Charge density of divalent metal cations determines RNA stability.

PubWeight™: 1.56‹?› | Rank: Top 4%

🔗 View Article (PMC 2523262)

Published in J Am Chem Soc on February 13, 2007

Authors

Eda Koculi1, Changbong Hyeon, D Thirumalai, Sarah A Woodson

Author Affiliations

1: T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.

Articles citing this

RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys (2008) 2.00

Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA (2010) 1.58

Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32

Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc (2010) 1.30

Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol (2009) 1.20

Sharing and archiving nucleic acid structure mapping data. RNA (2011) 1.20

Taming free energy landscapes with RNA chaperones. RNA Biol (2010) 1.19

Understanding nucleic acid-ion interactions. Annu Rev Biochem (2014) 1.18

Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria. Methods Enzymol (2009) 1.16

Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol (2008) 1.15

RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. Biophys J (2012) 1.12

Computational exploration of mobile ion distributions around RNA duplex. J Phys Chem B (2010) 1.10

Chemically accurate coarse graining of double-stranded DNA. Proc Natl Acad Sci U S A (2010) 1.09

Urea facilitates the translocation of single-stranded DNA and RNA through the alpha-hemolysin nanopore. Biophys J (2010) 1.08

Salt dependence of nucleic acid hairpin stability. Biophys J (2008) 1.03

Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc (2012) 0.98

Salt contribution to RNA tertiary structure folding stability. Biophys J (2011) 0.96

Predicting ion binding properties for RNA tertiary structures. Biophys J (2010) 0.93

Salt-dependent folding energy landscape of RNA three-way junction. Biophys J (2010) 0.93

Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion. J Mol Biol (2010) 0.92

Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields. J Phys Chem B (2015) 0.91

Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G. Nucleic Acids Res (2013) 0.89

Importance of diffuse metal ion binding to RNA. Met Ions Life Sci (2011) 0.88

The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry (2010) 0.87

Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. Biophys J (2014) 0.86

Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. J Am Chem Soc (2009) 0.86

Ion-mediated RNA structural collapse: effect of spatial confinement. Biophys J (2012) 0.85

Predicting ion-nucleic acid interactions by energy landscape-guided sampling. J Chem Theory Comput (2012) 0.84

The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility. J Mol Struct (2008) 0.84

Predicting electrostatic forces in RNA folding. Methods Enzymol (2009) 0.83

Comparison of interactions of diamine and Mg²⁺ with RNA tertiary structures: similar versus differential effects on the stabilities of diverse RNA folds. Biochemistry (2013) 0.82

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res (2014) 0.81

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding. J Chem Theory Comput (2015) 0.80

The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff. J Comput Chem (2008) 0.80

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA. Nucleic Acids Res (2015) 0.79

Role of ion valence in the submillisecond collapse and folding of a small RNA domain. Biochemistry (2013) 0.78

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Phys Rev Lett (2015) 0.78

Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA. J Mol Biol (2015) 0.78

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

Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? J Am Chem Soc (2016) 0.76

Potential of mean force between like-charged nanoparticles: Many-body effect. Sci Rep (2016) 0.75

Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores. J Chem Phys (2009) 0.75

Effects of Dimethyl Sulfoxide on Surface Water near Phospholipid Bilayers. Biophys J (2016) 0.75

Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding. Nucleic Acids Res (2017) 0.75

A divalent cation-dependent variant of the glmS ribozyme with stringent Ca2+ selectivity co-opts a pre-existing non-specific metal ion binding site. RNA (2016) 0.75

Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions. Biophys J (2016) 0.75

MCTBI: a web server for predicting metal ion effects in RNA structures. RNA (2017) 0.75

Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure. Proc Natl Acad Sci U S A (2017) 0.75

Articles cited by this

Determination of molecular weights and frictional ratios of proteins in impure systems by use of gel filtration and density gradient centrifugation. Application to crude preparations of sulfite and hydroxylamine reductases. Biochim Biophys Acta (1966) 16.27

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys (1978) 14.75

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys (1978) 9.44

Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry (1988) 9.18

DNA condensation by multivalent cations. Biopolymers (1997) 4.49

A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol (1997) 3.68

A guide to ions and RNA structure. RNA (2004) 3.61

Ions and RNA folding. Annu Rev Biophys Biomol Struct (2005) 3.37

Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry (1991) 3.31

Visualizing the higher order folding of a catalytic RNA molecule. Science (1991) 3.19

Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr Opin Chem Biol (2005) 3.00

Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell (2004) 2.68

Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature (1993) 2.62

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

The stability of globular proteins. CRC Crit Rev Biochem (1975) 2.42

Compact and ordered collapse of randomly generated RNA sequences. Nat Struct Mol Biol (2005) 2.36

Early events in RNA folding. Annu Rev Phys Chem (2001) 2.29

Metal ions in the structure and function of RNA. J Biol Inorg Chem (2002) 2.28

Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat Struct Biol (2000) 2.27

A collapsed non-native RNA folding state. Nat Struct Biol (2000) 2.16

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

Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science (2005) 2.05

Problems and prospects in the theory of gel electrophoresis of DNA. Q Rev Biophys (1992) 1.84

Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding. Biochemistry (1999) 1.81

Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena. Biochemistry (1993) 1.79

Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J Mol Biol (2001) 1.78

Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations. Structure (1998) 1.64

Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys J (2005) 1.64

Condensation of DNA by trivalent cations. 2. Effects of cation structure. Biopolymers (1990) 1.61

Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J Mol Biol (1993) 1.61

Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. J Mol Biol (2001) 1.61

The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory. J Mol Biol (1999) 1.58

A thermodynamic framework for the magnesium-dependent folding of RNA. Biopolymers (2003) 1.53

Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. J Chem Phys (2005) 1.52

Metal ion binding to catalytic RNA molecules. Curr Opin Struct Biol (2003) 1.51

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. RNA (2002) 1.49

Determining the Mg2+ stoichiometry for folding an RNA metal ion core. J Am Chem Soc (2005) 1.47

Metal ion requirements for sequence-specific endoribonuclease activity of the Tetrahymena ribozyme. Biochemistry (1989) 1.42

Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci U S A (1999) 1.38

A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res (2003) 1.36

Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain. RNA (1999) 1.34

Ion-mediated nucleic acid helix-helix interactions. Biophys J (2006) 1.32

The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc Natl Acad Sci U S A (2002) 1.30

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

The role of metal ions in RNA catalysis. Curr Opin Struct Biol (2002) 1.26

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J Mol Biol (2004) 1.23

Structural specificity conferred by a group I RNA peripheral element. Proc Natl Acad Sci U S A (2005) 1.19

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

Binding of ionic ligands to polyelectrolytes. Biophys J (1996) 1.18

Counterion charge density determines the position and plasticity of RNA folding transition states. J Mol Biol (2006) 1.07

Effects of divalent metal ions on individual steps of the Tetrahymena ribozyme reaction. Biochemistry (1997) 1.05

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

Comments on selected aspects of nucleic acid electrostatics. Biopolymers (2003) 0.97

Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation. Nucleic Acids Res (2004) 0.96

Cation radius effects on the helix-coil transition of DNA. Cryptates and other large cations. Biophys J (1990) 0.85

Dynamics of curved DNA molecules: prediction and experiment. J Am Chem Soc (2003) 0.79

Articles by these authors

Navigating the folding routes. Science (1995) 7.34

Metastability of the folded states of globular proteins. Proc Natl Acad Sci U S A (1990) 3.79

Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci U S A (2005) 3.29

Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. Structure (2003) 3.18

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des (1997) 3.14

Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci U S A (1993) 3.08

The nature of folded states of globular proteins. Biopolymers (1992) 2.91

Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A (2000) 2.66

RNA and protein folding: common themes and variations. Biochemistry (2005) 2.47

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci (1999) 2.41

The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA (2008) 2.27

Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci U S A (2010) 2.23

Folding of RNA involves parallel pathways. J Mol Biol (1997) 2.22

Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly. Nature (2008) 2.19

Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J Mol Biol (2004) 2.18

Native topology determines force-induced unfolding pathways in globular proteins. Proc Natl Acad Sci U S A (2000) 2.09

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci U S A (2008) 2.03

Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism. Proc Natl Acad Sci U S A (2006) 2.01

Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc Natl Acad Sci U S A (2002) 1.99

Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol (1996) 1.95

Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism. J Am Chem Soc (2007) 1.90

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A (2006) 1.90

Dynamics of allosteric transitions in GroEL. Proc Natl Acad Sci U S A (2006) 1.88

In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates. Mol Cell (2013) 1.85

Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. J Mol Biol (1999) 1.85

Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism. Proc Natl Acad Sci U S A (1996) 1.79

Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J Mol Biol (2001) 1.78

Dynamic Ca2+-dependent stimulation of vesicle fusion by membrane-anchored synaptotagmin 1. Science (2010) 1.77

Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci (2002) 1.77

Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci U S A (2003) 1.76

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc Natl Acad Sci U S A (2003) 1.75

Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci U S A (2007) 1.74

Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1995) 1.73

Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers. J Am Chem Soc (2006) 1.63

Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins (2001) 1.61

Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics. J Mol Biol (2001) 1.61

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (2005) 1.60

Dynamics of unbinding of cell adhesion molecules: transition from catch to slip bonds. Proc Natl Acad Sci U S A (2005) 1.59

Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure (2006) 1.58

Mechanical unfolding of RNA hairpins. Proc Natl Acad Sci U S A (2005) 1.57

Theoretical perspectives on protein folding. Annu Rev Biophys (2010) 1.53

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci U S A (2008) 1.52

Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol (1998) 1.50

Protein-independent folding pathway of the 16S rRNA 5' domain. J Mol Biol (2005) 1.47

Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc (2003) 1.44

Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem (2011) 1.43

Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J (2006) 1.42

Collapse transition in proteins. Phys Chem Chem Phys (2008) 1.41

Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding. Proc Natl Acad Sci U S A (1999) 1.41

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

Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci U S A (1999) 1.38

Rigor to post-rigor transition in myosin V: link between the dynamics and the supporting architecture. Structure (2010) 1.37

Ribosome exit tunnel can entropically stabilize alpha-helices. Proc Natl Acad Sci U S A (2005) 1.36

RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. J Mol Biol (2005) 1.36

Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci (2006) 1.35

Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold Des (1998) 1.34

Aqueous urea solution destabilizes Abeta(16-22) oligomers. Proc Natl Acad Sci U S A (2004) 1.34

Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci U S A (2008) 1.33

Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol (2004) 1.33

Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat Commun (2011) 1.32

Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions. Proc Natl Acad Sci U S A (2005) 1.32

Exploring the energy landscape in proteins. Proc Natl Acad Sci U S A (1993) 1.32

Size, shape, and flexibility of RNA structures. J Chem Phys (2006) 1.31

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J (2007) 1.31

Probing the instabilities in the dynamics of helical fragments from mouse PrPC. Proc Natl Acad Sci U S A (2004) 1.31

Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc (2010) 1.30

Rapid binding and release of Hfq from ternary complexes during RNA annealing. Nucleic Acids Res (2011) 1.30

Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res (2006) 1.28

Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27

Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry (2004) 1.26

Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc (2008) 1.24

Persistence length changes dramatically as RNA folds. Phys Rev Lett (2005) 1.23

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J Mol Biol (2004) 1.23

Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J Mol Biol (2007) 1.22

Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22

Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces. J Mol Biol (2006) 1.22

Cooperative tertiary interaction network guides RNA folding. Cell (2012) 1.21

Metal ion dependence of cooperative collapse transitions in RNA. J Mol Biol (2009) 1.20

Major role for mRNA binding and restructuring in sRNA recruitment by Hfq. RNA (2011) 1.20

Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B (2007) 1.20

Conserved arginines on the rim of Hfq catalyze base pair formation and exchange. Nucleic Acids Res (2013) 1.19

Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J Mol Biol (2005) 1.19

Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci (2002) 1.19

Effect of salt and RNA structure on annealing and strand displacement by Hfq. Nucleic Acids Res (2009) 1.18

Factors governing the foldability of proteins. Proteins (1996) 1.18

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol (1997) 1.18

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A (2009) 1.16

Structural requirement for Mg2+ binding in the group I intron core. J Mol Biol (2003) 1.16

Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol (2002) 1.16

Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism. Nat Commun (2013) 1.15

Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res (2007) 1.15

Dynamics of locking of peptides onto growing amyloid fibrils. Proc Natl Acad Sci U S A (2009) 1.15

Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Fold Des (1998) 1.14