Published in J Am Chem Soc on September 14, 2007
Advances in Bioconjugation. Curr Org Chem (2010) 1.60
Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. J Am Chem Soc (2010) 1.46
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc (2008) 1.41
Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. J Phys Chem Lett (2011) 1.36
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proc Natl Acad Sci U S A (2012) 1.29
Nitrile bonds as infrared probes of electrostatics in ribonuclease S. J Phys Chem B (2010) 1.24
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization. Proc Natl Acad Sci U S A (2010) 1.23
Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase. Proc Natl Acad Sci U S A (2009) 1.17
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Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics. Biochemistry (2009) 1.02
Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase. Proc Natl Acad Sci U S A (2011) 1.02
Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations. J Am Chem Soc (2010) 1.00
Measuring electric fields and noncovalent interactions using the vibrational stark effect. Acc Chem Res (2015) 0.96
Site-specific infrared probes of proteins. Annu Rev Phys Chem (2015) 0.96
Solvation response along the reaction coordinate in the active site of ketosteroid isomerase. J Am Chem Soc (2010) 0.94
Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proc Natl Acad Sci U S A (2013) 0.91
Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water. J Phys Chem Lett (2010) 0.90
Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding. J Am Chem Soc (2012) 0.86
Using infrared spectroscopy of cyanylated cysteine to map the membrane binding structure and orientation of the hybrid antimicrobial peptide CM15. Biochemistry (2011) 0.86
Combinatorial catalysis employing a visible enzymatic beacon in real time: synthetically versatile (pseudo)halometalation/carbocyclizations. Angew Chem Int Ed Engl (2011) 0.85
Electrostatic fields near the active site of human aldose reductase: 2. New inhibitors and complications caused by hydrogen bonds. Biochemistry (2011) 0.79
Protein apparent dielectric constant and its temperature dependence from remote chemical shift effects. J Am Chem Soc (2014) 0.77
Solvatochromism and the solvation structure of benzophenone. J Chem Phys (2013) 0.75
The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes. Front Neurosci (2016) 0.75
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Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLoS Biol (2006) 2.41
Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (2006) 2.32
Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc (2003) 2.30
Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins. Biochemistry (2003) 2.14
Electrostatic screening of charge and dipole interactions with the helix backbone. Science (1993) 1.95
High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue. Biochemistry (1997) 1.71
Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins. J Am Chem Soc (2006) 1.68
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Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate. J Am Chem Soc (2003) 1.04
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Mutational analysis of the three cysteines and active-site aspartic acid 103 of ketosteroid isomerase from Pseudomonas putida biotype B. J Bacteriol (1997) 0.98
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Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 7.45
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34
Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol (2009) 4.32
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA (2005) 3.95
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
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.27
Phase separation of lipid membranes analyzed with high-resolution secondary ion mass spectrometry. Science (2006) 3.07
Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A (2001) 2.78
Micropattern formation in supported lipid membranes. Acc Chem Res (2002) 2.72
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res (2005) 2.52
Probing protein electrostatics with a synthetic fluorescent amino acid. Science (2002) 2.46
Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLoS Biol (2006) 2.41
Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (2006) 2.32
Rapid compaction during RNA folding. Proc Natl Acad Sci U S A (2002) 2.27
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
Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins. Biochemistry (2003) 2.14
Early steps of supported bilayer formation probed by single vesicle fluorescence assays. Biophys J (2002) 2.09
Challenges in enzyme mechanism and energetics. Annu Rev Biochem (2003) 2.00
Green fluorescent protein variants as ratiometric dual emission pH sensors. 1. Structural characterization and preliminary application. Biochemistry (2002) 1.96
Model membrane systems and their applications. Curr Opin Chem Biol (2007) 1.96
Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem (2011) 1.94
Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J Mol Biol (2004) 1.90
The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol (2003) 1.80
Arrays of mobile tethered vesicles on supported lipid bilayers. J Am Chem Soc (2003) 1.71
Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature (2010) 1.69
Site-specific conversion of cysteine thiols into thiocyanate creates an IR probe for electric fields in proteins. J Am Chem Soc (2006) 1.68
Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J Mol Biol (2003) 1.67
Effects of linker sequences on vesicle fusion mediated by lipid-anchored DNA oligonucleotides. Proc Natl Acad Sci U S A (2009) 1.65
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
General method for modification of liposomes for encoded assembly on supported bilayers. J Am Chem Soc (2005) 1.42
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
The ligand-free state of the TPP riboswitch: a partially folded RNA structure. J Mol Biol (2009) 1.39
Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis. J Am Chem Soc (2003) 1.34
Dynamic Stokes shift in green fluorescent protein variants. Proc Natl Acad Sci U S A (2007) 1.32
Potent inhibition of scrapie prion replication in cultured cells by bis-acridines. Proc Natl Acad Sci U S A (2003) 1.32
Protonation, photobleaching, and photoactivation of yellow fluorescent protein (YFP 10C): a unifying mechanism. Biochemistry (2005) 1.30
Vesicle adsorption and lipid bilayer formation on glass studied by atomic force microscopy. Langmuir (2004) 1.29
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
Variable incidence angle fluorescence interference contrast microscopy for z-imaging single objects. Biophys J (2005) 1.27
Origins of catalysis by computationally designed retroaldolase enzymes. Proc Natl Acad Sci U S A (2010) 1.27
Lipid-anchored DNA mediates vesicle fusion as observed by lipid and content mixing. Biointerphases (2008) 1.26
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc (2008) 1.26
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A (2006) 1.26
Green fluorescent protein variants as ratiometric dual emission pH sensors. 2. Excited-state dynamics. Biochemistry (2002) 1.25
Nitrile bonds as infrared probes of electrostatics in ribonuclease S. J Phys Chem B (2010) 1.24
DNA-tethered membranes formed by giant vesicle rupture. J Struct Biol (2009) 1.21
Structural specificity conferred by a group I RNA peripheral element. Proc Natl Acad Sci U S A (2005) 1.19
Deconstructing green fluorescent protein. J Am Chem Soc (2008) 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
Controlling two-dimensional tethered vesicle motion using an electric field: interplay of electrophoresis and electro-osmosis. Langmuir (2006) 1.17
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
Structural and spectroscopic analysis of the kinase inhibitor bosutinib and an isomer of bosutinib binding to the Abl tyrosine kinase domain. PLoS One (2012) 1.17
Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 1. Mutagenesis and structural studies. Biochemistry (2007) 1.16
Electrostatic fields near the active site of human aldose reductase: 1. New inhibitors and vibrational stark effect measurements. Biochemistry (2008) 1.16
Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 2. Unusual photophysical properties. Biochemistry (2007) 1.16
A repulsive field: advances in the electrostatics of the ion atmosphere. Curr Opin Chem Biol (2008) 1.16
Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis. J Am Chem Soc (2006) 1.15
Direct measurement of tertiary contact cooperativity in RNA folding. J Am Chem Soc (2008) 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
Calculations of the electric fields in liquid solutions. J Phys Chem B (2013) 1.13
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
Probing the structure of supported membranes and tethered oligonucleotides by fluorescence interference contrast microscopy. Langmuir (2005) 1.12
Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. J Am Chem Soc (2009) 1.10
Kinetics of DNA-mediated docking reactions between vesicles tethered to supported lipid bilayers. Proc Natl Acad Sci U S A (2007) 1.10
Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes. J Am Chem Soc (2013) 1.10
Diffusive dynamics of vesicles tethered to a fluid supported bilayer by single-particle tracking. Langmuir (2006) 1.10
Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Curr Opin Struct Biol (2008) 1.10
Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy. J Phys Chem B (2012) 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
Polarized absorption spectra of green fluorescent protein single crystals: transition dipole moment directions. Biochemistry (2003) 1.06
Measurement of solvation responses at multiple sites in a globular protein. J Phys Chem B (2007) 1.06
Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol (2005) 1.05
Bandlike transport in strongly coupled and doped quantum dot solids: a route to high-performance thin-film electronics. Nano Lett (2012) 1.04