Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing.

PubWeight™: 0.91‹?›

🔗 View Article (PMC 2678012)

Published in J Mol Biol on September 27, 2008

Authors

Kirk A Vander Meulen1, Jared H Davis, Trenton R Foster, M Thomas Record, Samuel E Butcher

Author Affiliations

1: Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.

Articles citing this

Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction. Biochemistry (2009) 1.10

Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J Virol (2009) 1.09

Entropic origin of Mg2+-facilitated RNA folding. Proc Natl Acad Sci U S A (2012) 0.93

Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry. Methods Enzymol (2009) 0.90

Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex. Biophys J (2012) 0.88

Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr). J Mol Biol (2011) 0.86

Thermodynamic origins of monovalent facilitated RNA folding. Biochemistry (2012) 0.85

Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry. Nucleic Acids Res (2011) 0.83

Fluorescence competition assay measurements of free energy changes for RNA pseudoknots. Biochemistry (2010) 0.81

Exploring the electrostatic energy landscape for tetraloop-receptor docking. Phys Chem Chem Phys (2013) 0.79

Entropic stabilization of folded RNA in crowded solutions measured by SAXS. Nucleic Acids Res (2016) 0.76

Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis. RNA Biol (2013) 0.75

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme. Biophys Chem (2017) 0.75

Articles cited by this

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

Crystal structure of a group I ribozyme domain: principles of RNA packing. Science (1996) 13.99

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci (1995) 9.23

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci U S A (2001) 6.58

The riboswitch control of bacterial metabolism. Trends Biochem Sci (2004) 4.95

Energetics of protein structure. Adv Protein Chem (1995) 4.82

Crystal structure of a self-splicing group I intron with both exons. Nature (2004) 3.92

Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys (2008) 3.75

RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science (1998) 3.67

Frequent use of the same tertiary motif by self-folding RNAs. EMBO J (1995) 3.63

RNA tertiary structure mediation by adenosine platforms. Science (1996) 3.40

Predicting thermodynamic properties of RNA. Methods Enzymol (1995) 3.38

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science (2003) 3.32

Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry (1992) 3.26

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol (1974) 3.25

Kinetic intermediates in RNA folding. Science (1994) 3.07

A network of heterogeneous hydrogen bonds in GNRA tetraloops. J Mol Biol (1996) 2.98

Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol (2006) 2.81

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat Struct Biol (1998) 2.71

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry (1999) 2.54

Salt-nucleic acid interactions. Annu Rev Phys Chem (1995) 2.50

Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions. Structure (2001) 2.49

TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res (2001) 2.31

A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques. Proc Natl Acad Sci U S A (1999) 2.16

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry (1993) 2.13

Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: general thermodynamic models and data for the binding of nucleotides to ribonuclease A. Biochemistry (1983) 2.09

Heat capacity effects on the melting of DNA. 1. General aspects. Biophys J (1999) 2.00

Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc Natl Acad Sci U S A (1989) 1.92

Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Proteins (1998) 1.84

GNRA tetraloops make a U-turn. RNA (1995) 1.82

The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol (2003) 1.80

Thermodynamics of three-way multibranch loops in RNA. Biochemistry (2001) 1.78

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res (2006) 1.67

RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J Mol Biol (2005) 1.65

Solution structure of a GAAA tetraloop receptor RNA. EMBO J (1997) 1.63

Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study. Biochemistry (2001) 1.62

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. Biochemistry (1999) 1.60

Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J Mol Biol (1994) 1.48

Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid. Biopolymers (1977) 1.44

Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. Eur J Biochem (2002) 1.43

Tertiary interactions determine the accuracy of RNA folding. J Am Chem Soc (2008) 1.40

Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme. Biochemistry (2002) 1.31

The thermodynamic origin of the stability of a thermophilic ribozyme. Proc Natl Acad Sci U S A (2001) 1.30

Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J Am Chem Soc (2008) 1.25

Thermodynamics of folding a pseudoknotted mRNA fragment. J Mol Biol (1994) 1.19

Heat capacity changes associated with nucleic acid folding. Biopolymers (2006) 1.19

Helical junctions as determinants for RNA folding: origin of tertiary structure stability of the hairpin ribozyme. Biochemistry (2000) 1.18

An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs. RNA (1995) 1.18

The energetics of HMG box interactions with DNA: thermodynamic description of the target DNA duplexes. J Mol Biol (1999) 1.16

Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Biochemistry (2006) 1.15

Direct measurement of tertiary contact cooperativity in RNA folding. J Am Chem Soc (2008) 1.15

Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme. Biochemistry (2004) 1.14

Applications of isothermal titration calorimetry in RNA biochemistry and biophysics. Biopolymers (2007) 1.12

Thermodynamic stabilities of internal loops with GU closing pairs in RNA. Biochemistry (2001) 1.12

Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein. Proteins (2000) 1.11

Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure. J Mol Biol (2005) 1.10

Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis. Biochemistry (1998) 1.08

Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation. Nat Struct Biol (2000) 1.08

Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry (1999) 1.05

Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg(2+)-dependent docking of a GAAA tetraloop. J Mol Biol (2005) 1.05

Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects. Biochemistry (2006) 1.04

Thermodynamic analysis of transfer RNA unfolding. J Mol Biol (1978) 1.03

Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme. Proc Natl Acad Sci U S A (2001) 1.02

Thermodynamics of ion-induced RNA folding in the hammerhead ribozyme: an isothermal titration calorimetric study. Biochemistry (2001) 0.99

Role of metal ions in the tetraloop-receptor complex as analyzed by NMR. RNA (2006) 0.98

Water and proteins. I. The significance and structure of water; its interaction with electrolytes and non-electrolytes. Adv Biophys (1978) 0.96

A simple method to measure the absolute heat capacity of proteins. Anal Biochem (1999) 0.76

Articles by these authors

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem (2002) 3.00

Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure. Nat Struct Biol (2002) 2.75

Pseudoknots: RNA structures with diverse functions. PLoS Biol (2005) 2.60

Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol (2011) 2.50

Crowding and confinement effects on protein diffusion in vivo. J Bacteriol (2006) 1.84

Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates. J Mol Biol (2002) 1.83

Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface. J Phys Chem B (2007) 1.77

U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction. Nat Struct Mol Biol (2004) 1.66

RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J Mol Biol (2005) 1.65

The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute. Biochemistry (2004) 1.52

Thermodynamic origin of hofmeister ion effects. J Phys Chem B (2008) 1.50

Roles of cytoplasmic osmolytes, water, and crowding in the response of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine. Biochemistry (2003) 1.48

Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A (2007) 1.44

Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J Mol Biol (2005) 1.42

Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes. J Am Chem Soc (2004) 1.40

Protein surface salt bridges and paths for DNA wrapping. Curr Opin Struct Biol (2002) 1.37

Cytoplasmic protein mobility in osmotically stressed Escherichia coli. J Bacteriol (2008) 1.34

Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability. Biochemistry (2004) 1.31

Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding. Biochemistry (2005) 1.31

Protein diffusion in the periplasm of E. coli under osmotic stress. Biophys J (2011) 1.30

Why Hofmeister effects of many salts favor protein folding but not DNA helix formation. Proc Natl Acad Sci U S A (2010) 1.30

Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. Biochemistry (2009) 1.29

Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer. Proc Natl Acad Sci U S A (2011) 1.27

Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proc Natl Acad Sci U S A (2011) 1.26

Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation. Genes Dev (2012) 1.25

Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J Am Chem Soc (2008) 1.25

Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface. Proc Natl Acad Sci U S A (2006) 1.23

Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop. J Mol Biol (2007) 1.23

The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A (2004) 1.22

Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent conversion to RPo. Biochemistry (2006) 1.22

Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. Proc Natl Acad Sci U S A (2013) 1.22

Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus. J Mol Biol (2009) 1.20

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nat Struct Mol Biol (2004) 1.19

Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments. J Mol Biol (2007) 1.18

Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. J Mol Biol (2008) 1.17

Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas. J Phys Chem B (2007) 1.16

Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein-DNA interactions and growth rate in osmotically stressed Escherichia coli K-12. J Mol Recognit (2004) 1.16

Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes. Biochemistry (2003) 1.15

Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR. J Mol Biol (2005) 1.15

Structure and interactions of the first three RNA recognition motifs of splicing factor prp24. J Mol Biol (2007) 1.14

Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. Biochemistry (2004) 1.11

Effect of the number of nucleic acid oligomer charges on the salt dependence of stability (DeltaG 37degrees) and melting temperature (Tm): NLPB analysis of experimental data. Biochemistry (2004) 1.10

Solution structure of the HIV-1 frameshift inducing stem-loop RNA. Nucleic Acids Res (2003) 1.10

Structure of the yeast U2/U6 snRNA complex. RNA (2012) 1.09

Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. RNA (2007) 1.08

Generalized derivation of an exact relationship linking different coefficients that characterize thermodynamic effects of preferential interactions. Biophys Chem (2002) 1.08

Probing DNA binding, DNA opening, and assembly of a downstream clamp/jaw in Escherichia coli RNA polymerase-lambdaP(R) promoter complexes using salt and the physiological anion glutamate. Biochemistry (2010) 1.07

Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change. Biochemistry (2004) 1.05

One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex. Proc Natl Acad Sci U S A (2010) 1.05

Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA. J Mol Biol (2007) 1.04

A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA (2007) 1.03

Methods of changing biopolymer volume fraction and cytoplasmic solute concentrations for in vivo biophysical studies. Methods Enzymol (2007) 1.00

A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop. Nucleic Acids Res (2011) 0.99

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants. Proc Natl Acad Sci U S A (2013) 0.98

Selection and characterization of small molecules that bind the HIV-1 frameshift site RNA. ACS Chem Biol (2009) 0.98

Role of metal ions in the tetraloop-receptor complex as analyzed by NMR. RNA (2006) 0.98

DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer. Nucleic Acids Res (2007) 0.97

Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication. ACS Chem Biol (2011) 0.96

Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt. Nucleic Acids Res (2004) 0.96

Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24. RNA (2010) 0.96

Guanidinoneomycin B recognition of an HIV-1 RNA helix. Chembiochem (2008) 0.96

Structural basis for a lethal mutation in U6 RNA. Biochemistry (2003) 0.95

Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification. RNA (2003) 0.95

DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA. J Mol Biol (2008) 0.95

Targeting frameshifting in the human immunodeficiency virus. Expert Opin Ther Targets (2012) 0.93

HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome. Nucleic Acids Res (2012) 0.92

Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods (2010) 0.92

Preferential interactions in aqueous solutions of urea and KCl. Biophys Chem (2003) 0.90

Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping. J Mol Biol (2009) 0.90

Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation. Biochemistry (2012) 0.90

Quantifying functional group interactions that determine urea effects on nucleic acid helix formation. J Am Chem Soc (2013) 0.89

Gibbs-Duhem-based relationships among derivatives expressing the concentration dependences of selected chemical potentials for a multicomponent system. Biophys Chem (2004) 0.89

Bacterial toxin RelE: a highly efficient ribonuclease with exquisite substrate specificity using atypical catalytic residues. Biochemistry (2013) 0.89

Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry (2014) 0.87

Quantifying additive interactions of the osmolyte proline with individual functional groups of proteins: comparisons with urea and glycine betaine, interpretation of m-values. Biochemistry (2013) 0.87

Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration. Biochemistry (2006) 0.86

Flipping off the riboswitch: RNA structures that control gene expression. ACS Chem Biol (2006) 0.84

Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Nucleic Acids Res (2007) 0.84

Using surface tension data to predict differences in surface and bulk concentrations of nonelectrolytes in water. J Phys Chem C Nanomater Interfaces (2009) 0.84

Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry. Nucleic Acids Res (2011) 0.83

Quantifying the roles of water and solutes (denaturants, osmolytes, and Hofmeister salts) in protein and model processes using the solute partitioning model. Methods Mol Biol (2009) 0.83

Nonspecific DNA binding and bending by HUαβ: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J Mol Biol (2011) 0.83

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts. J Biomol NMR (2012) 0.82

Asymptotic solution of the cylindrical nonlinear Poisson-Boltzmann equation at low salt concentration: analytic expressions for surface potential and preferential interaction coefficient. Proc Natl Acad Sci U S A (2002) 0.82

Nucleic acid structure characterization by small angle X-ray scattering (SAXS). Curr Protoc Nucleic Acid Chem (2012) 0.81

Resonance assignments for the two N-terminal RNA recognition motifs (RRM) of the S. cerevisiae pre-mRNA processing protein Prp24. J Biomol NMR (2006) 0.81

Positioning the Intracellular Salt Potassium Glutamate in the Hofmeister Series by Chemical Unfolding Studies of NTL9. Biochemistry (2016) 0.80

Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H. Appl Microbiol Biotechnol (2015) 0.79

(1)H, (13)C and (15)N resonance assignments of a ribonucleoprotein complex consisting of Prp24-RRM2 bound to a fragment of U6 RNA. Biomol NMR Assign (2009) 0.78

Correction to "quantifying functional group interactions that determine urea effects on nucleic Acid helix formation". J Am Chem Soc (2013) 0.78

Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation. Methods Mol Biol (2015) 0.78

Rapid quench mixing to quantify kinetics of steps in association of Escherichia coli RNA polymerase with promoter DNA. Methods Enzymol (2003) 0.77

STAR-studded circuitry. Nat Struct Mol Biol (2004) 0.77

Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH. Biochemistry (2010) 0.76

Expanded DNA and RNA Trinucleotide Repeats in Myotonic Dystrophy Type 1 Select Their Own Multitarget, Sequence-Selective Inhibitors. Biochemistry (2020) 0.75