Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations.

No abstract is available for this paper.

• Publication year

  1998

• Venue

  Structure

• Publication date

  1998-10-15

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/S0969-2126(98)00130-0PMID 9782053
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Oxford handbook of nucleic acid structure

  1998cited by this paper
• Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA.

  1998cited by this paper
• Molecular dynamics investigations of hammerhead ribozyme RNA

  1998cited by this paper
• The structural basis of hammerhead ribozyme self-cleavage.

  1998cited by this paper
• Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy.

  1998cited by this paper
• Structure, recognition and adaptive binding in RNA aptamer complexes.

  1997cited by this paper
• RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin.

  1997cited by this paper
• Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.

  1997cited by this paper
• Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

  1997cited by this paper
• Ion‐induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study

  1997cited by this paper
• Relating conformation, Mg2+ binding, and functional group modification in the hammerhead ribozyme.

  1997cited by this paper
• The structure, function and application of the hammerhead ribozyme.

  1997cited by this paper
• Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine.

  1997influential reference
• Recent solution structures of RNA and its complexes with drugs, peptides and proteins.

  1997cited by this paper
• Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.

  1997cited by this paper
• The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation.

  1996cited by this paper
• Metal-binding sites in the major groove of a large ribozyme domain.

  1996influential reference
• Mg(2+)-dependent conformational changes in the hammerhead ribozyme.

  1996cited by this paper
• Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

  1996cited by this paper
• Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme

  1996influential reference
• Structural basis of RNA folding and recognition in an AMP–RNA aptamer complex

  1996influential reference
• Molecular recognition in the FMN-RNA aptamer complex.

  1996influential reference
• A second generation force field for the simulation of proteins

  1995cited by this paper
• Divalent metal ions and the internal equilibrium of the hammerhead ribozyme.

  1995cited by this paper
• The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus.

  1995influential reference
• The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage.

  1995cited by this paper
• The sarcin/ricin loop, a modular RNA.

  1995influential reference
• Classical electrostatics in biology and chemistry.

  1995cited by this paper
• RNA structure at high resolution

  1995cited by this paper
• Three-dimensional structure of a hammerhead ribozyme

  1994cited by this paper
• Isolation of RNA Aptamers for Biological Cofactors by In Vitro Selection

  1994influential reference
• 12 Divalent Metal Ions in RNA Folding and Catalysis

  1993cited by this paper
• An RNA motif that binds ATP

  1993influential reference
• Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism.

  1993cited by this paper
• 18 RNA Structural Elements and RNA Function

  1993cited by this paper
• Ribozymes: a distinct class of metalloenzymes.

  1993cited by this paper
• Ribosomal RNA identity elements for ricin A-chain recognition and catalysis. Analysis with tetraloop mutants.

  1992cited by this paper
• X-ray analysis of substrate analogs in the ricin A-chain active site.

  1992cited by this paper
• Ribosomal RNA identity elements for ricin A-chain recognition and catalysis.

  1991cited by this paper
• Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons

  1991cited by this paper
• Role of divalent metal ions in the hammerhead RNA cleavage reaction.

  1991cited by this paper
• Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".

  1990cited by this paper
• RNA pseudoknots. Stability and loop size requirements.

  1990cited by this paper
• RNA world

  1987cited by this paper
• Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.

  1987cited by this paper
• Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles.

  1986cited by this paper
• Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA.

  1985cited by this paper
• Crystallographic refinement of yeast aspartic acid transfer RNA.

  1985cited by this paper
• Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations.

  1985cited by this paper
• A small angle x-ray scattering study of a fragment derived from E. coli 5S RNA.

  1984cited by this paper
• X-ray diffraction study of the zinc(II) binding sites in yeast phenylalanine transfer RNA. Preferential binding of zinc to guanines in purine-purine sequences.

  1983cited by this paper
• Significance and mechanism of divalent-ion binding to transfer RNA.

  1982cited by this paper
• Nucleic Acid-Metal Ion Interactions

  1980cited by this paper
• Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA.

  1978cited by this paper
• RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe.

  1977cited by this paper
• A crystallographic study of metal-binding to yeast phenylalanine transfer RNA.

  1977cited by this paper
• Equilibrium binding of magnesium(II) by Escherichia coli tRNAfMet.

  1976cited by this paper
• Interaction of manganese with fragments, complementary fragment recombinations, and whole molecules of yeast phenylalanine specific transfer RNA.

  1974cited by this paper
• Three-Dimensional Structure of Yeast Phenylalanine Transfer RNA: Folding of the Polynucleotide Chain

  1973cited by this paper
• Solution

  1902cited by this paper

• Geometric deep learning for the prediction of magnesium-binding sites in RNA structures.

  2024cites this paper
• Intricate 3D architecture of a DNA mimic of GFP

  2023cites this paper
• Modulation of biomolecular phase behavior by metal ions.

  2023cites this paper
• Bulge-Forming miRNases Cleave Oncogenic miRNAs at the Central Loop Region in a Sequence-Specific Manner

  2022cites this paper
• Graph deep learning locates magnesium ions in RNA

  2022influential citation
• Context-sensitivity of isosteric substitutions of non-Watson–Crick basepairs in recurrent RNA 3D motifs

  2021cites this paper
• Recent advances in metallodrug-like molecules targeting non-coding RNAs in cancer chemotherapy

  2019cites this paper
• Challenges and current status of computational methods for docking small molecules to nucleic acids.

  2019cites this paper
• Evaluation of cytotoxic potential of structurally well-characterized RNA targeted ionic non-steroidal anti-inflammatory (NSAID) Cu(ii) & Zn(ii) DACH–mefenamato drug conjugates against human cancer cell lines

  2019cites this paper
• Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.

  2018cites this paper
• Machine learning for Mg2+-binding sites prediction in RNA structures

  2018cites this paper
• Drug Design Targeting RNA

  2016cites this paper
• Small molecules targeting viral RNA

  2016cites this paper
• Computational methods for prediction of RNA interactions with metal ions and small organic ligands.

  2015cites this paper
• Modeling of ribonucleic acid–ligand interactions

  2015cites this paper
• Cellular RNA Targeting by Platinum (II) Anticancer Therapeutics

  2014cites this paper
• Platinum-RNA Modifications Following Drug Treatment in S. cerevisiae Identified by Click Chemistry and Enzymatic Mapping

  2014cites this paper
• Novel adsorbent for DNA adsorption: Fe3+-attached sporopollenin particles embedded composite cryogels

  2013cites this paper
• Part I Nucleic Acid Site-Selective Binding Studies of Isomers of Dihydrodioxin-Masked Ortho-Quinones as Potential Antitumor Drugs Part II The Role of Non-Watson-Crick Base Pairs in Stabilizing Recurrent RNA Motif

  2012cites this paper
• Simulating Dynamics in RNA–Protein Complexes

  2012cites this paper
• Exploring potential drug target sites in the ribosome using cisplatin and its analogues

  2011cites this paper
• Effects of magnesium ions on two EMCV IRES key activity fragments

  2011influential citation
• Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA.

  2011cites this paper
• NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

  2011cites this paper
• Brownian dynamics study of the association between the 70S ribosome and elongation factor G

  2011cites this paper
• Computational studies of RNA dynamics and RNA-ligand interactions

  2011cites this paper
• Application of Cu 2+ -attached Magnetite Nanoparticles Embedded Supermacroporous Monolithic Composite Cryogels for DNA Adsorption

  2011cites this paper
• Local rather than global folding enables the lead-dependent activity of the 8-17 deoxyribozyme: evidence from contact photo-crosslinking.

  2010cites this paper
• Identification of catalytic metal ion ligands in ribozymes.

  2009cites this paper
• Preparation and characterization of metal-chelated poly(HEMA-MAH) monolithic cryogels and their use for DNA adsorption

  2009cites this paper
• Mg2+  modulation of EMCV IRES key activity fragment equilibria and r(G·C) base-pair kinetics

  2009cites this paper
• Dynamics, Degradation, and Chemical Modification of Non-Coding RNA

  2008cites this paper
• Dynamics of Recognition between tRNA and elongation factor Tu.

  2008cites this paper
• Charge density of divalent metal cations determines RNA stability.

  2007cites this paper
• Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry.

  2007cites this paper
• Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution.

  2007cites this paper
• Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s(4)U8-C13 photocrosslinking.

  2007cites this paper
• Metal interactions and activities of truncated and extended hammerhead ribozyme constructs

  2007cites this paper
• Folding of a universal ribozyme: the ribonuclease P RNA

  2007cites this paper
• Accelerating molecular modeling applications with graphics processors

  2007cites this paper
• The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.

  2007cites this paper
• Foldingof a universal ribozyme: theribonuclease PRNA

  2007cites this paper
• Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands

  2006cites this paper
• Nucleic Acid–Metal Ion Interactions

  2006cites this paper
• Conformationally Constrained Aminoglycosides: Ribosomal Binding Probes and Potential Antibiotics

  2006cites this paper
• RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case

  2006cites this paper
• The ribosomal A-site as an inspiration for the design of RNA binders.

  2006cites this paper
• Counterion charge density determines the position and plasticity of RNA folding transition states.

  2006cites this paper
• Metal Cation–Nucleic Acids Interactions

  2005cites this paper
• Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.

  2005influential citation
• Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features

  2005cites this paper
• RNA as a target for small-molecule therapeutics

  2005cites this paper
• MeRNA: a database of metal ion binding sites in RNA structures

  2005cites this paper
• A guide to ions and RNA structure.

  2004cites this paper
• Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations.

  2004cites this paper
• Anion binding to nucleic acids.

  2004cites this paper
• Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids

  2004cites this paper
• Anion Binding to Nucleic Acids recorded in the Nucleic acid DataBase ( NDB ) ( Berman

  2004influential citation
• in the 5 S rRNA Loop E Inferred from Molecular Dynamics Simulations

  2004cites this paper
• Structural changes of tRNA and 5S rRNA induced with magnesium and visualized with synchrotron mediated hydroxyl radical cleavage

  2004cites this paper
• Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

  2003cites this paper
• Microenvironment analysis and identification of magnesium binding sites in RNA.

  2003cites this paper
• A crystallographic study of the binding of 13 metal ions to two related RNA duplexes.

  2003cites this paper
• A thermodynamic framework for the magnesium-dependent folding of RNA.

  2003cites this paper
• Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.

  2003cites this paper
• Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.

  2003cites this paper
• Structural requirement for Mg2+ binding in the group I intron core.

  2003cites this paper
• Nucleic Acid Separations Utilizing Immobilized Metal Affinity Chromatography

  2003cites this paper
• The rate-limiting step in the folding of a large ribozyme without kinetic traps

  2002cites this paper
• The bulge region of HIV-1 TAR RNA binds metal ions in solution.

  2002influential citation
• Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

  2002influential citation
• Brownian-dynamics simulations of metal-ion binding to four-way junctions.

  2002cites this paper
• Sequestering of Eu(III) by a GAAA RNA tetraloop.

  2002cites this paper
• Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence.

  2001cites this paper
• Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

  2001cites this paper
• Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

  2001cites this paper
• Beyond nucleic acid base pairs: From triads to heptads

  2001cites this paper
• A thermodynamic framework for Mg2+ binding to RNA

  2001cites this paper
• Mg2+-induced tRNA folding.

  2001cites this paper
• Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations.

  2001cites this paper
• RNA solvation: A molecular dynamics simulation perspective

  2000cites this paper
• RNA secondary structure: physical and computational aspects

  2000cites this paper
• Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.

  2000cites this paper
• An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment.

  2000cites this paper
• Modulation of RNA function by aminoglycoside antibiotics

  2000cites this paper
• Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs.

  2000cites this paper
• NEW EMBO MEMBER'S REVIEW Modulation of RNA function by aminoglycoside antibiotics

  2000cites this paper
• Cation—π and Amino-Acceptor Interactions Between Hydrated Metal Cations and DNA Bases. A Quantum-Chemical View

  2000cites this paper
• Simulation of the structure and dynamics of nonhelical RNA motifs.

  2000cites this paper
• Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.

  2000cites this paper
• Metal-phosphate interactions in the hammerhead ribozyme observed by 31P NMR and phosphorothioate substitutions.

  2000cites this paper
• Multiplicity of metal ion binding patterns to nucleobases

  2000cites this paper
• Strategien für die Entwicklung gegen RNA und RNA-Protein-Komplexe gerichteter pharmakologischer Wirkstoffe

  2000cites this paper
• RNA bulges as architectural and recognition motifs.

  2000cites this paper
• A dimeric DNA interface stabilized by stacked A.(G.G.G.G).A hexads and coordinated monovalent cations.

  2000cites this paper
• Rational drug design and high-throughput techniques for RNA targets.

  2000cites this paper
• Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus.

  2000cites this paper
• Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting1

  2000cites this paper
• On the wobble GoU and related pairs.

  2000cites this paper
• Aminoglycoside-RNA interactions.

  1999cites this paper