Geometrical Constraints Limiting the Poly(ADP-ribose) Conformation Investigated by Molecular Dynamics Simulation Ilda D’Annessa, Andrea Coletta, Alessandro Desideri Department of Biology and Centro di Bioinformatica e Biostatistica, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy Received 12 February 2013; revised 22 April 2013; accepted 5 May 2013 Published online 12 May 2013 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/bip.22280 ABSTRACT: Poly(ADP-ribosylation) is a post-transductional modification that regulates protein’s function. Most of the proteins sub- jected to this control mechanism belong to machineries involved in DNA damage repair, or DNA interacting pro- teins. 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 con- cerning its structure. To understand, which are the geometri- cal parameters that confer to the polymer the structural constraints that determine its interaction with the target pro- teins, 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. V C 2013 Wiley Periodicals, Inc. Biopolymers 101: 78–86, 2014. Keywords: poly(ADP-ribose); molecular dynamics; poly- mer; dihedral angles This article was originally published online as an accepted pre- print. 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 INTRODUCTION P rotein’s function is regulated by a series of modifica- tions that can occur either after transcription or translation. The post-translational modification of proteins is an advantageous strategy for the cell to increase the functional diversity of the proteome and to regulate the level of activity of proteins. These modifi- cations include phosphorylation, glycosylation, ubiquitina- tion, nitrosylation, methylation, acetylation, lipidation, sumoylation, poly(ADP-ribosylation), and proteolysis. Poly(ADP-ribosylation) is an important modification occurring in proteins involved in DNA damage control=repair machineries, chromatin modification, transcription, cell death pathways, insulator function, mitotic apparatus function, and in general in proteins whose function is directly related to the interaction with the DNA, such as histones, transcription fac- tors, and DNA repair proteins. 1–8 In detail, DNA damage induced by chemical carcinogens and ionizing radiation acti- vates Poly ADP Ribose Polymerase (PARP) that catalyzes the synthesis of Poly(ADP-ribose) polymer (PAR) using NAD 1 as a precursor, 5,7,9–11 forming both linear or branched chains of different length ranging from 20 to 100 monomers. 12,13 The role of PAR is to recruit several proteins in proximity of the DNA damage and the polymer is then degraded by PARG, once the damage has been repaired. 14 Each Poly(ADP-ribose) chain starts with an O1D terminal (on the “distal” ribose moiety of the first monomer) and ends with one or more (in case of branching) O2 0 terminal (on the adenosine moiety of the last monomer). The monomers are joined each other by an a(1 ! 2) ribose–ribose linkage, and the same bond also occurs in the branching. 10,15 In the case of the linear linkage the bond happens between the O2 atom of the ribose joined to adenine, labeled O2 0 , and the C1 atom of the free ribose of the following monomer, labeled C1D (Figure S1). At the level of the branching, the bond occurs between the two free riboses, being O2D and C1D the atoms involved (Figure S1). Additional Supporting Information may be found in the online version of this article. Correspondence to: Alessandro Desideri; e-mail: desideri@uniroma2.it Contract grant sponsor: Associazione Italiana Ricerca Cancro AIRC Contract grant number: N. 10121 V C 2013 Wiley Periodicals, Inc. 78 Biopolymers Volume 101 / Number 1