Published in Biochemistry on December 02, 2008
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Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase. Biochemistry (2013) 0.77
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Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem (2011) 1.94
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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
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Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc (2008) 1.41
Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole. Proc Natl Acad Sci U S A (2010) 1.41
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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
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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
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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
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA (2010) 1.13
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Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Curr Opin Struct Biol (2008) 1.10
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
Hydrogen bond dynamics in the active site of photoactive yellow protein. Proc Natl Acad Sci U S A (2009) 1.04
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
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Probing the dynamics of the P1 helix within the Tetrahymena group I intron. J Am Chem Soc (2009) 0.94
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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
Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. Biochemistry (2010) 0.88
From a structural average to the conformational ensemble of a DNA bulge. Proc Natl Acad Sci U S A (2014) 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
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
Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase. Biochemistry (2013) 0.85
Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy. Methods Enzymol (2009) 0.85
Electrostatics of nucleic acid folding under conformational constraint. J Am Chem Soc (2012) 0.85