@article{,
title = {The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12837388},
isbn = {12837388},
year = {2003},
date = {2003-01-01},
journal = {Chem Biol},
volume = {10},
number = {6},
pages = {551-561},
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.},
note = {1074-5521
Journal Article},
keywords = {5S/*chemistry/metabolism Support, Bacterial/*chemistry RNA, Binding Sites Cations, Divalent Computer Simulation Crystallization Electrostatics Hydrogen Bonding Magnesium/*chemistry/metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't Thermodynamics Water/chemistry, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
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.