
- The Substrate-Assisted General Base Catalysis Model for Phosphate Monoester Hydrolysis: Evaluation Using Reactivity Comparisons
- Structural specificity conferred by a group I RNA peripheral element
- C H A P T E R E I G H T E E N Probing Nucleic AcidIon Interactions
- Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: Implications for
- Alkaline Phosphatase Revisited: Hydrolysis of Alkyl Phosphates Patrick J. O'Brien and Daniel Herschlag*
- Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an
- Multiple Unfolding Events during Native Folding of the Tetrahymena Group I Ribozyme
- Does the Active Site Arginine Change the Nature of the Transition State for Alkaline
- conference papers J. Appl. Cryst. (2007). 40, s229s234 Jan Lipfert et al. RNA low-resolution models from SAXS s229
- Alkaline Phosphatase Mono-and Diesterase Reactions: Comparative Transition State Analysis
- A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect
- Nanomechanical measurements of the sequence-dependent folding landscapes
- Probing the Origin of the Compromised Catalysis of E. coli Alkaline Phosphatase in its Promiscuous Sulfatase Reaction
- Dissection of a metal-ion-mediated conformational change in Tetrahymena
- J. Am. Chem. SOC.1989, 11 1, 7587-1596 7587 Phosphoryl Transfer to Anionic Oxygen Nucleophiles. Nature
- RNA Simulations: Probing Hairpin Unfolding and the Dynamics of a GNRA Tetraloop
- Biochemistry 1993,32, 8737-8741 8737 Catalysis of the Hydrolysis of Phosphorylated Pyridines by Alkaline Phosphatase
- BIOORGANIC CHEMISTRY 16, 62-96 (1988) The Role of Induced Fit and Conformational Changes of
- Structural and Functional Comparisons of Nucleotide Pyrophosphatase/ Phosphodiesterase and Alkaline Phosphatase: Implications for Mechanism and
- pubs.acs.org/Biochemistry Published on Web 05/26/2009 r 2009 American Chemical Society 6932 Biochemistry 2009, 48, 69326939
- Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids
- 10.1261/rna.632007Access the most recent version at doi: 2007 13: 1656-1667; originally published online Aug 24, 2007;RNA
- pubs.acs.org/BiochemistryPublished on Web 11/04/2010r 2010 American Chemical Society Biochemistry 2010, 49, 1033910348 10339
- Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
- nature structural biology volume 7 number 5 may 2000 367 Small angle X-ray
- Kinetic Isotope Effects for Alkaline Phosphatase Reactions: Implications for the Role of Active-Site Metal Ions in Catalysis
- 37643773 Nucleic Acids Research, 2007, Vol. 35, No. 11 Published online 21 May 2007 doi:10.1093/nar/gkm335
- Do Electrostatic Interactions with Positively Charged Active Site Groups Tighten the Transition State for Enzymatic
- Adenosine 5 -O-(3-thio)triphosphate (ATP S) is a substrate for the nucleotide hydrolysis and RNA unwinding activities
- Functional Identification of Ligands for a Catalytic Metal Ion in Group I Introns Marcello Forconi,
- Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts
- RNA Catalysisby a Group I DEVELOPING A MODEL FOR TRANSITION STATE
- 01992 Oxford University Press . Nucleic Acids Research, 1992, Val. 20, No. 24 4613-4619 Mutations at the guanosine-binding site of the
- VOLUME116, NUMBER26 DECEMBER28, 1994
- Evaluating the Potential for Halogen Bonding in the Oxyanion Hole of Ketosteroid
- The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure
- J. Am. Chem. SOC.1989, 11 1, 7519-7586 1519 Evidence That Metaphosphate Monoanion Is Not an
- An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I
- Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding
- Chemical Rescue of Phosphoryl Transfer in a Cavity Mutant: A Cautionary Tale for Site-Directed Mutagenesis,
- 7938 J. Am. Chem. Soc. 1986, 108, 7938-7946 in this unsymmetrical azoalkane.
- 1942 J. Am. Chem. SOC.1990, 112, 1942-1950 (PA)2FeOFe(PA)2(1) (eq 2 and 4, and Scheme Ia).
- 5172 Biochemistry 1990, 29, 5172-5 119 Catalysis of the Hydrolysis of Phosphorylated Pyridines by Mg(OH)+: A Possible
- Biochemistry 1990, 29, 10159-10171 10159 Catalysis of RNA Cleavage by the Tetrahymena thermophila Ribozyme.
- 10172 Biochemistry 1990, 29, 10172-10180 Catalysis of RNA Cleavage by the Tetrahymena thermophila Ribozyme.
- 4844 Biochemistry 1991, 30, 4844-4854 Ribozyme-Catalyzed and Nonenzymatic Reactions of Phosphate
- Reprinted from Biochemistry, 1992, 31. Copyright 0 1992 by the American Chemical Society and reprinted by permission of the copyright owner.1386
- Reprintedfrom Biochemistry,1994,33. Copyright 0 1994by the American Chemical Society and reprintedby permissionof the copyrightowner.
- RNA Chaperones and the RNA Folding Problem*
- Group I Ribozymes: Substrate Recognition, Catalytic Strategies,
- A Core Folding Model for Catalysis by the Hammerhead Ribozyme Accounts for Its Extraordinary Sensitivity to Abasic Mutations
- Nature Macmillan Publishers Ltd 1998 news and views
- 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
- Effects of oligonucleotide length and atomic composition on stimulation of the ATPase activity
- Impaired Transition State Complementarity in the Hydrolysis of O-Arylphosphorothioates by Protein-Tyrosine Phosphatases
- Three metal ions at the active site of the Tetrahymena group I ribozyme
- Characterization of a Local Folding Event of the Tetrahymena Group I Ribozyme: Effects of Oligonucleotide Substrate Length, pH, and Temperature on the Two
- Stereospecificity of Reactions Catalyzed by HIV-1 Integrase* (Received for publication, August 6, 1999)
- Research Paper 85 The role of the cleavage site 2-hydroxyl in the Tetrahymena
- semaphorins (26, 27). Given the presence of all three types of molecules in the SA library, it is
- Defining the Catalytic Metal Ion Interactions in the Tetrahymena Ribozyme Shu-ou Shan,, Alexander V. Kravchuk, Joseph A. Piccirilli,*,| and Daniel Herschlag*,
- Precision and functional specificity in mRNA decay , Chih Long Liu
- Probing the Tetrahymena Group I Ribozyme Reaction in Both Directions Katrin Karbstein, Kate S. Carroll, and Daniel Herschlag*
- Environmental Effects on Phosphoryl Group Bonding Probed by Vibrational Spectroscopy: Implications for Understanding
- Functional Identification of Catalytic Metal Ion Binding Sites within RNA
- Promiscuous Catalysis by the Tetrahymena Group I Ribozyme Marcello Forconi and Daniel Herschlag*
- Alkaline Phosphatase Catalysis Is Ultrasensitive to Charge Sequestered between the Active Site Zinc Ions
- Interdomain Communication in DNA Topoisomerase II DNA BINDING AND ENZYME ACTIVATION*S
- The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond Mechanisms
- DOI: 10.1126/science.1133601 , 1001 (2006);314Science
- Measuring the Folding Transition Time of Single RNA Molecules Tae-Hee Lee,* Lisa J. Lapidus,* Wei Zhao,* Kevin J. Travers,y
- 10.1261/rna.566007Access the most recent version at doi: published online Jul 6, 2007;RNA
- Evaluation of Ion Binding to DNA Duplexes Using a Size-Modified Poisson-Boltzmann Theory
- Structural inference of native and partially folded RNA by high-throughput contact mapping
- Direct Measurement of Tertiary Contact Cooperativity in RNA Bernie D. Sattin,,
- Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded
- Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid
- Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs,
- Available online at www.sciencedirect.com A repulsive field: advances in the electrostatics of the ion
- 10.1261/rna.1270809Access the most recent version at doi: 2009 15: 189-199RNA
- Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering
- Motions of the Substrate Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling
- Obtaining enzymes in pure form was an essential prerequisite for understanding the
- RNA Catalysis DOI: 10.1002/anie.200903006
- Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human
- 10.1261/rna.1747509Access the most recent version at doi: 2009 15: 2195-2205 originally published online October 22, 2009RNA
- C H A P T E R F I V E Metal Ion-Based RNA Cleavage
- Multiple native states reveal persistent ruggedness of an RNA folding landscape
- 10.1261/rna.1985110Access the most recent version at doi: 2010 16: 708-719 originally published online March 1, 2010RNA
- Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole
- Origins of catalysis by computationally designed retroaldolase enzymes
- pubs.acs.org/BiochemistryPublished on Web 02/22/2010r 2010 American Chemical Society Biochemistry 2010, 49, 27532762 2753
- Use of Duplex Rigidity for Stability and Specificity in RNA Tertiary Structure Geeta J. Narlikar,, Laura E. Bartley,| and Daniel Herschlag*,,|
- Provided for non-commercial research and educational use only. Not for reproduction, distribution or commercial use.
- Hydrogen bond dynamics in the active site of photoactive yellow protein
- J. Am. Chem. Soc. 1986, 108,479-483 479 Decreasing Reactivity with Increasing Nucleophile Basicity.
- Identification of the Hammerhead Ribozyme Metal Ion Binding Site Responsible for Rescue of the Deleterious Effect of a Cleavage Site Phosphorothioate
- COMMUNICATION Probing the Folding Landscape of the Tetrahymena
- 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
- Coupling between ATP Binding and DNA Cleavage by DNA Topoisomerase II
- Genome-wide identification of mRNAs associated with the translational regulator PUMILIO
- 8312 Biochemistry 1993,32,8312-8321 The Importance of Being Ribose at the Cleavage Site in the Tetrahymena
- J. Am. Chem. SOC.1987, 109, 4665-4674 4665 30), 247 (100); exact mass 578.2025, calcd for C46H26 578.2034.
- Functional Interrelationships in the Alkaline Phosphatase Superfamily: Phosphodiesterase Activity of Escherichia coli Alkaline Phosphatase
- C H A P T E R F O U R T E E N Fluorescence Polarization
- Role of SRP RNA in the GTPase Cycles of Ffh and FtsY Paul Peluso, Shu-ou Shan, Silke Nock, Daniel Herschlag, and Peter Walter*,
- The EMBO Journal vol.13 no.12 pp.2913-2924,1994 An RNA chaperone activity of non-specific RNA binding
- Comparison of the hammerhead cleavage reactions stimulated by monovalent
- New Pathways in Folding of the Tetrahymena Group I Rick Russell and Daniel Herschlag*
- Promiscuous Sulfatase Activity and Thio-Effects in a Phosphodiesterase of the Alkaline Phosphatase Superfamily
- Dissecting eukaryotic translation and its control by ribosome density mapping
- J. Am. Chem. SOC.1990, 112, 1951-1956 1951 Nucleophiles of High Reactivity in Phosphoryl Transfer
- Nucleophilic Activation by Positioning in Phosphoryl Transfer Catalyzed by Nucleoside Diphosphate Kinase,
- Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia coli Alkaline Phosphatase,
- Biochemistry 1993,32. 8299-83 11 8299 Contributions of 2'-Hydroxyl Groups of the RNA Substrate to Binding and
- Probing the Dynamics of the P1 Helix within the Tetrahymena Group I Intron
- Extensive Association of Functionally and Cytotopically Related mRNAs
- CHALLENGES IN ENZYME MECHANISM AND Daniel A. Kraut, Kate S. Carroll, and Daniel Herschlag
- SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid
- Supporting Information Schwans et al. 10.1073/pnas.0901032106
- SUPPORTING INFORMATION Testing Geometrical Discrimination within an Enzyme Active Site
- Figure S1: Histogram of the lengths of FRET traces. The line shows the best single-exponential fit, from which the rate constant kbleach was determined.
- Supporting Text for: Origins of Catalysis by Computationally Designed
- C H A P T E R T H R E E Methods of Site-Specific Labeling
- Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
- THE LIGAND-FREE STATE OF THE TPP RIBOSWITCH, A PARTIALLY FOLDED RNA STRUCTURE
- Supporting Information Hydrogen Bonding in the Active Site of Ketosteroid Isomerase
- Supporting Information Wiley-VCH 2009
- Supporting Information for "Tightening of Active Site Interactions En-route to the Transition State Revealed by Single-Atom Substitution in the Guanosine-Binding Site of
- C H A P T E R E L E V E N Measuring the Energetic Coupling of
- Published: May 03, 2011 r 2011 American Chemical Society 7791 dx.doi.org/10.1021/ja111316y |J. Am. Chem. Soc. 2011, 133, 77917800
- Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA*S
- SUPPORTING INFORMATION Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site
- Supplemental Material: Annu. Rev. Biochem. 2011. 80: doi: 10.1146/annurev-biochem-060409-092741
- Supporting Information Sigala et al. 10.1073/pnas.0900168106
- Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin-labeling
- Supporting Information For: Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA
- B R I E F COM MU N I CAT I ON S Implications of molecular
- Supporting Information Saturation of LacI with model constructs
- Supplementary Material for "Dissecting Electrostatic Screening, Specific Ion
- Supplementary Information for "Do Conformational Biases of Simple Helical
- Implications of molecular heterogeneity for the cooperativity of biological macromolecules
- BI80CH08-Herschlag ARI 1 March 2011 16:25 Biological Phosphoryl-
- Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA*S
- A Role for a Single-Stranded Junction in RNA Binding and Specificity by the Tetrahymena Group I Ribozyme
- Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data
- Biological Phosphoryl-Transfer Reactions
- Published: June 21, 2011 r 2011 American Chemical Society 11621 dx.doi.org/10.1021/ja203370b |J. Am. Chem. Soc. 2011, 133, 1162111631
- Structure-Function Analysis from the Outside In: Long-Range Tertiary Contacts in RNA Exhibit Distinct Catalytic Roles
- Thermodynamic Evidence for Negative Charge Stabilization by a Catalytic Metal Ion within an RNA Active Site
- C H A P T E R E L E V E N Measuring the Energetic Coupling of
- High-Resolution Analysis of Zn2+ Coordination in the
- Chemistry & Biology Brief Communication
- Published: May 03, 2011 r 2011 American Chemical Society 7791 dx.doi.org/10.1021/ja111316y |J. Am. Chem. Soc. 2011, 133, 77917800
- B R I E F COM MU N I CAT I ON S Implications of molecular