-08028 Barcelona, Spain.;Aleman, C, Univ Barcelona, Fac Quim, Dept Engn Quim, Marti i Franquees 1, E-08028 Barcelona, Spain.;carlos.aleman@upc.es
    1. Year: 2007
    2. Date: Sep
  1. Journal: Journal of Physical Chemistry B
    1. 111
    2. 35
    3. Pages: 10538-10549
  2. Type of Article: Article
  3. ISSN: 1520-6106
  1. Abstract:

    A general strategy to develop coarse-grained models of beta-helical protein fragments is presented. The procedure has been applied to a building block formed by a two-turn repeat motif from E. coli galactoside acetyltransferase, which is able to provide a very stable self-assembled tubular nanoconstruct upon stacking of its replicas. For this purpose, first, we have developed a computational scheme to sample very efficiently the configurational space of the building block. This method, which is inspired by a strategy recently designed to study amorphous polymers and by an advanced Monte Carlo algorithm, provides a large ensemble of uncorrelated configurations at a very reasonable computational cost. The atomistic configurations provided by this method have been used to obtain a coarse-grained model that describes the amino acids with fewer particles than those required for full atomistic detail, i.e., two, three, or four depending on the chemical nature of the amino acid. Coarse-grained potentials have been developed considering the following types of interactions: (i) electrostatic and van der Waals interactions between residues i and i + n with n >= 2; (ii) interactions between residues i and i + 1; and (c) intra-residue interactions. The reliability of the proposed model has been tested by comparing the atomistic and coarse-grained energies calculated for a large number of independent configurations of the beta-helical building block.

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External Sources

  1. DOI: 10.1021/jp072832q
  2. WOS: 000249169800026

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