title: The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations.
abstract: Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.
authors.affiliation: Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, 67084 Cedex, Strasbourg, France. p.auffinger@ibmc.u-strasbg.fr
authors.forename: Pascal
authors.initials: P
authors.lastname: Auffinger
authors.forename: Lukasz
authors.initials: L
authors.lastname: Bielecki
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
mesh_terms: D001665:Binding Sites; D002413:Cations, Divalent; D003198:Computer Simulation; D003460:Crystallization; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D002413:Cations, Divalent; D012329:RNA, Bacterial; D012341:RNA, Ribosomal, 5S; D014867:Water; D008274:Magnesium