Published in Proc Natl Acad Sci U S A on May 26, 2009
Hydrogen bond coupling in the ketosteroid isomerase active site. Biochemistry (2009) 1.02
Proton affinity of the oxyanion hole in the active site of ketosteroid isomerase. Biochemistry (2010) 0.98
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Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proc Natl Acad Sci U S A (2013) 0.91
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Proton transfer reactions and hydrogen-bond networks in protein environments. J R Soc Interface (2013) 0.83
Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy. Biophys J (2012) 0.81
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Initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy. Biochemistry (2003) 1.18
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Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein. Biochemistry (2000) 0.92
Functional tuning of photoactive yellow protein by active site residue 46. Biochemistry (2008) 0.92
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The hydrogen-bonding network in heme oxygenase also functions as a modulator of enzyme dynamics: chaotic motions upon disrupting the H-bond network in heme oxygenase from Pseudomonas aeruginosa. J Am Chem Soc (2007) 0.87
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Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol (2009) 4.32
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Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci U S A (2006) 3.56
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science (2006) 3.49
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One (2008) 3.38
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Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A (2001) 2.78
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Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLoS Biol (2006) 2.41
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Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J Am Chem Soc (2007) 2.20
Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol (2006) 2.19
Challenges in enzyme mechanism and energetics. Annu Rev Biochem (2003) 2.00
Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem (2011) 1.94
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The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol (2003) 1.80
Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature (2010) 1.69
Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J Mol Biol (2003) 1.67
Alkaline phosphatase revisited: hydrolysis of alkyl phosphates. Biochemistry (2002) 1.61
The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol (2006) 1.61
Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution. Biochemistry (2006) 1.60
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophys J (2007) 1.60
Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci U S A (2008) 1.54
Determining the Mg2+ stoichiometry for folding an RNA metal ion core. J Am Chem Soc (2005) 1.47
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc Natl Acad Sci U S A (2005) 1.46
Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. J Am Chem Soc (2010) 1.46
RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J Mol Biol (2002) 1.45
Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes. PLoS Biol (2013) 1.42
Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole. Proc Natl Acad Sci U S A (2010) 1.41
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc (2008) 1.41
The ligand-free state of the TPP riboswitch: a partially folded RNA structure. J Mol Biol (2009) 1.39
Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site? J Am Chem Soc (2007) 1.31
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proc Natl Acad Sci U S A (2012) 1.29
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Res (2010) 1.28
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc (2008) 1.27
Origins of catalysis by computationally designed retroaldolase enzymes. Proc Natl Acad Sci U S A (2010) 1.27
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc (2008) 1.26
Structural specificity conferred by a group I RNA peripheral element. Proc Natl Acad Sci U S A (2005) 1.19
Do conformational biases of simple helical junctions influence RNA folding stability and specificity? RNA (2009) 1.19
Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion. J Mol Biol (2008) 1.19
Understanding nucleic acid-ion interactions. Annu Rev Biochem (2014) 1.18
Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase. Proc Natl Acad Sci U S A (2009) 1.17
Probing the Tetrahymena group I ribozyme reaction in both directions. Biochemistry (2002) 1.17
Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data. PLoS One (2012) 1.17
A repulsive field: advances in the electrostatics of the ion atmosphere. Curr Opin Chem Biol (2008) 1.16
Direct measurement of tertiary contact cooperativity in RNA folding. J Am Chem Soc (2008) 1.15
Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis. J Am Chem Soc (2006) 1.15
Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis. J Am Chem Soc (2002) 1.15
Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry (2014) 1.13
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA (2010) 1.13
Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. J Am Chem Soc (2009) 1.10
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Robust design and optimization of retroaldol enzymes. Protein Sci (2012) 1.09
Measuring the folding transition time of single RNA molecules. Biophys J (2007) 1.09
Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer? J Am Chem Soc (2004) 1.08
Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol (2005) 1.05
Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis. J Am Chem Soc (2007) 1.03
Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism. J Biol Chem (2008) 1.02
Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase. Biochemistry (2008) 1.02
Hydrogen bond coupling in the ketosteroid isomerase active site. Biochemistry (2009) 1.02
Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function. Proc Natl Acad Sci U S A (2003) 1.01
Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions. J Am Chem Soc (2005) 0.99
Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. J Am Chem Soc (2007) 0.98
Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry (2008) 0.98
Ground state destabilization from a positioned general base in the ketosteroid isomerase active site. Biochemistry (2013) 0.96
Interdomain communication in DNA topoisomerase II. DNA binding and enzyme activation. J Biol Chem (2006) 0.96
Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA. J Biol Chem (2011) 0.95
Probing the dynamics of the P1 helix within the Tetrahymena group I intron. J Am Chem Soc (2009) 0.94
Low specificity of metal ion binding in the metal ion core of a folded RNA. RNA (2007) 0.94
Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site. Proc Natl Acad Sci U S A (2013) 0.94
Riboswitch conformations revealed by small-angle X-ray scattering. Methods Mol Biol (2009) 0.93
Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily. Biochemistry (2008) 0.93
Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis. RNA (2002) 0.93
Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. RNA (2012) 0.92
DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity. Nucleic Acids Res (2007) 0.92
Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.92
High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. J Mol Biol (2011) 0.92
Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proc Natl Acad Sci U S A (2013) 0.91
Multiple unfolding events during native folding of the Tetrahymena group I ribozyme. J Mol Biol (2010) 0.91
Methods of site-specific labeling of RNA with fluorescent dyes. Methods Enzymol (2009) 0.90
Implications of molecular heterogeneity for the cooperativity of biological macromolecules. Nat Struct Mol Biol (2011) 0.90
Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase. J Am Chem Soc (2011) 0.89
From a structural average to the conformational ensemble of a DNA bulge. Proc Natl Acad Sci U S A (2014) 0.88
Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. Biochemistry (2010) 0.88
Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations. Proc Natl Acad Sci U S A (2013) 0.88
The far reaches of enzymology. Nat Chem Biol (2009) 0.87
Structure and function converge to identify a hydrogen bond in a group I ribozyme active site. Angew Chem Int Ed Engl (2009) 0.87
Metal ion-based RNA cleavage as a structural probe. Methods Enzymol (2009) 0.86
Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry (2011) 0.86
Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site. J Am Chem Soc (2014) 0.85
Choosing orientation: influence of cargo geometry and ActA polarization on actin comet tails. Mol Biol Cell (2012) 0.85
Electrostatics of nucleic acid folding under conformational constraint. J Am Chem Soc (2012) 0.85
A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme. J Am Chem Soc (2012) 0.85