Daniel Herschlag

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) is a substrate for the nucleotide hydrolysis and RNA unwinding activities of eukaryotic translation initiation factor eIF4A
    Matthew L Peck
    Department of Biochemistry, Stanford University, Stanford, California 94305 5307, USA
    RNA 9:1180-7. 2003
  2. pmc Functional identification of catalytic metal ion binding sites within RNA
    James L Hougland
    Department of Chemistry, University of Chicago, Illinois, USA
    PLoS Biol 3:e277. 2005
  3. pmc Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    Andre P Gerber
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E79. 2004
  4. ncbi request reprint Probing the Tetrahymena group I ribozyme reaction in both directions
    Katrin Karbstein
    Department of Biochemistry, Stanford University, Beckman Center B400, Stanford, California 94305 5307, USA
    Biochemistry 41:11171-83. 2002
  5. pmc High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography
    Elena Bobyr
    Department of Chemistry, Stanford University, Stanford, CA 94305, USA
    J Mol Biol 415:102-17. 2012
  6. pmc Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole
    Paul A Sigala
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 130:13696-708. 2008
  7. pmc Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion
    Jesse G Zalatan
    Department of Chemistry, Stanford University, Beckman Center B400, Stanford, CA 94305, USA
    J Mol Biol 384:1174-89. 2008
  8. pmc Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site
    Paul A Sigala
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:E2552-61. 2013
  9. pmc Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction
    Irina Catrina
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 129:5760-5. 2007
  10. pmc Ground state destabilization from a positioned general base in the ketosteroid isomerase active site
    Eliza A Ruben
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Biochemistry 52:1074-81. 2013

Collaborators

Detail Information

Publications90

  1. pmc Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) is a substrate for the nucleotide hydrolysis and RNA unwinding activities of eukaryotic translation initiation factor eIF4A
    Matthew L Peck
    Department of Biochemistry, Stanford University, Stanford, California 94305 5307, USA
    RNA 9:1180-7. 2003
    ..These results raise caution concerning the assumption that ATPgammaS is a nonhydrolyzable ATP analog and underscore the utility of thio-substituted NTPs as mechanistic probes...
  2. pmc Functional identification of catalytic metal ion binding sites within RNA
    James L Hougland
    Department of Chemistry, University of Chicago, Illinois, USA
    PLoS Biol 3:e277. 2005
    ....
  3. pmc Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    Andre P Gerber
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E79. 2004
    ....
  4. ncbi request reprint Probing the Tetrahymena group I ribozyme reaction in both directions
    Katrin Karbstein
    Department of Biochemistry, Stanford University, Beckman Center B400, Stanford, California 94305 5307, USA
    Biochemistry 41:11171-83. 2002
    ..These and prior results suggest that the Tetrahymena group I ribozyme, analogous to protein enzymes, uses multiple catalytic strategies to achieve its large rate enhancement...
  5. pmc High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography
    Elena Bobyr
    Department of Chemistry, Stanford University, Stanford, CA 94305, USA
    J Mol Biol 415:102-17. 2012
    ..Overall, the results suggest that the binuclear Zn(2+) catalytic site remains very similar between AP and NPP during the course of a reaction cycle...
  6. pmc Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole
    Paul A Sigala
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 130:13696-708. 2008
    ....
  7. pmc Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion
    Jesse G Zalatan
    Department of Chemistry, Stanford University, Beckman Center B400, Stanford, CA 94305, USA
    J Mol Biol 384:1174-89. 2008
    ..These results establish a new mechanistic model for this prototypical bimetallo enzyme and demonstrate the power of a comparative approach for probing biochemical function...
  8. pmc Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site
    Paul A Sigala
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:E2552-61. 2013
    ....
  9. pmc Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction
    Irina Catrina
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 129:5760-5. 2007
    ..We suggest that the lower charge density of this oxygen atom on a transferred sulfuryl group accounts for a large fraction of the decreased stabilization of the transition state for its reaction relative to phosphoryl transfer...
  10. pmc Ground state destabilization from a positioned general base in the ketosteroid isomerase active site
    Eliza A Ruben
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Biochemistry 52:1074-81. 2013
    ..This ground state destabilization mechanism may be common to the many enzymes with anionic side chains that deprotonate carbon acids...
  11. pmc Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase
    Aaron T Fafarman
    Department of Chemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 109:E299-308. 2012
    ....
  12. pmc Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole
    Daniel A Kraut
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:1960-5. 2010
    ..These results underscore the complex energetics of hydrogen bonding interactions and site-directed mutagenesis experiments...
  13. doi request reprint Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase
    Jason P Schwans
    Department of Biochemistry and Department of Chemistry, Stanford University, Stanford, California 94305, United States
    Biochemistry 52:7840-55. 2013
    ..The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects...
  14. pmc Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis
    Jesse G Zalatan
    Department of Chemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 129:9789-98. 2007
    ....
  15. pmc Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase
    Jason P Schwans
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 106:14271-5. 2009
    ..These results suggest that remote binding interactions contribute >5 kcal/mol to catalysis by KSI but that local rather than remote interactions dictate the catalytic contributions from KSI's general base and oxyanion hole...
  16. ncbi request reprint Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution
    Jesse G Zalatan
    Department of Chemistry, Stanford University, Stanford, California 94305 5307, USA
    Biochemistry 45:9788-803. 2006
    ....
  17. pmc Functional identification of ligands for a catalytic metal ion in group I introns
    Marcello Forconi
    Department of Biochemistry and Chemistry, Stanford University, Stanford, California 94305, USA
    Biochemistry 47:6883-94. 2008
    ..Elucidating these active site connections is a crucial step toward an in-depth understanding of how specific structural features of the group I intron lead to catalysis...
  18. pmc Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    Magdalena A Jonikas
    Department of Bioengineering, Stanford University, California 94305, USA
    RNA 15:189-99. 2009
    ..thermophila group I intron, creating an integrated model of the entire molecule. Our software package is freely available at https://simtk.org/home/nast...
  19. pmc Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase
    PATRICK J O'BRIEN
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    Biochemistry 47:7663-72. 2008
    ....
  20. pmc Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble
    Yu Bai
    Department of Biochemistry, Stanford University, California 94305, USA
    J Am Chem Soc 130:12334-41. 2008
    ..The increase of conformational entropy presents an additional barrier to folding by stabilizing the unfolded state. Neglecting this effect will adversely impact the accuracy of folding analyses and models...
  21. ncbi request reprint Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions
    Ivana Nikolic-Hughes
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 127:9314-5. 2005
    ..Future work comparing the sensitivity of related enzymes that have been optimized to catalyze different reactions will help reveal how natural selection has tuned related active sites to favor different reactions...
  22. pmc Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling
    Philip Hanoian
    Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
    Biochemistry 49:10339-48. 2010
    ..These studies also provide experimentally testable predictions about the impact of mutating the distal tyrosine residues in this hydrogen bonding network on the NMR chemical shifts and electronic absorption spectra...
  23. pmc Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism
    Felix Mueller-Planitz
    Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, USA
    J Biol Chem 283:17463-76. 2008
    ....
  24. pmc A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect
    Katrin Karbstein
    Stanford University, School of Medicine, Beckman Center B400, Department of Biochemistry, 279 Campus Drive, Stanford, CA 94305, USA
    RNA 10:1730-9. 2004
    ....
  25. pmc A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site
    Marcello Forconi
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    Biochemistry 49:2753-62. 2010
    ....
  26. pmc Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding
    Jan Lipfert
    Department of Physics, Stanford University, Stanford, California 94305, USA
    RNA 16:708-19. 2010
    ..The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected...
  27. pmc Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
    Vincent B Chu
    Department of Applied Physics, Stanford University, California, USA
    Biophys J 93:3202-9. 2007
    ..The accompanying numerical solver has been released publicly, providing the general scientific community the ability to compute SMPB solutions around a variety of different biological structures with only modest computational resources...
  28. pmc 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA
    Marcello Forconi
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Chem Biol 18:949-54. 2011
    ..Our results give insight about the properties of organofluorine and suggest a possible general biochemical signature for tertiary interactions between 2'-hydroxyl groups and exocyclic amino groups within RNA...
  29. pmc Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site
    Jason P Schwans
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:11308-13. 2013
    ....
  30. pmc The ligand-free state of the TPP riboswitch: a partially folded RNA structure
    Mona Ali
    Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
    J Mol Biol 396:153-65. 2010
    ..Our results also demonstrate the power of combining experimental small-angle X-ray scattering data with theoretical structure prediction tools in the determination of RNA structures beyond riboswitches...
  31. pmc Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function
    Katrin Karbstein
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    Proc Natl Acad Sci U S A 100:2300-5. 2003
    ....
  32. pmc Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site?
    Paul A Sigala
    Departments of Chemistry and Biochemistry, Stanford University, Stanford, California 94305 5307, USA
    J Am Chem Soc 129:12104-5. 2007
  33. ncbi request reprint Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA
    Laura E Bartley
    Department of Biochemistry, B400 Beckman Center, Stanford University, Stanford, CA 94305 5307, USA
    J Mol Biol 328:1011-26. 2003
    ..The results described here, combined with previous work, provide an in-depth view of an RNA tertiary structure formation event and suggest that large, highly structured RNAs may have local regions that are misordered...
  34. pmc Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
    Yu Bai
    Biophysics Program, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 129:14981-8. 2007
    ....
  35. pmc Do conformational biases of simple helical junctions influence RNA folding stability and specificity?
    Vincent B Chu
    Department of Applied Physics, Stanford University, Stanford, California 94305, USA
    RNA 15:2195-205. 2009
    ..Thus, junction topology provides a fundamental strategy for transcending the limitations imposed by the low information content of RNA primary sequence...
  36. pmc Multiple native states reveal persistent ruggedness of an RNA folding landscape
    Sergey V Solomatin
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    Nature 463:681-4. 2010
    ..These data demonstrate that severe ruggedness of RNA folding landscapes extends into conformational space occupied by native conformations...
  37. pmc Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole
    Daniel A Kraut
    Department of Biochemistry, Stanford University, Stanford, California, United States of America
    PLoS Biol 4:e99. 2006
    ....
  38. pmc Implications of molecular heterogeneity for the cooperativity of biological macromolecules
    Sergey V Solomatin
    Department of Biochemistry, Stanford University, Stanford, California, USA
    Nat Struct Mol Biol 18:732-4. 2011
    ..As heterogeneity is common in smFRET experiments, appreciation of its influence on fundamental measures of cooperativity is critical for deriving accurate molecular models...
  39. pmc Biological phosphoryl-transfer reactions: understanding mechanism and catalysis
    JONATHAN K LASSILA
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    Annu Rev Biochem 80:669-702. 2011
    ..Finally, we present important future challenges for this field...
  40. pmc Direct measurement of tertiary contact cooperativity in RNA folding
    Bernie D Sattin
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 130:6085-7. 2008
    ..Using wild-type and mutant RNAs, we found that cooperativity between the two tertiary contacts enhances P4-P6 stability by 3.2 +/- 0.2 kcal/mol...
  41. pmc Hydrogen bond coupling in the ketosteroid isomerase active site
    Paul A Sigala
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    Biochemistry 48:6932-9. 2009
    ....
  42. pmc Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily
    JONATHAN K LASSILA
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    Biochemistry 47:12853-9. 2008
    ..The results further suggest that active site contacts to substrate oxygen atoms that do not contact the Zn(2+) ions may play an important role in defining the selectivity of the enzymes...
  43. pmc Origins of catalysis by computationally designed retroaldolase enzymes
    JONATHAN K LASSILA
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 107:4937-42. 2010
    ..Thus, future design efforts may benefit from a focus on achieving precision in binding interactions and placement of catalytic groups...
  44. pmc Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects
    Aaron T Fafarman
    Department of Chemistry, Stanford University, Stanford, California 94305 5080, USA
    J Am Chem Soc 132:12811-3. 2010
    ....
  45. pmc Structural inference of native and partially folded RNA by high-throughput contact mapping
    Rhiju Das
    Departments of Biochemistry, Bioengineering, and Genetics, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 105:4144-9. 2008
    ..With its applicability to nearly any solution state, we expect MOHCA to be a powerful tool for illuminating the many functional structures of large RNA molecules and RNA/protein complexes...
  46. pmc Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
    Yu Bai
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:1035-40. 2005
    ..An upper limit on the magnitude of the attractive potential under all tested ionic conditions is estimated...
  47. ncbi request reprint Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer?
    Ivana Nikolic-Hughes
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 126:11814-9. 2004
    ....
  48. pmc Dissecting eukaryotic translation and its control by ribosome density mapping
    Yoav Arava
    Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
    Nucleic Acids Res 33:2421-32. 2005
    ..These results provide new insights into eukaryotic translation in vivo...
  49. ncbi request reprint Challenges in enzyme mechanism and energetics
    Daniel A Kraut
    Department of Biochemistry, Stanford University, B400 Beckman Center, 279 Campus Drive, Stanford, California 94305 5307, USA
    Annu Rev Biochem 72:517-71. 2003
    ..The promise of advancing and integrating cutting edge conceptual, experimental, and computational tools brings mechanistic enzymology to a new era, one poised for novel fundamental insights into biological catalysis...
  50. ncbi request reprint The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme
    Rhiju Das
    Department of Physics, Stanford University, Stanford, CA 94305 4060, USA
    J Mol Biol 332:311-9. 2003
    ..These results help delineate an analogy between the early conformational changes in RNA folding and the "burst phase" changes and molten globule formation in protein folding...
  51. pmc Determining the Mg2+ stoichiometry for folding an RNA metal ion core
    Rhiju Das
    Department of Physics and Biochemistry, Stanford University, Stanford, CA 94305, USA
    J Am Chem Soc 127:8272-3. 2005
    ..By pinpointing the metal ion stoichiometry, these measurements provide a critical but previously missing step in the thermodynamic dissection of the coupling between metal ion binding and RNA folding...
  52. pmc Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA
    David G Hendrickson
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 7:e1000238. 2009
    ....
  53. pmc A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme
    Xuesong Shi
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 134:1910-3. 2012
    ..Our results reveal substantial functional effects from a seemingly simple single-stranded RNA junction and suggest that junction sequences may evolve rapidly to provide important interactions in functional RNAs...
  54. pmc Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling
    Gian Paola G Grant
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 0744, USA
    J Am Chem Soc 131:3136-7. 2009
    ..This approach may help in understanding the relationship between RNA structure, dynamics, and function...
  55. pmc Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis
    Jesse G Zalatan
    Department of Chemistry, Stanford University, California 94305, USA
    J Am Chem Soc 128:1293-303. 2006
    ..The AP active site therefore has the ability to recognize different transition states, a property that could assist in the evolutionary optimization of promiscuous activities...
  56. pmc Hydrogen bond dynamics in the active site of photoactive yellow protein
    Paul A Sigala
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    Proc Natl Acad Sci U S A 106:9232-7. 2009
    ....
  57. pmc Measuring the folding transition time of single RNA molecules
    Tae Hee Lee
    Department of Physics and Applied Physics, Stanford University, Stanford, California, USA
    Biophys J 92:3275-83. 2007
    ..We applied the method to the P4-P6 domain of the Tetrahymena group I self-splicing intron to yield the folding transition time of 240 micros. The unfolding time is found to be too short to measure with this method...
  58. pmc 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
    Marcello Forconi
    Department of Biochemistry, Stanford University, Stanford, California, USA
    J Am Chem Soc 133:7791-800. 2011
    ....
  59. pmc DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
    Felix Mueller-Planitz
    Stanford University, School of Medicine, Department of Biochemistry, Stanford, CA 94305, USA
    Nucleic Acids Res 35:3764-73. 2007
    ....
  60. pmc Rapid compaction during RNA folding
    Rick Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:4266-71. 2002
    ..The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding...
  61. pmc Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
    Daniel J Hogan
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Biol 6:e255. 2008
    ..These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate...
  62. pmc Modulation of individual steps in group I intron catalysis by a peripheral metal ion
    Marcello Forconi
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    RNA 13:1656-67. 2007
    ..These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle...
  63. ncbi request reprint Alkaline phosphatase revisited: hydrolysis of alkyl phosphates
    PATRICK J O'BRIEN
    Department of Biochemistry, Stanford University, Stanford, California 94305 5307, USA
    Biochemistry 41:3207-25. 2002
    ..The new (32)P-based assay employed herein will facilitate continued dissection of the AP reaction by providing a means to readily follow the chemical step for phosphorylation of the enzyme...
  64. pmc Low specificity of metal ion binding in the metal ion core of a folded RNA
    Kevin J Travers
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    RNA 13:1205-13. 2007
    ..These limits presumably arise from steric or electrostatic features of the metal ion binding sites...
  65. pmc Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization
    Logan D Andrews
    Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 133:11621-31. 2011
    ..These results suggest that electrostatic repulsion between Ser102 and negatively charged phosphate ester substrates contributes to catalysis by the preferential destabilization of the reaction's E·S ground state...
  66. pmc Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae
    Jan Lipfert
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    J Mol Biol 365:1393-406. 2007
    ..These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies...
  67. pmc Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
    Yoav Arava
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    Proc Natl Acad Sci U S A 100:3889-94. 2003
    ..Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length. Models to account for this surprising observation are discussed...
  68. pmc Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA
    Max Greenfeld
    Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
    J Biol Chem 286:19872-9. 2011
    ..The simplicity of P4-P6 allowed us to reliably determine the thermodynamic and kinetic effects of metal ions on folding and to now begin to build more detailed models for RNA folding behavior...
  69. doi request reprint Metal ion-based RNA cleavage as a structural probe
    Marcello Forconi
    Department of Biochemistry, Stanford University, Stanford, California, USA
    Methods Enzymol 468:91-106. 2009
    ..In this chapter, we review this information, briefly giving strengths and limitations for each of these approaches. Finally, we provide a general protocol to perform metal ion-mediated cleavage of RNA...
  70. pmc Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis
    Shu ou Shan
    Department of Biochemistry, Stanford University, California 94305 5307, USA
    RNA 8:861-72. 2002
    ..This model provides a conceptual and quantitative framework that will facilitate understanding and further probing of the energetic and structural features of this conformational change and its role in catalysis...
  71. pmc A repulsive field: advances in the electrostatics of the ion atmosphere
    Vincent B Chu
    Department of Applied Physics, Stanford University, GLAM, McCullough 318, 476 Lomita Mall, Stanford, CA 94305, USA
    Curr Opin Chem Biol 12:619-25. 2008
    ..The continued development of experiments will help guide the development of improved theories, with the ultimate goal of understanding RNA folding and function and nucleic acid/protein interactions from a quantitative perspective...
  72. pmc Evaluating the potential for halogen bonding in the oxyanion hole of ketosteroid isomerase using unnatural amino acid mutagenesis
    Daniel A Kraut
    Department of Biochemistry, Stanford University, Stanford, CA, USA
    ACS Chem Biol 4:269-73. 2009
    ..We conclude that, at least in this active site, a halogen bond cannot functionally replace a hydrogen bond...
  73. ncbi request reprint Promiscuous catalysis by the tetrahymena group I ribozyme
    Marcello Forconi
    Department of Biochemistry, B400 Beckman Center, Stanford University, Stanford, California 94305 5307, USA
    J Am Chem Soc 127:6160-1. 2005
    ..We conclude that both charge and geometry are important factors for catalysis of the normal reaction and that promiscuous catalytic activities of ribozymes could have been created or enhanced by reorienting and swapping RNA domains...
  74. pmc 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
    Katrin Karbstein
    Department of Biochemistry, Stanford University, Stanford, California 94305 5307, USA
    Biochemistry 46:4861-75. 2007
    ..This effect may facilitate replacement of the P1 extension with P10 after the first chemical step of self-splicing and release of the ligated exons after the second step of self-splicing...
  75. doi request reprint Riboswitch conformations revealed by small-angle X-ray scattering
    Jan Lipfert
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    Methods Mol Biol 540:141-59. 2009
    ..In addition, we have employed ab initio shape reconstruction algorithms to obtain low-resolution models of the riboswitch structure from SAXS data under different solution conditions...
  76. pmc Exploring the folding landscape of a structured RNA
    Rick Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:155-60. 2002
    ..Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape...
  77. ncbi request reprint RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop
    Eric J Sorin
    Department of Chemistry, Stanford University, Stanford, CA 94305 5080, USA
    J Mol Biol 317:493-506. 2002
    ..These results are considered in the context of current experimental knowledge of this and similar nucleic acid hairpins...
  78. pmc Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs
    Vincent B Chu
    Department of Applied Physics, Stanford University, GLAM, McCullough 318, 476 Lomita Mall, Stanford, CA 94305, United States
    Curr Opin Struct Biol 18:305-14. 2008
    ..Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology...
  79. ncbi request reprint Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis
    Hu Cheng
    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 1602, USA
    J Am Chem Soc 124:11295-306. 2002
    ..We suggest that ground-state distortions of substrates bound to enzymes can provide a readout of the electrostatic active site environment, an environment that is otherwise difficult to assess...
  80. pmc Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
    Daniel P Riordan
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    Nucleic Acids Res 39:1501-9. 2011
    ....
  81. doi request reprint Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer
    Max Greenfeld
    Department of Chemical Engineering, Stanford University, Stanford, California, USA
    Methods Enzymol 472:205-20. 2010
    ..This chapter aims to provide a general experimental approach to measuring the energetic coupling of tertiary contacts, using smFRET...
  82. pmc SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    Rhiju Das
    Department of Physics, Stanford University, Stanford, CA 94305, USA
    RNA 11:344-54. 2005
    ..Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu...
  83. pmc Probing the dynamics of the P1 helix within the Tetrahymena group I intron
    Xuesong Shi
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 131:9571-8. 2009
    ....
  84. ncbi request reprint Interdomain communication in DNA topoisomerase II. DNA binding and enzyme activation
    Felix Mueller-Planitz
    Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305 5307, USA
    J Biol Chem 281:23395-404. 2006
    ..Both DNA binding sites therefore signal to the ATPase domains. The results support and extend current mechanistic models for topoisomerase II-catalyzed DNA transport and provide a framework for future mechanistic dissection...
  85. pmc Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB, Canada, T6G 2M9
    Science 314:1001-4. 2006
    ....
  86. ncbi request reprint The paradoxical behavior of a highly structured misfolded intermediate in RNA folding
    Rick Russell
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    J Mol Biol 363:531-44. 2006
    ..We speculate that the complex topology of RNA secondary structures and the inherent rigidity of RNA helices render kinetic traps due to topological isomers considerably more common for RNA than for proteins...
  87. ncbi request reprint Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations
    Keiji Takamoto
    Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA
    J Mol Biol 343:1195-206. 2004
    ..The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA...
  88. pmc Structural specificity conferred by a group I RNA peripheral element
    Travis H Johnson
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 102:10176-81. 2005
    ..Such "structural specificity" may be a general function of RNA peripheral domains...
  89. pmc Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance
    David G Hendrickson
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 3:e2126. 2008
    ..Microarray analysis of Ago2 immunopurified samples provides a simple, direct method for experimentally identifying the targets of miRNAs and for elucidating roles of miRNAs in cellular regulation...
  90. pmc Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
    Michael T Woodside
    National Institute for Nanotechnology, National Research Council of Canada, Edmonton, AB, Canada T6G 2V4
    Proc Natl Acad Sci U S A 103:6190-5. 2006
    ..We find quantitative agreement over the entire range of measurements with a hybrid landscape model that combines thermodynamic nearest-neighbor free energies and nanomechanical DNA stretching energies...