Geometrical constraints limiting the poly(ADP-ribose) conformation investigated by molecular dynamics simulation

Authors

  • Ilda D'Annessa,

    1. Department of Biology and Centro di Bioinformatica e Biostatistica, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome, Italy
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  • Andrea Coletta,

    1. Department of Biology and Centro di Bioinformatica e Biostatistica, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome, Italy
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  • Alessandro Desideri

    Corresponding author
    1. Department of Biology and Centro di Bioinformatica e Biostatistica, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome, Italy
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

ABSTRACT

Poly(ADP-ribosylation) is a post-transductional modification that regulates protein's function. Most of the proteins subjected to this control mechanism belong to machineries involved in DNA damage repair, or DNA interacting proteins. Poly(ADP-ribose) polymers are long chains of even 100 monomer length that can be branched at several positions but, not withstanding its importance, nothing is known concerning its structure. To understand, which are the geometrical parameters that confer to the polymer the structural constraints that determine its interaction with the target proteins, we have performed molecular dynamics of three chains of different length, made by 5, 25, and 30 units, the last one being branched. Analysis of the simulations allowed us to identify the main intra- and inter-monomer dihedral angles that govern the structure of the polymer that however, does not reach a unique definite conformation. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 78–86, 2014.

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