Daniel Herschlag
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American biochemist
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Daniel Herschlagbiology Degrees
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Biochemistry
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Biology
Daniel Herschlag's Degrees
- PhD Chemistry University of California, Berkeley
- Bachelors Chemistry University of California, Berkeley
Why Is Daniel Herschlag Influential?
(Suggest an Edit or Addition)According to Wikipedia, Daniel Herschlag is an American biochemist and Professor of Biochemistry at the Stanford University School of Medicine. His research uses an interdisciplinary approach to advance our understanding of the fundamental behavior of RNA and proteins. He is well known for his application of rigorous kinetic and mechanistic approaches to RNA and protein systems.
Daniel Herschlag's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Precision and functional specificity in mRNA decay (2002) (767)
- Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae (2003) (699)
- Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast (2004) (689)
- Catalytic promiscuity and the evolution of new enzymatic activities. (1999) (673)
- RNA Chaperones and the RNA Folding Problem (*) (1995) (656)
- A single-molecule study of RNA catalysis and folding. (2000) (652)
- Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System (2008) (591)
- Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA (2009) (437)
- Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. (2006) (361)
- Direct Measurement of the Full, Sequence-Dependent Folding Landscape of a Nucleic Acid (2006) (338)
- SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. (2005) (316)
- Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. (2011) (314)
- Understanding nucleic acid-ion interactions. (2014) (314)
- Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis (2003) (303)
- Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. (2006) (301)
- Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. (2009) (301)
- Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele (2008) (247)
- Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. (1990) (244)
- A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. (1994) (228)
- Challenges in enzyme mechanism and energetics. (2003) (224)
- Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. (2007) (223)
- An RNA chaperone activity of non‐specific RNA binding proteins in hammerhead ribozyme catalysis. (1994) (223)
- Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. (1997) (218)
- Exploring the folding landscape of a structured RNA (2001) (216)
- The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. (1998) (216)
- Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance (2008) (205)
- Rapid compaction during RNA folding (2002) (203)
- The roles of structural dynamics in the cellular functions of RNAs (2019) (201)
- Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. (1991) (200)
- Multiple Native States Reveal Persistent Ruggedness of an RNA Folding Landscape (2010) (193)
- Ras-catalyzed hydrolysis of GTP: a new perspective from model studies. (1996) (190)
- Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom. (1991) (185)
- The Energetics of Hydrogen Bonds in Model Systems: Implications for Enzymatic Catalysis (1996) (179)
- Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. (1999) (177)
- Protein enhancement of hammerhead ribozyme catalysis. (1993) (174)
- Counterion distribution around DNA probed by solution X-ray scattering. (2003) (170)
- Synergism in transcriptional activation: a kinetic view. (1993) (168)
- The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. (1998) (162)
- Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. (1994) (161)
- Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase. (2001) (155)
- Role of SRP RNA in the GTPase cycles of Ffh and FtsY. (2001) (155)
- Three metal ions at the active site of the Tetrahymena group I ribozyme. (1999) (150)
- Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis. (1995) (150)
- Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution. (2006) (144)
- Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. (2007) (143)
- The role of induced fit and conformational changes of enzymes in specificity and catalysis (1988) (139)
- Role of 4.5S RNA in assembly of the bacterial signal recognition particle with its receptor. (2000) (136)
- Small angle X-ray scattering reveals a compact intermediate in RNA folding (2000) (136)
- Robust design and optimization of retroaldol enzymes (2012) (135)
- Dissecting eukaryotic translation and its control by ribosome density mapping (2005) (134)
- The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis. (1996) (132)
- Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis. (2006) (131)
- Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. (2001) (130)
- Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. (2010) (128)
- The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. (2003) (127)
- Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. (2001) (125)
- Alkaline Phosphatase Revisited: Hydrolysis of Alkyl Phosphates †. (2002) (123)
- Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. (1990) (121)
- How to measure and evaluate binding affinities (2020) (119)
- Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole (2006) (117)
- Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. (2007) (115)
- SULFATASE ACTIVITY OF E. COLI ALKALINE PHOSPHATASE DEMONSTRATES A FUNCTIONAL LINK TO ARYLSULFATASES, AN EVOLUTIONARILY RELATED ENZYME FAMILY (1998) (108)
- Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. (2012) (108)
- Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. (2004) (107)
- Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. (2003) (106)
- Hydrogen Bonds: Simple after All? (2018) (106)
- Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion. (2008) (106)
- DNA cleavage catalysed by the ribozyme from Tetrahymena (1990) (106)
- Assembly Line Polyketide Synthases: Mechanistic Insights and Unsolved Problems (2014) (104)
- RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. (2002) (102)
- The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction. (1993) (100)
- Spatial distribution of competing ions around DNA in solution. (2004) (100)
- Involvement of a Specific Metal Ion in the Transition of the Hammerhead Ribozyme to Its Catalytic Conformation* (1997) (99)
- RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. (1992) (97)
- New pathways in folding of the Tetrahymena group I RNA enzyme. (1999) (97)
- The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphorothioates by alkaline phosphatase. (1995) (96)
- Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. (2001) (93)
- Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. (1992) (92)
- Ion counting from explicit-solvent simulations and 3D-RISM. (2014) (92)
- Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA. (1993) (91)
- The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. (2006) (90)
- Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. (2005) (90)
- Determining the Mg2+ stoichiometry for folding an RNA metal ion core. (2005) (90)
- Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. (2008) (89)
- Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch (2016) (89)
- Origins of catalysis by computationally designed retroaldolase enzymes (2010) (88)
- Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase (2012) (86)
- Structural inference of native and partially folded RNA by high-throughput contact mapping (2008) (85)
- The effect of divalent metal ions on the rate and transition-state structure of phosphoryl-transfer reactions (1987) (85)
- Catalysis of the hydrolysis of phosphorylated pyridines by Mg(OH)+: a possible model for enzymatic phosphoryl transfer. (1990) (82)
- Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. (2008) (80)
- Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data (2012) (78)
- Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases. (1996) (78)
- Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments (2008) (77)
- Specificity of hammerhead ribozyme cleavage. (1996) (77)
- Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome (2010) (77)
- High-throughput analysis and protein engineering using microcapillary arrays (2015) (77)
- A repulsive field: advances in the electrostatics of the ion atmosphere. (2008) (76)
- Evidence that metaphosphate monoanion is not an intermediate in solvolysis reactions in aqueous solution (1989) (73)
- Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site? (2007) (73)
- Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding. (1993) (71)
- Hydrogen bond dynamics in the active site of photoactive yellow protein (2009) (71)
- The ligand-free state of the TPP riboswitch: a partially folded RNA structure. (2010) (69)
- Phosphoryl Transfer to Anionic Oxygen Nucleophiles. Nature of the Transition State and Electrostatic Repulsion (1989) (69)
- Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. (2007) (67)
- Direct measurement of tertiary contact cooperativity in RNA folding. (2008) (67)
- Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. (2017) (66)
- Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. (2013) (66)
- Mutations in a nonconserved sequence of the Tetrahymena ribozyme increase activity and specificity (1991) (66)
- A New Heat Shock Protein That Binds Nucleic Acids* (1999) (66)
- Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro (1999) (65)
- Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis. (2007) (65)
- Functional Identification of Catalytic Metal Ion Binding Sites within RNA (2005) (64)
- The Substrate-Assisted General Base Catalysis Model for Phosphate Monoester Hydrolysis: Evaluation Using Reactivity Comparisons (2000) (63)
- Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole (2010) (63)
- Dissection of the role of the conserved G.U pair in group I RNA self-splicing. (1994) (62)
- Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. (2010) (61)
- High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding (2018) (61)
- Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase. (1999) (60)
- Ribonuclease Revisited: Catalysis via the Classical General Acid-Base Mechanism or a Triester-like Mechanism? (1994) (60)
- The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. (2000) (60)
- Do conformational biases of simple helical junctions influence RNA folding stability and specificity? (2009) (59)
- Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting. (2015) (58)
- Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2'-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme. (1999) (57)
- Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. (1999) (57)
- Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability. (2015) (56)
- Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization. (1995) (56)
- Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase (2009) (56)
- Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets (2015) (55)
- Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics (2020) (54)
- Energetic Effects of Multiple Hydrogen Bonds. Implications for Enzymatic Catalysis (1996) (54)
- Group I Ribozymes: Substrate Recognition, Catalytic Strategies, and Comparative Mechanistic Analysis (1996) (54)
- Evaluating the potential for halogen bonding in the oxyanion hole of ketosteroid isomerase using unnatural amino acid mutagenesis. (2009) (53)
- Use of anion–aromatic interactions to position the general base in the ketosteroid isomerase active site (2013) (53)
- Metal ion-based RNA cleavage as a structural probe. (2009) (53)
- Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase. (2008) (53)
- High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. (2012) (52)
- Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily. (2008) (52)
- The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction. (2000) (51)
- Nucleophiles of high reactivity in phosphoryl transfer reactions: .alpha.-effect compounds and fluoride ion (1990) (51)
- Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site (2015) (49)
- Methods of site-specific labeling of RNA with fluorescent dyes. (2009) (49)
- Decreasing reactivity with increasing nucleophile basicity. The effect of solvation on .beta.nuc for phosphoryl transfer to amines. (1986) (49)
- Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step. (1994) (49)
- Use of intrinsic binding energy for catalysis by an RNA enzyme. (1997) (48)
- Impaired transition state complementarity in the hydrolysis of O-arylphosphorothioates by protein-tyrosine phosphatases. (1999) (48)
- Measuring the folding transition time of single RNA molecules. (2007) (47)
- Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. (2012) (46)
- A quantitative and predictive model for RNA binding by human Pumilio proteins (2018) (45)
- Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: Implications for RNA preorganization and function (2003) (45)
- Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. (2008) (45)
- Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme. (1997) (44)
- Probing the Tetrahymena group I ribozyme reaction in both directions. (2002) (44)
- 6 How the Group I Intron Works: A Case Study of RNA Structure and Function (2006) (44)
- Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? (2016) (44)
- pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa. (1996) (44)
- Mechanistic investigations of a ribozyme derived from the Tetrahymena group I intron: insights into catalysis and the second step of self-splicing. (1996) (44)
- Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. (2009) (43)
- Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer? (2004) (43)
- Isolation of a local tertiary folding transition in the context of a globally folded RNA (1996) (43)
- Computational design of three-dimensional RNA structure and function (2019) (42)
- Structural specificity conferred by a group I RNA peripheral element. (2005) (42)
- Pyrophosphate Formation from Acetyl Phosphate and Orthophosphate Anions in Concentrated Aqueous Salt Solutions Does Not Provide Evidence for a Metaphosphate Intermediate (1986) (42)
- Stereospecificity of Reactions Catalyzed by HIV-1 Integrase* (1999) (42)
- Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions. (2005) (41)
- Effects of divalent metal ions on individual steps of the Tetrahymena ribozyme reaction. (1997) (41)
- Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA* (2011) (41)
- Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions. (2017) (40)
- Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase. (2013) (40)
- An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction. (2000) (39)
- From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. (2015) (38)
- A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations. (1998) (38)
- Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site (2013) (37)
- Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis. (2002) (37)
- Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling (2007) (37)
- Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction. (1998) (36)
- Structural ensemble and microscopic elasticity of freely diffusing DNA by direct measurement of fluctuations (2013) (36)
- Functional identification of ligands for a catalytic metal ion in group I introns. (2008) (36)
- Does the Active Site Arginine Change the Nature of the Transition State for Alkaline Phosphatase-Catalyzed Phosphoryl Transfer? (1999) (36)
- Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. (2010) (35)
- The Solution Structural Ensembles of RNA Kink-turn Motifs and Their Protein Complexes (2015) (35)
- Implications of Molecular Heterogeneity for the Cooperativity of Biological Macromolecules (2011) (35)
- Low specificity of metal ion binding in the metal ion core of a folded RNA. (2007) (34)
- Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme. (1999) (33)
- Parallel molecular mechanisms for enzyme temperature adaptation (2021) (33)
- Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) is a substrate for the nucleotide hydrolysis and RNA unwinding activities of eukaryotic translation initiation factor eIF4A. (2003) (33)
- Electrostatics of nucleic acid folding under conformational constraint. (2012) (33)
- Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. (2018) (31)
- Hydrogen bonding in enzymatic catalysis: analysis of energetic contributions. (1999) (31)
- Hydrogen bond coupling in the ketosteroid isomerase active site. (2009) (31)
- The Story of RNA Folding, as Told in Epochs. (2018) (30)
- Ground State Destabilization by Anionic Nucleophiles Contributes to the Activity of Phosphoryl Transfer Enzymes (2013) (30)
- Using Unnatural Amino Acids to Probe the Energetics of Oxyanion Hole Hydrogen Bonds in the Ketosteroid Isomerase Active Site (2014) (30)
- The effects of magnesium2+, hydrogen bonding, and steric factors on rate and equilibrium constants for phosphoryl transfer between carboxylate ions and pyridines (1990) (30)
- Mechanistic and Evolutionary Insights from Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases across the Alkaline Phosphatase Superfamily (2016) (30)
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction (2020) (29)
- Multiple unfolding events during native folding of the Tetrahymena group I ribozyme. (2010) (28)
- From a structural average to the conformational ensemble of a DNA bulge (2014) (27)
- Slow molecular recognition by RNA (2017) (27)
- Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation (2019) (27)
- Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase. (2011) (27)
- Probing the Origins of Catalytic Discrimination between Phosphate and Sulfate Monoester Hydrolysis: Comparative Analysis of Alkaline Phosphatase and Protein Tyrosine Phosphatases (2014) (27)
- Riboswitch conformations revealed by small-angle X-ray scattering. (2009) (27)
- Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis. (2002) (27)
- Ion counting demonstrates a high electrostatic field generated by the nucleosome (2019) (27)
- DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity (2007) (26)
- Coupling between ATP Binding and DNA Cleavage by DNA Topoisomerase II (2008) (26)
- Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme. (1999) (26)
- Biophysical, chemical, and functional probes of RNA structure, interactions and folding: Part A. Preface. (2009) (26)
- Effects of oligonucleotide length and atomic composition on stimulation of the ATPase activity of translation initiation factor elF4A. (1999) (25)
- The far reaches of enzymology. (2009) (24)
- Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy. (2009) (24)
- Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization. (2011) (23)
- Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis. (2001) (23)
- Structure-function relationships in the hammerhead ribozyme probed by base rescue. (1998) (23)
- Characterization of a local folding event of the Tetrahymena group I ribozyme: effects of oligonucleotide substrate length, pH, and temperature on the two substrate binding steps. (1999) (22)
- Three αSNAP and 10 ATP Molecules Are Used in SNARE Complex Disassembly by N-ethylmaleimide-sensitive Factor (NSF)* (2014) (21)
- Experimental and Computational Mutagenesis To Investigate the Positioning of a General Base within an Enzyme Active Site (2014) (21)
- Fluorescence polarization anisotropy to measure RNA dynamics. (2009) (21)
- Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase. (2016) (20)
- Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA (2017) (20)
- Catalysis of Phosphoryl Transfer from ATP by Amine Nucleophiles (1999) (20)
- Interdomain Communication in DNA Topoisomerase II (2006) (20)
- Ground state destabilization from a positioned general base in the ketosteroid isomerase active site. (2013) (20)
- Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway (2016) (19)
- Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting. (2019) (19)
- A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site. (2010) (19)
- Catalysis of the hydrolysis of phosphorylated pyridines by alkaline phosphatase has little or no dependence on the pKa of the leaving group. (1993) (19)
- Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET. (2015) (18)
- Hidden Structural Modules in a Cooperative RNA Folding Transition (2018) (18)
- Probing the dynamics of the P1 helix within the Tetrahymena group I intron. (2009) (18)
- Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. (2015) (17)
- Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution (2017) (17)
- Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles (2019) (17)
- Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase. (2016) (16)
- Mutations at the guanosine-binding site of the Tetrahymena ribozyme also affect site-specific hydrolysis. (1992) (15)
- Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry (2017) (15)
- Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. (2011) (15)
- Modulation of individual steps in group I intron catalysis by a peripheral metal ion. (2007) (15)
- Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics (2017) (14)
- Blind tests of RNA–protein binding affinity prediction (2019) (14)
- Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2 (2019) (14)
- RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. (2016) (14)
- Use of phosphorothioates to identify sites of metal-ion binding in RNA. (2009) (13)
- Probing the role of a secondary structure element at the 5'- and 3'-splice sites in group I intron self-splicing: the tetrahymena L-16 ScaI ribozyme reveals a new role of the G.U pair in self-splicing. (2007) (13)
- Structure and function converge to identify a hydrogen bond in a group I ribozyme active site. (2009) (12)
- Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway (2017) (12)
- Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data (2015) (12)
- A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect. (2004) (11)
- Use of duplex rigidity for stability and specificity in RNA tertiary structure. (2000) (11)
- Promiscuous catalysis by the tetrahymena group I ribozyme. (2005) (11)
- Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation on βnuc for Phosphoryl Transfer to Amines. (1986) (11)
- 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. (2011) (11)
- Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase. (2013) (11)
- High throughput and quantitative enzymology in the genomic era. (2021) (10)
- Alkaline phosphatase revisited: hydrolysis of alkyl phosphates. (2002) (10)
- Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study. (2012) (10)
- Roles of Long-Range Tertiary Interactions in Limiting Dynamics of the Tetrahymena Group I Ribozyme (2014) (10)
- A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction (2014) (10)
- A Single‐Stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme (2013) (9)
- Computational Design of Asymmetric Three-dimensional RNA Structures and Machines (2017) (9)
- A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme. (2012) (8)
- The structural ensemble of a Holliday junction determined by X-ray scattering interference (2020) (8)
- RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix (2018) (8)
- Kemp Eliminase Activity of Ketosteroid Isomerase. (2017) (8)
- Thermodynamic evidence for negative charge stabilization by a catalytic metal ion within an RNA active site. (2012) (8)
- Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme. (2011) (8)
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics (2018) (7)
- Biosciences Proposal Bootcamp: Structured peer and faculty feedback improves trainees’ proposals and grantsmanship self-efficacy (2020) (7)
- Gold nanocrystal labels provide a sequence–to–3D structure map in SAXS reconstructions (2018) (7)
- The individual and the team in collaborative science (2020) (7)
- Comment on “Extreme electric fields power catalysis in the active site of ketosteroid isomerase” (2015) (7)
- High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs (2021) (6)
- Correction to "Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase". (2016) (6)
- RNA radiolabeling. (2013) (6)
- The Effect of Divalent Metal Ions on the Rate and Transition-State Structure of Phosphoryl-Transfer Reactions. (1987) (6)
- Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding (2019) (6)
- An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions (2016) (5)
- Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures. (2020) (5)
- RNA structure: Ribozyme crevices and catalysis (1998) (5)
- Systematic investigation of the link between enzyme catalysis and cold adaptation (2021) (5)
- Recording and Analyzing Nucleic Acid Distance Distributions with X‐Ray Scattering Interferometry (XSI) (2018) (4)
- Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking (2022) (4)
- Learning from ribozymes (2015) (4)
- A Robust Method for Collecting X-ray Diffraction Data from Protein Crystals across Physiological Temperatures (2020) (4)
- Correction: Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance (2008) (4)
- Serum electrolytes can promote hydroxyl radical-initiated biomolecular damage from inflammation. (2019) (4)
- Fluorescently labeling synthetic RNAs. (2013) (4)
- Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer. (2010) (3)
- Quantitative studies of an RNA duplex electrostatics by ion counting (2019) (3)
- Author response: Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site (2015) (3)
- Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes (2016) (2)
- Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor (2019) (2)
- A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4 (2021) (2)
- Ensemble-function relationships to dissect mechanisms of enzyme catalysis (2022) (2)
- Galactofuranosyl-containing glycopeptide of Penicillium charlesii. Vacuum ultraviolet circular dichroism. (2009) (2)
- The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond Mechanisms (2006) (2)
- An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. (2017) (2)
- folding stability and specificity ? Do conformational biases of simple helical junctions influence RNA Material Supplemental (2009) (2)
- Assessing positioning in enzymatic catalysis via ketosteroid isomerase conformational ensembles (2019) (2)
- uPIC–M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry (2021) (1)
- Phosphoryl Transfer to Anionic Oxygen Nucleophiles. Nature of the Transition State and Electrostatic Repulsion. (1990) (1)
- E. coli alkaline phosphatase with bound inorganic phosphate (2011) (1)
- Structure of E322Y Alkaline Phosphatase in Complex with Inorganic Phosphate (2008) (1)
- The Stanford Institute for Chemical Biology. (2013) (1)
- Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data (2015) (1)
- Cation enrichment in the ion atmosphere is promoted by local hydration of DNA (2021) (1)
- “ Structure-Function from the Outside In : Long-range Tertiary Contacts in RNA Exhibit Distinct Catalytic Roles ” (2011) (1)
- The Study of Single Biomolecules with Fluorescence Methods (2001) (1)
- Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase (2006) (1)
- RNA conformational propensities determine cellular activity (2022) (1)
- Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate Effects upon Substitution of Sulfur for a Nonbridging Phosphoryl (1991) (1)
- The Effect of Magnesium on the Thermodynamics of Nucleic Acid Tertiary Contact Formation (2014) (1)
- Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in complex with inorganic phosphate (2015) (1)
- RNA. Preface. (2009) (1)
- Damaged goods? Evaluating the impact of X-ray damage on conformational heterogeneity in room temperature and cryo-cooled protein crystals (2021) (1)
- The roles of structural dynamics in the cellular functions of RNAs (2019) (1)
- DNA cleavage catalysed by the ribozyme from Tetrahymena (1990) (0)
- High Throughput Characterization of RNA Tertiary Elements (2016) (0)
- Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate (2006) (0)
- Ion counting demonstrates a high electrostatic potential of the nucleosome (2019) (0)
- Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound (2011) (0)
- Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) at 280 K (2020) (0)
- Crystal Structure of Ketosteroid Isomerase Y32F/Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol (2018) (0)
- How enzymes work (2010) (0)
- Crystal Structure of Ketosteroid Isomerase P39GV40GS42G from Pseudomonas Testosteroni (tKSI) bound to Equilenin (2011) (0)
- Multi-conformer model of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 250 K (2020) (0)
- Crystal Structure of Ketosteroid Isomerase Y16S/D40N from Pseudomonas putida with Bound Equilenin (2010) (0)
- X-Ray Diffraction data from E. Coli Alkaline Phosphatase in complex with tungstate, source of 5C66 structure (2017) (0)
- Removal of Covalent Heterogeneity Reveals Simple Folding (2011) (0)
- Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with Equilenin Bound (2010) (0)
- Observing folding and catalysis of a single RNA enzyme molecule (2000) (0)
- Nucleic Acid Conformation Ensembles Revealed by Au-SAXS Interferometry (2013) (0)
- E. coli alkaline phosphatase D101A, D153A, R166S, E322A, K328A mutant (2017) (0)
- Ensemble-function relationships to connect structure to mechanism: application of EnsemblePDB to the serine protease reaction coordinate and its catalytic features (2022) (0)
- Robust computational design, optimization, and structural characterization of retroaldol enzymes (2011) (0)
- Nanosecond Motions of the Substrate-Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling (2010) (0)
- Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 2,6-difluorophenol (2007) (0)
- Ensemble–function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole (2021) (0)
- E. coli alkaline phosphatase mutant S102G/R166S in complex with inorganic phosphate (2013) (0)
- Insights from Global Studies of Eukaryotic Translation (2007) (0)
- PNAS Plus Significance Statements (2013) (0)
- The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond (2007) (0)
- SAXS Studies of the Primary Forces Involved in RNA Folding (2004) (0)
- Investigating mechanistic and evolutionary relationships between members of the alkaline phosphatase superfamily (2006) (0)
- Author response: Ion counting demonstrates a high electrostatic field generated by the nucleosome (2019) (0)
- Competition and spatial distribution of ions diffusively bound to DNA (2005) (0)
- LESSONS FROM CATALYSIS BY RNA ENZYMES (2018) (0)
- A High-Throughput Assay Platform for Next-Generation Mechanistic Enzymology and Applications (2020) (0)
- Depa Depa Fluorescence Polarization Anisotropy to Measure RNA Dynamics (2009) (0)
- E. Coli Alkaline Phosphatase in complex with tungstate (2016) (0)
- A Quantitative and Predict ive Model for RNA Binding by Human Pumilio Proteins Graphical (2019) (0)
- Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 280 K (2020) (0)
- Impacts of high ATP supply from chloroplasts and mitochondria on the leaf metabolism of Arabidopsis thaliana (0)
- High-throughput enzymology reveals mutations throughout a phosphatase that decouple catalysis and transition state analog affinity (2022) (0)
- Crystal Structure of Ketosteroid Isomerase D38GF54A mutant from Pseudomonas Testosteroni (tKSI) bound to Equilenin (2017) (0)
- Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI) (2016) (0)
- Crystal structure of ketosteroid isomerase Y14AY55FD99A from Pseudomonas testosteroni (2011) (0)
- Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound phenol. (2006) (0)
- Crystal structure of alkaline phosphatase PafA T79S, N100A, K162A, R164A mutant (2017) (0)
- • Correlations between Enzyme Catalysis, Heterogeneous Catalysis and Homogeneous Catalysis • New Methods of Catalyst Synthesis • Characterization of Catalysts under Reaction Conditions • Global Catalytic Processes (2001) (0)
- A Microfluidics-Based Assay for Mapping Connectivity in Highly Proficient Enzymes Reveals Functional Modularity (2019) (0)
- Catalysis by Alkaline Phosphatase is Ultrasensitive to Charge Sequestered Between the Active Site Zinc Ions in the Transition State ” (2005) (0)
- Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to Equilenin at 280 K (2020) (0)
- Multi-conformer model of Apo Ketosteroid Isomerase from Pseudomonas Putida (pKSI) at 250 K (2020) (0)
- Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M116C-CN from P. putida (2011) (0)
- Crystal structure of ketosteroid isomerase F54G from Pseudomonas testosteroni (2012) (0)
- Specificity Principles in RNA-Guided Targeting (2016) (0)
- RNA Structure, Function, and (Thermo-) Dynamics: A SAXS and Single-Molecule Perspective (2011) (0)
- Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals. (2022) (0)
- Single Molecule Analysis of Group I Ribozyme Folding Reveals Pronounced Ruggedness Throughout Its Folding Landscape (2009) (0)
- Crystal structure of ketosteroid isomerase Y16AD103A from Pseudomonas putida (2011) (0)
- The Structure of Nucleotide Pyrophosphatase/ Phosphodiesterase and Implications for Enzyme Evolution in the Alkaline Phosphatase Superfamily (2006) (0)
- An RNA dynamic ensemble at atomic resolution (2020) (0)
- Evolution of RNA Binding Proteins and Their Regulatory Networks (2013) (0)
- Crystal Structure of Ketosteroid Isomerase P39A from Pseudomonas Testosteroni (tKSI) (2011) (0)
- Blind Predictions of RNA/Protein Relative Binding Affinities (2017) (0)
- Building a quantitative and predictive model of 5'SS selection by human U1 snRNP using RNA-map. (2023) (0)
- Bringing Enzymology into the Genomic Era: Developing and Deploying New Tools to Quantitatively Map Functional Connections Throughout an Enzyme (2019) (0)
- Crystal Structure of Ketosteroid Isomerase from Mycobacterium hassiacum (mhKSI) (2020) (0)
- E. coli alkaline phosphatase mutant R166S in complex with phosphate (2008) (0)
- Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI) (2011) (0)
- Multi-conformer model of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to Equilenin at 250 K (2020) (0)
- STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE (2001) (0)
- Correction to Uncovering the Determinants of a Highly Perturbed Tyrosine p Ka in the Active Site of Ketosteroid Isomerase. (2018) (0)
- The Diversity of Nuclear Magnetic Resonance Spectroscopy (2009) (0)
- Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements (2022) (0)
- Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) (2011) (0)
- From sequence to nanostructure: a critical base pair in RNA k-turns that confers folding and structural characteristics, and correlates with biological function (2015) (0)
- Dissecting the Electrostatics of Nucleic Acids (2018) (0)
- PHOSPHATE RECOGNITION BY A RIBOZYME (1992) (0)
- Additions and Corrections: Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation on (nuc) for Phosphoryl Transfer to Amines. (1986) (0)
- chaperones . facilitate in vitro splicing of phage T 4 introns by acting as RNA Escherichia coli proteins , including ribosomal protein S 12 (2008) (0)
- binding in an energetic model for glycine riboswitch folding Dissecting electrostatic screening , specific ion binding , and ligand Material Supplemental (2010) (0)
- Crystal Structure of Ketosteroid Isomerase D38N mutant from Mycobacterium hassiacum (mhKSI) bound to 3,4-dinitrophenol (2020) (0)
- Author response: How to measure and evaluate binding affinities (2020) (0)
- Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI) (2011) (0)
- Scaling Behavior of Single Stranded DNA Measured by Small Angle X-ray Scattering (2009) (0)
- A Kinetic and Thermodynamic Framework for the Hammerhead Ribozyme Reaction 7 (2002) (0)
- Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M105C-CN from P. putida with Bound Equilenin (2011) (0)
- SAXS S tudies of C ounterion-induced F orces in F olding of Nu cleic A cids (2004) (0)
- Crystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomonas Testosteroni (tKSI) (2011) (0)
- Crystal structure of wild type alkaline phosphatase PafA to 1.7A resolution (2016) (0)
- Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 100 K (2020) (0)
- Crystal Structure of Ketosteroid Isomerase D40N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol (2018) (0)
- Listening to domain communication in DNA topoisomerase II (2005) (0)
- Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures. (2023) (0)
- Specificity ofhammerheadribozyme cleavage (1996) (0)
- Crystal Structure of Ketosteroid Isomerase D40N/D103N mutant from Pseudomonas Putida (pKSI) bound to 3,4-dinitrophenol (2018) (0)
- Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI) (2013) (0)
- Future Directions of Catalysis Science—Workshop (2001) (0)
- The Storyof RNAFolding, as Told in Epochs (2018) (0)
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