| Year |
Citation |
Score |
| 2023 |
Markin CJ, Mokhtari DA, Du S, Doukov T, Sunden F, Cook JA, Fordyce PM, Herschlag D. Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology. Proceedings of the National Academy of Sciences of the United States of America. 120: e2219074120. PMID 37428919 DOI: 10.1073/pnas.2219074120 |
0.303 |
|
| 2023 |
Ken ML, Roy R, Geng A, Ganser LR, Manghrani A, Cullen BR, Schulze-Gahmen U, Herschlag D, Al-Hashimi HM. RNA conformational propensities determine cellular activity. Nature. PMID 37198487 DOI: 10.1038/s41586-023-06080-x |
0.314 |
|
| 2023 |
Shin JH, Bonilla SL, Denny SK, Greenleaf WJ, Herschlag D. Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements. Proceedings of the National Academy of Sciences of the United States of America. 120: e2220485120. PMID 36897989 DOI: 10.1073/pnas.2220485120 |
0.337 |
|
| 2020 |
Jarmoskaite I, AlSadhan I, Vaidyanathan PP, Herschlag D. How to measure and evaluate binding affinities. Elife. 9. PMID 32758356 DOI: 10.7554/Elife.57264 |
0.324 |
|
| 2020 |
Zettl T, Shi X, Bonilla S, Sedlak SM, Lipfert J, Herschlag D. The structural ensemble of a Holliday junction determined by X-ray scattering interference. Nucleic Acids Research. PMID 32597986 DOI: 10.1093/Nar/Gkaa509 |
0.33 |
|
| 2019 |
Gebala M, Herschlag D. Quantitative Studies of an RNA Duplex Electrostatics by Ion Counting. Biophysical Journal. 117: 1116-1124. PMID 31466697 DOI: 10.1016/J.Bpj.2019.08.007 |
0.421 |
|
| 2019 |
Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. Nature Nanotechnology. PMID 31427748 DOI: 10.1038/S41565-019-0517-8 |
0.564 |
|
| 2019 |
Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R. Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31375637 DOI: 10.1073/Pnas.1901530116 |
0.573 |
|
| 2019 |
Gebala M, Johnson SL, Narlikar GJ, Herschlag D. Ion counting demonstrates a high electrostatic field generated by the nucleosome. Elife. 8. PMID 31184587 DOI: 10.7554/Elife.44993 |
0.588 |
|
| 2019 |
Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nature Reviews. Molecular Cell Biology. PMID 31182864 DOI: 10.1038/S41580-019-0136-0 |
0.393 |
|
| 2019 |
Sengupta RN, Herschlag D. Enhancement of RNA•Ligand Association Kinetics via an Electrostatic Anchor. Biochemistry. PMID 31117387 DOI: 10.1021/Acs.Biochem.9B00231 |
0.424 |
|
| 2019 |
Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Molecular Cell. PMID 31078383 DOI: 10.1016/J.Molcel.2019.04.012 |
0.578 |
|
| 2019 |
Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind tests of RNA-protein binding affinity prediction. Proceedings of the National Academy of Sciences of the United States of America. PMID 30962376 DOI: 10.1073/Pnas.1819047116 |
0.573 |
|
| 2019 |
Becker WR, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D. Demonstration of Protein Cooperativity Mediated by RNA Structure Using the Human Protein PUM2. Rna (New York, N.Y.). PMID 30914482 DOI: 10.1261/Rna.068585.118 |
0.431 |
|
| 2019 |
Gebala M, Johnson SL, Narlikar GJ, Herschlag D. Author response: Ion counting demonstrates a high electrostatic field generated by the nucleosome Elife. DOI: 10.7554/Elife.44993.020 |
0.581 |
|
| 2018 |
Herschlag D, Bonilla S, Bisaria N. The Story of RNA Folding, as Told in Epochs. Cold Spring Harbor Perspectives in Biology. 10. PMID 30275276 DOI: 10.1101/Cshperspect.A032433 |
0.39 |
|
| 2018 |
Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM. Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. Rna (New York, N.Y.). PMID 30012568 DOI: 10.1261/Rna.066258.118 |
0.386 |
|
| 2018 |
Pinney M, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov TI, Schwans JP, Martínez TJ, Herschlag D. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. Journal of the American Chemical Society. PMID 29990421 DOI: 10.1021/Jacs.8B01596 |
0.325 |
|
| 2018 |
Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell. PMID 29961580 DOI: 10.1016/J.Cell.2018.05.038 |
0.569 |
|
| 2018 |
Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X. Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Current Protocols in Nucleic Acid Chemistry. 73: e54. PMID 29927110 DOI: 10.1002/Cpnc.54 |
0.506 |
|
| 2018 |
Zettl T, Mathew RS, Shi X, Doniach S, Herschlag D, Harbury PAB, Lipfert J. Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions. Science Advances. 4: eaar4418. PMID 29806025 DOI: 10.1126/Sciadv.Aar4418 |
0.56 |
|
| 2018 |
Herschlag D, Pinney M. Hydrogen bonds: Simple after all? Biochemistry. PMID 29678112 DOI: 10.1021/Acs.Biochem.8B00217 |
0.311 |
|
| 2018 |
Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Correction to Uncovering the Determinants of a Highly Perturbed Tyrosine p Kin the Active Site of Ketosteroid Isomerase. Biochemistry. PMID 29584413 DOI: 10.1021/Acs.Biochem.8B00246 |
0.312 |
|
| 2018 |
Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R. Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Reports. 22: 3240-3250. PMID 29562180 DOI: 10.1016/J.Celrep.2018.02.101 |
0.576 |
|
| 2017 |
Bonilla S, Limouse C, Bisaria N, Gebala M, Mabuchi H, Herschlag D. Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway. Journal of the American Chemical Society. PMID 29185740 DOI: 10.1021/Jacs.7B08870 |
0.451 |
|
| 2017 |
Sunden F, AlSadhan I, Lyubimov A, Doukov T, Swan J, Herschlag D. Differential Catalytic Promiscuity of the Alkaline Phosphatase Superfamily Bimetallo Core Reveals Mechanistic Features Underlying Enzyme Evolution. The Journal of Biological Chemistry. PMID 29070681 DOI: 10.1074/Jbc.M117.788240 |
0.389 |
|
| 2017 |
Gleitsman KR, Sengupta RN, Herschlag D. Slow Molecular Recognition by RNA. Rna (New York, N.Y.). PMID 28971853 DOI: 10.1261/Rna.062026.117 |
0.367 |
|
| 2017 |
Bisaria N, Greenfeld M, Limouse C, Mabuchi H, Herschlag D. Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics. Proceedings of the National Academy of Sciences of the United States of America. PMID 28839094 DOI: 10.1073/Pnas.1703507114 |
0.415 |
|
| 2017 |
Lamba V, Yabukarski F, Herschlag D. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. Journal of the American Chemical Society. PMID 28719738 DOI: 10.1021/Jacs.7B03547 |
0.363 |
|
| 2017 |
Allred B, Gebala M, Herschlag D. Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH(+)•C Wobble Formation in Double-stranded DNA. Journal of the American Chemical Society. PMID 28489947 DOI: 10.1021/Jacs.7B01830 |
0.379 |
|
| 2017 |
Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi H, Herschlag D. Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions. Rna (New York, N.Y.). PMID 28138061 DOI: 10.1261/Rna.060053.116 |
0.399 |
|
| 2017 |
Bisaria N, Jarmoskaite I, Herschlag D. Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Cell Systems. 4: 21-29. PMID 28125791 DOI: 10.1016/J.Cels.2016.12.010 |
0.394 |
|
| 2017 |
Shi X, Walker P, Harbury PB, Herschlag D. Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry. Nucleic Acids Research. PMID 28108663 DOI: 10.1093/Nar/Gkw1352 |
0.395 |
|
| 2017 |
Lamba V, Sanchez E, Fanning LR, Howe K, Gonzalez MA, Herschlag D, Forconi M. Kemp Eliminase Activity of Ketosteroid Isomerase. Biochemistry. PMID 28045505 DOI: 10.1021/Acs.Biochem.6B00762 |
0.761 |
|
| 2017 |
Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind Predictions of RNA/Protein Relative Binding Affinities Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.434 |
0.566 |
|
| 2016 |
Sunden F, AlSadhan I, Lyubimov AY, Ressl S, Wiersma-Koch H, Borland J, Brown CL, Johnson TA, Singh Z, Herschlag D. Mechanistic and evolutionary insights from comparative enzymology of phosphomonoesterases and phosphodiesterases across the alkaline phosphatase superfamily. Journal of the American Chemical Society. PMID 27670607 DOI: 10.1021/Jacs.6B06186 |
0.425 |
|
| 2016 |
van Schie SN, Sengupta RN, Herschlag D. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes. Plos One. 11: e0160457. PMID 27501145 DOI: 10.1371/Journal.Pone.0160457 |
0.497 |
|
| 2016 |
Bisaria N, Greenfeld M, Limouse C, Pavlichin DS, Mabuchi H, Herschlag D. Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway. Proceedings of the National Academy of Sciences of the United States of America. PMID 27493222 DOI: 10.1073/Pnas.1525082113 |
0.442 |
|
| 2016 |
Gebala M, Bonilla S, Bisaria N, Herschlag D. Does cation size affect occupancy and electrostatic screening of the nucleic acid ion atmosphere? Journal of the American Chemical Society. PMID 27479701 DOI: 10.1021/Jacs.6B04289 |
0.365 |
|
| 2016 |
Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. Journal of Molecular Biology. PMID 27452365 DOI: 10.1016/J.Jmb.2016.07.013 |
0.402 |
|
| 2016 |
Lamba V, Yabukarski F, Pinney M, Herschlag D. Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase. Journal of the American Chemical Society. PMID 27410422 DOI: 10.1021/Jacs.6B04796 |
0.395 |
|
| 2016 |
Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nature Communications. 7: ncomms11768. PMID 27292179 DOI: 10.1038/Ncomms11768 |
0.387 |
|
| 2016 |
Peck A, Sunden F, Andrews LD, Pande VS, Herschlag D. Tungstate as a transition state analog for catalysis by alkaline phosphatase. Journal of Molecular Biology. PMID 27189921 DOI: 10.1016/J.Jmb.2016.05.007 |
0.426 |
|
| 2016 |
Shi X, Huang L, Lilley DM, Harbury PB, Herschlag D. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nature Chemical Biology. PMID 26727239 DOI: 10.1038/Nchembio.1997 |
0.412 |
|
| 2016 |
Denny S, Bisaria N, Yesselman J, Das R, Herschlag D, Greenleaf W. High Throughput Characterization of RNA Tertiary Elements Biophysical Journal. 110: 363a. DOI: 10.1016/J.Bpj.2015.11.1957 |
0.568 |
|
| 2015 |
Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. Plos Biology. 13: e1002307. PMID 26587879 DOI: 10.1371/Journal.Pbio.1002307 |
0.372 |
|
| 2015 |
Sengupta RN, van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. Rna (New York, N.Y.). PMID 26567314 DOI: 10.1261/Rna.053710.115 |
0.836 |
|
| 2015 |
Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies. Journal of the American Chemical Society. PMID 26517731 DOI: 10.1021/Jacs.5B08395 |
0.793 |
|
| 2015 |
Natarajan A, Yabukarski F, Lamba V, Schwans JP, Sunden F, Herschlag D. BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science (New York, N.Y.). 349: 936. PMID 26315426 DOI: 10.1126/Science.Aab1584 |
0.342 |
|
| 2015 |
Shi X, Bonilla S, Herschlag D, Harbury P. Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. Methods in Enzymology. 558: 75-97. PMID 26068738 DOI: 10.1016/Bs.Mie.2015.02.001 |
0.341 |
|
| 2015 |
Sunden F, Peck A, Salzman J, Ressl S, Herschlag D. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site. Elife. 4. PMID 25902402 DOI: 10.7554/Elife.06181 |
0.378 |
|
| 2015 |
Sigala PA, Ruben EA, Liu CW, Piccoli PM, Hohenstein EG, Martínez TJ, Schultz AJ, Herschlag D. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability. Journal of the American Chemical Society. 137: 5730-40. PMID 25871450 DOI: 10.1021/Ja512980H |
0.73 |
|
| 2015 |
Bisaria N, Herschlag D. Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET. Biochemical Society Transactions. 43: 172-8. PMID 25849913 DOI: 10.1042/Bst20140268 |
0.467 |
|
| 2015 |
Herschlag D. Learning from ribozymes. Rna (New York, N.Y.). 21: 527-8. PMID 25780124 DOI: 10.1261/Rna.050914.115 |
0.451 |
|
| 2015 |
Herschlag D, Allred BE, Gowrishankar S. From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. Current Opinion in Structural Biology. 30: 125-33. PMID 25744941 DOI: 10.1016/J.Sbi.2015.02.006 |
0.391 |
|
| 2015 |
Sunden F, Peck A, Salzman J, Ressl S, Herschlag D. Author response: Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site Elife. DOI: 10.7554/Elife.06181.024 |
0.322 |
|
| 2014 |
Andrews LD, Zalatan JG, Herschlag D. Probing the origins of catalytic discrimination between phosphate and sulfate monoester hydrolysis: comparative analysis of alkaline phosphatase and protein tyrosine phosphatases. Biochemistry. 53: 6811-9. PMID 25299936 DOI: 10.1021/Bi500765P |
0.765 |
|
| 2014 |
Gleitsman KR, Herschlag DH. A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction. Rna (New York, N.Y.). 20: 1732-46. PMID 25246656 DOI: 10.1261/Rna.044362.114 |
0.348 |
|
| 2014 |
Natarajan A, Schwans JP, Herschlag D. Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site. Journal of the American Chemical Society. 136: 7643-54. PMID 24787954 DOI: 10.1021/Ja413174B |
0.332 |
|
| 2014 |
Khosla C, Herschlag D, Cane DE, Walsh CT. Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry. 53: 2875-83. PMID 24779441 DOI: 10.1021/Bi500290T |
0.317 |
|
| 2014 |
Shi X, Bisaria N, Benz-Moy TL, Bonilla S, Pavlichin DS, Herschlag D. Roles of long-range tertiary interactions in limiting dynamics of the Tetrahymena group I ribozyme. Journal of the American Chemical Society. 136: 6643-8. PMID 24738560 DOI: 10.1021/Ja413033D |
0.391 |
|
| 2014 |
Shi X, Beauchamp KA, Harbury PB, Herschlag D. From a structural average to the conformational ensemble of a DNA bulge. Proceedings of the National Academy of Sciences of the United States of America. 111: E1473-80. PMID 24706812 DOI: 10.1073/Pnas.1317032111 |
0.319 |
|
| 2014 |
Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annual Review of Biochemistry. 83: 813-41. PMID 24606136 DOI: 10.1146/Annurev-Biochem-060409-092720 |
0.649 |
|
| 2014 |
Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry. 53: 2541-55. PMID 24597914 DOI: 10.1021/Bi401671T |
0.391 |
|
| 2014 |
Giamba?u GM, Luchko T, Herschlag D, York DM, Case DA. Ion counting from explicit-solvent simulations and 3D-RISM. Biophysical Journal. 106: 883-94. PMID 24559991 DOI: 10.1016/J.Bpj.2014.01.021 |
0.327 |
|
| 2014 |
Watkins HM, Mendez D, Ratner D, Herschlag D, Doniach S. The Effect of Magnesium on the Thermodynamics of Nucleic Acid Tertiary Contact Formation Biophysical Journal. 106: 385a. DOI: 10.1016/J.Bpj.2013.11.2178 |
0.604 |
|
| 2013 |
Wiersma-Koch H, Sunden F, Herschlag D. Site-directed mutagenesis maps interactions that enhance cognate and limit promiscuous catalysis by an alkaline phosphatase superfamily phosphodiesterase. Biochemistry. 52: 9167-76. PMID 24261692 DOI: 10.1021/Bi4010045 |
0.419 |
|
| 2013 |
Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase. Biochemistry. 52: 7840-55. PMID 24151972 DOI: 10.1021/Bi401083B |
0.444 |
|
| 2013 |
Greenfeld M, Herschlag D. Fluorescently labeling synthetic RNAs. Methods in Enzymology. 530: 281-97. PMID 24034327 DOI: 10.1016/B978-0-12-420037-1.00015-4 |
0.342 |
|
| 2013 |
Porecha R, Herschlag D. RNA radiolabeling. Methods in Enzymology. 530: 255-79. PMID 24034326 DOI: 10.1016/B978-0-12-420037-1.00014-2 |
0.357 |
|
| 2013 |
Nguyen P, Shi X, Sigurdsson ST, Herschlag D, Qin PZ. A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme. Chembiochem : a European Journal of Chemical Biology. 14: 1720-3. PMID 23900919 DOI: 10.1002/Cbic.201300376 |
0.316 |
|
| 2013 |
Andrews LD, Fenn TD, Herschlag D. Ground state destabilization by anionic nucleophiles contributes to the activity of phosphoryl transfer enzymes. Plos Biology. 11: e1001599. PMID 23843744 DOI: 10.1371/Journal.Pbio.1001599 |
0.427 |
|
| 2013 |
Schwans JP, Sunden F, Lassila JK, Gonzalez A, Tsai Y, Herschlag D. Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America. 110: 11308-13. PMID 23798413 DOI: 10.1073/Pnas.1206710110 |
0.435 |
|
| 2013 |
Sigala PA, Fafarman AT, Schwans JP, Fried SD, Fenn TD, Caaveiro JM, Pybus B, Ringe D, Petsko GA, Boxer SG, Herschlag D. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site. Proceedings of the National Academy of Sciences of the United States of America. 110: E2552-61. PMID 23798390 DOI: 10.1073/Pnas.1302191110 |
0.752 |
|
| 2013 |
Herschlag D, Natarajan A. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. Biochemistry. 52: 2050-67. PMID 23488725 DOI: 10.1021/Bi4000113 |
0.338 |
|
| 2013 |
Ruben EA, Schwans JP, Sonnett M, Natarajan A, Gonzalez A, Tsai Y, Herschlag D. Ground state destabilization from a positioned general base in the ketosteroid isomerase active site. Biochemistry. 52: 1074-81. PMID 23311398 DOI: 10.1021/Bi301348X |
0.39 |
|
| 2013 |
Shi X, Harbury P, Herschlag D. Nucleic Acid Conformation Ensembles Revealed by Au-SAXS Interferometry Biophysical Journal. 104: 502a. DOI: 10.1016/J.Bpj.2012.11.2770 |
0.318 |
|
| 2012 |
Sim AY, Lipfert J, Herschlag D, Doniach S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 021901. PMID 23005779 DOI: 10.1103/Physreve.86.021901 |
0.544 |
|
| 2012 |
Forconi M, Benz-Moy T, Gleitsman KR, Ruben E, Metz C, Herschlag D. Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study. Rna (New York, N.Y.). 18: 1222-9. PMID 22543863 DOI: 10.1261/Rna.031567.111 |
0.79 |
|
| 2012 |
Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. Rna (New York, N.Y.). 18: 1123-41. PMID 22539523 DOI: 10.1261/Rna.028738.111 |
0.704 |
|
| 2012 |
Althoff EA, Wang L, Jiang L, Giger L, Lassila JK, Wang Z, Smith M, Hari S, Kast P, Herschlag D, Hilvert D, Baker D. Robust design and optimization of retroaldol enzymes. Protein Science : a Publication of the Protein Society. 21: 717-26. PMID 22407837 DOI: 10.1002/Pro.2059 |
0.424 |
|
| 2012 |
Anthony PC, Sim AY, Chu VB, Doniach S, Block SM, Herschlag D. Electrostatics of nucleic acid folding under conformational constraint. Journal of the American Chemical Society. 134: 4607-14. PMID 22369617 DOI: 10.1021/Ja208466H |
0.587 |
|
| 2012 |
Fafarman AT, Sigala PA, Schwans JP, Fenn TD, Herschlag D, Boxer SG. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proceedings of the National Academy of Sciences of the United States of America. 109: E299-308. PMID 22308339 DOI: 10.1073/Pnas.1111566109 |
0.757 |
|
| 2012 |
Shi X, Solomatin SV, Herschlag D. A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme. Journal of the American Chemical Society. 134: 1910-3. PMID 22220837 DOI: 10.1021/Ja2083575 |
0.429 |
|
| 2012 |
Bobyr E, Lassila JK, Wiersma-Koch HI, Fenn TD, Lee JJ, Nikolic-Hughes I, Hodgson KO, Rees DC, Hedman B, Herschlag D. High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. Journal of Molecular Biology. 415: 102-17. PMID 22056344 DOI: 10.1016/J.Jmb.2011.10.040 |
0.412 |
|
| 2012 |
Sengupta RN, Herschlag D, Piccirilli JA. Thermodynamic evidence for negative charge stabilization by a catalytic metal ion within an RNA active site. Acs Chemical Biology. 7: 294-9. PMID 22029738 DOI: 10.1021/Cb200202Q |
0.665 |
|
| 2011 |
Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase. Journal of the American Chemical Society. 133: 20052-5. PMID 22053826 DOI: 10.1021/Ja208050T |
0.378 |
|
| 2011 |
Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. Chemistry & Biology. 18: 949-54. PMID 21867910 DOI: 10.1016/J.Chembiol.2011.07.014 |
0.804 |
|
| 2011 |
Benz-Moy TL, Herschlag D. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry. 50: 8733-55. PMID 21815635 DOI: 10.1021/Bi2008245 |
0.419 |
|
| 2011 |
Andrews LD, Deng H, Herschlag D. Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization. Journal of the American Chemical Society. 133: 11621-31. PMID 21692505 DOI: 10.1021/Ja203370B |
0.386 |
|
| 2011 |
Solomatin SV, Greenfeld M, Herschlag D. Implications of molecular heterogeneity for the cooperativity of biological macromolecules. Nature Structural & Molecular Biology. 18: 732-4. PMID 21572445 DOI: 10.1038/Nsmb.2052 |
0.309 |
|
| 2011 |
Forconi M, Porecha RH, Piccirilli JA, Herschlag D. 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. Journal of the American Chemical Society. 133: 7791-800. PMID 21539364 DOI: 10.1021/Ja111316Y |
0.82 |
|
| 2011 |
Lassila JK, Zalatan JG, Herschlag D. Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annual Review of Biochemistry. 80: 669-702. PMID 21513457 DOI: 10.1146/Annurev-Biochem-060409-092741 |
0.725 |
|
| 2011 |
Greenfeld M, Solomatin SV, Herschlag D. Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA. The Journal of Biological Chemistry. 286: 19872-9. PMID 21478155 DOI: 10.1074/Jbc.M111.235465 |
0.397 |
|
| 2011 |
Riordan DP, Herschlag D, Brown PO. Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Research. 39: 1501-9. PMID 20959291 DOI: 10.1093/Nar/Gkq920 |
0.344 |
|
| 2011 |
Lipfert J, Herschlag D, Doniach S, Dekker NH. RNA Structure, Function, and (Thermo-) Dynamics: A SAXS and Single-Molecule Perspective Biophysical Journal. 100: 1a-2a. DOI: 10.1016/J.Bpj.2010.11.060 |
0.596 |
|
| 2010 |
Hanoian P, Sigala PA, Herschlag D, Hammes-Schiffer S. Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. Biochemistry. 49: 10339-48. PMID 21049962 DOI: 10.1021/Bi101428E |
0.736 |
|
| 2010 |
Fafarman AT, Sigala PA, Herschlag D, Boxer SG. Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. Journal of the American Chemical Society. 132: 12811-3. PMID 20806897 DOI: 10.1021/Ja104573B |
0.732 |
|
| 2010 |
Greenfeld M, Herschlag D. Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer. Methods in Enzymology. 472: 205-20. PMID 20580966 DOI: 10.1016/S0076-6879(10)72009-7 |
0.372 |
|
| 2010 |
Wan Y, Suh H, Russell R, Herschlag D. Multiple unfolding events during native folding of the Tetrahymena group I ribozyme. Journal of Molecular Biology. 400: 1067-77. PMID 20541557 DOI: 10.1016/J.Jmb.2010.06.010 |
0.377 |
|
| 2010 |
Lassila JK, Baker D, Herschlag D. Origins of catalysis by computationally designed retroaldolase enzymes. Proceedings of the National Academy of Sciences of the United States of America. 107: 4937-42. PMID 20194782 DOI: 10.1073/Pnas.0913638107 |
0.491 |
|
| 2010 |
Lipfert J, Sim AY, Herschlag D, Doniach S. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. Rna (New York, N.Y.). 16: 708-19. PMID 20194520 DOI: 10.1261/Rna.1985110 |
0.621 |
|
| 2010 |
Forconi M, Sengupta RN, Piccirilli JA, Herschlag D. A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site. Biochemistry. 49: 2753-62. PMID 20175542 DOI: 10.1021/Bi902200N |
0.831 |
|
| 2010 |
Solomatin SV, Greenfeld M, Chu S, Herschlag D. Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature. 463: 681-4. PMID 20130651 DOI: 10.1038/Nature08717 |
0.417 |
|
| 2010 |
Kraut DA, Sigala PA, Fenn TD, Herschlag D. Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole. Proceedings of the National Academy of Sciences of the United States of America. 107: 1960-5. PMID 20080683 DOI: 10.1073/Pnas.0911168107 |
0.795 |
|
| 2010 |
Ali M, Lipfert J, Seifert S, Herschlag D, Doniach S. The ligand-free state of the TPP riboswitch: a partially folded RNA structure. Journal of Molecular Biology. 396: 153-65. PMID 19925806 DOI: 10.1016/J.Jmb.2009.11.030 |
0.584 |
|
| 2009 |
Greenfeld M, Herschlag D. Probing nucleic acid-ion interactions with buffer exchange-atomic emission spectroscopy. Methods in Enzymology. 469: 375-89. PMID 20946799 DOI: 10.1016/S0076-6879(09)69018-2 |
0.342 |
|
| 2009 |
Shi X, Herschlag D. Fluorescence polarization anisotropy to measure RNA dynamics. Methods in Enzymology. 469: 287-302. PMID 20946795 DOI: 10.1016/S0076-6879(09)69014-5 |
0.375 |
|
| 2009 |
Solomatin S, Herschlag D. Methods of site-specific labeling of RNA with fluorescent dyes. Methods in Enzymology. 469: 47-68. PMID 20946784 DOI: 10.1016/S0076-6879(09)69003-0 |
0.357 |
|
| 2009 |
Forconi M, Herschlag D. Use of phosphorothioates to identify sites of metal-ion binding in RNA. Methods in Enzymology. 468: 311-33. PMID 20946776 DOI: 10.1016/S0076-6879(09)68015-0 |
0.779 |
|
| 2009 |
Forconi M, Herschlag D. Metal ion-based RNA cleavage as a structural probe. Methods in Enzymology. 468: 91-106. PMID 20946766 DOI: 10.1016/S0076-6879(09)68005-8 |
0.773 |
|
| 2009 |
Herschlag D. Biophysical, chemical, and functional probes of RNA structure, interactions and folding: Part A. Preface. Methods in Enzymology. 468: xv. PMID 19925921 DOI: 10.1016/S0076-6879(09)68020-4 |
0.398 |
|
| 2009 |
Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D. Do conformational biases of simple helical junctions influence RNA folding stability and specificity? Rna (New York, N.Y.). 15: 2195-205. PMID 19850914 DOI: 10.1261/Rna.1747509 |
0.607 |
|
| 2009 |
Forconi M, Sengupta RN, Liu MC, Sartorelli AC, Piccirilli JA, Herschlag D. Structure and function converge to identify a hydrogen bond in a group I ribozyme active site. Angewandte Chemie (International Ed. in English). 48: 7171-5. PMID 19708048 DOI: 10.1002/Anie.200903006 |
0.808 |
|
| 2009 |
Schwans JP, Kraut DA, Herschlag D. Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase. Proceedings of the National Academy of Sciences of the United States of America. 106: 14271-5. PMID 19706511 DOI: 10.1073/Pnas.0901032106 |
0.759 |
|
| 2009 |
Zalatan JG, Herschlag D. The far reaches of enzymology. Nature Chemical Biology. 5: 516-20. PMID 19620986 DOI: 10.1038/Nchembio0809-516 |
0.721 |
|
| 2009 |
Shi X, Mollova ET, Pljevaljci? G, Millar DP, Herschlag D. Probing the dynamics of the P1 helix within the Tetrahymena group I intron. Journal of the American Chemical Society. 131: 9571-8. PMID 19537712 DOI: 10.1021/Ja902797J |
0.409 |
|
| 2009 |
Sigala PA, Tsuchida MA, Herschlag D. Hydrogen bond dynamics in the active site of photoactive yellow protein. Proceedings of the National Academy of Sciences of the United States of America. 106: 9232-7. PMID 19470452 DOI: 10.1073/Pnas.0900168106 |
0.738 |
|
| 2009 |
Sigala PA, Caaveiro JM, Ringe D, Petsko GA, Herschlag D. Hydrogen bond coupling in the ketosteroid isomerase active site. Biochemistry. 48: 6932-9. PMID 19469568 DOI: 10.1021/Bi900713J |
0.74 |
|
| 2009 |
Lipfert J, Herschlag D, Doniach S. Riboswitch conformations revealed by small-angle X-ray scattering. Methods in Molecular Biology (Clifton, N.J.). 540: 141-59. PMID 19381558 DOI: 10.1007/978-1-59745-558-9_11 |
0.618 |
|
| 2009 |
Kraut DA, Churchill MJ, Dawson PE, Herschlag D. Evaluating the potential for halogen bonding in the oxyanion hole of ketosteroid isomerase using unnatural amino acid mutagenesis. Acs Chemical Biology. 4: 269-73. PMID 19260691 DOI: 10.1021/Cb900016Q |
0.73 |
|
| 2009 |
Grant GP, Boyd N, Herschlag D, Qin PZ. Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. Journal of the American Chemical Society. 131: 3136-7. PMID 19220053 DOI: 10.1021/Ja808217S |
0.401 |
|
| 2009 |
Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Rna (New York, N.Y.). 15: 189-99. PMID 19144906 DOI: 10.1261/Rna.1270809 |
0.552 |
|
| 2009 |
Solomatin S, Greenfeld M, Chu S, Herschlag D. Single Molecule Analysis of Group I Ribozyme Folding Reveals Pronounced Ruggedness Throughout Its Folding Landscape Biophysical Journal. 96: 9a. DOI: 10.1016/J.Bpj.2008.12.942 |
0.399 |
|
| 2009 |
Sim AYL, Lipfert J, Herschlag D, Doniach S. Scaling Behavior of Single Stranded DNA Measured by Small Angle X-ray Scattering Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.1744 |
0.528 |
|
| 2009 |
Liu CW, Alekseyev VY, Allwardt JR, Bankovich AJ, Cade-Menun BJ, Davis RW, Du LS, Garcia KC, Herschlag D, Khosla C, Kraut DA, Li Q, Null B, Puglisi JD, Sigala PA, et al. The diversity of nuclear magnetic resonance spectroscopy Nato Science For Peace and Security Series B: Physics and Biophysics. 65-81. |
0.745 |
|
| 2008 |
Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. A repulsive field: advances in the electrostatics of the ion atmosphere. Current Opinion in Chemical Biology. 12: 619-25. PMID 19081286 DOI: 10.1016/J.Cbpa.2008.10.010 |
0.586 |
|
| 2008 |
Lassila JK, Herschlag D. Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily. Biochemistry. 47: 12853-9. PMID 18975918 DOI: 10.1021/Bi801488C |
0.413 |
|
| 2008 |
Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. Plos Biology. 6: e255. PMID 18959479 DOI: 10.1371/Journal.Pbio.0060255 |
0.367 |
|
| 2008 |
Zalatan JG, Fenn TD, Herschlag D. Comparative enzymology in the alkaline phosphatase superfamily to determine the catalytic role of an active-site metal ion. Journal of Molecular Biology. 384: 1174-89. PMID 18851975 DOI: 10.1016/J.Jmb.2008.09.059 |
0.761 |
|
| 2008 |
Sigala PA, Kraut DA, Caaveiro JM, Pybus B, Ruben EA, Ringe D, Petsko GA, Herschlag D. Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. Journal of the American Chemical Society. 130: 13696-708. PMID 18808119 DOI: 10.1021/Ja803928M |
0.823 |
|
| 2008 |
Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nature Protocols. 3: 1395-401. PMID 18772866 DOI: 10.1038/Nprot.2008.134 |
0.456 |
|
| 2008 |
Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. Journal of the American Chemical Society. 130: 12334-41. PMID 18722445 DOI: 10.1021/Ja800854U |
0.619 |
|
| 2008 |
O'Brien PJ, Lassila JK, Fenn TD, Zalatan JG, Herschlag D. Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase. Biochemistry. 47: 7663-72. PMID 18627128 DOI: 10.1021/Bi800545N |
0.806 |
|
| 2008 |
Chu VB, Herschlag D. Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Current Opinion in Structural Biology. 18: 305-14. PMID 18555681 DOI: 10.1016/J.Sbi.2008.05.002 |
0.379 |
|
| 2008 |
Forconi M, Lee J, Lee JK, Piccirilli JA, Herschlag D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry. 47: 6883-94. PMID 18517225 DOI: 10.1021/Bi800519A |
0.815 |
|
| 2008 |
Sattin BD, Zhao W, Travers K, Chu S, Herschlag D. Direct measurement of tertiary contact cooperativity in RNA folding. Journal of the American Chemical Society. 130: 6085-7. PMID 18429611 DOI: 10.1021/Ja800919Q |
0.424 |
|
| 2008 |
Mueller-Planitz F, Herschlag D. Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism. The Journal of Biological Chemistry. 283: 17463-76. PMID 18403371 DOI: 10.1074/Jbc.M710014200 |
0.331 |
|
| 2008 |
Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105: 4144-9. PMID 18322008 DOI: 10.1073/Pnas.0709032105 |
0.728 |
|
| 2007 |
Bai Y, Greenfeld M, Travers KJ, Chu VB, Lipfert J, Doniach S, Herschlag D. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. Journal of the American Chemical Society. 129: 14981-8. PMID 17990882 DOI: 10.1021/Ja075020G |
0.573 |
|
| 2007 |
Sigala PA, Fafarman AT, Bogard PE, Boxer SG, Herschlag D. Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site? Journal of the American Chemical Society. 129: 12104-5. PMID 17854190 DOI: 10.1021/Ja075605A |
0.744 |
|
| 2007 |
Forconi M, Piccirilli JA, Herschlag D. Modulation of individual steps in group I intron catalysis by a peripheral metal ion. Rna (New York, N.Y.). 13: 1656-67. PMID 17720880 DOI: 10.1261/Rna.632007 |
0.829 |
|
| 2007 |
Zalatan JG, Catrina I, Mitchell R, Grzyska PK, O'brien PJ, Herschlag D, Hengge AC. Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis. Journal of the American Chemical Society. 129: 9789-98. PMID 17630738 DOI: 10.1021/Ja072196+ |
0.805 |
|
| 2007 |
Travers KJ, Boyd N, Herschlag D. Low specificity of metal ion binding in the metal ion core of a folded RNA. Rna (New York, N.Y.). 13: 1205-13. PMID 17616553 DOI: 10.1261/Rna.566007 |
0.39 |
|
| 2007 |
Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophysical Journal. 93: 3202-9. PMID 17604318 DOI: 10.1529/Biophysj.106.099168 |
0.541 |
|
| 2007 |
Catrina I, O'Brien PJ, Purcell J, Nikolic-Hughes I, Zalatan JG, Hengge AC, Herschlag D. Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. Journal of the American Chemical Society. 129: 5760-5. PMID 17411045 DOI: 10.1021/Ja069111+ |
0.795 |
|
| 2007 |
Karbstein K, Lee J, Herschlag D. 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. Biochemistry. 46: 4861-75. PMID 17385892 DOI: 10.1021/Bi062169G |
0.71 |
|
| 2007 |
Lee TH, Lapidus LJ, Zhao W, Travers KJ, Herschlag D, Chu S. Measuring the folding transition time of single RNA molecules. Biophysical Journal. 92: 3275-83. PMID 17307831 DOI: 10.1529/Biophysj.106.094623 |
0.334 |
|
| 2007 |
Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology. 365: 1393-406. PMID 17118400 DOI: 10.1016/J.Jmb.2006.10.022 |
0.692 |
|
| 2007 |
Lipfert J, Chu VB, Bai Y, Herschlag D, Doniach S. Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling Journal of Applied Crystallography. 40: s229-s234. DOI: 10.1107/S0021889807001707 |
0.55 |
|
| 2007 |
Fierke CA, Herschlag D. The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond. [Current Opinion in Chemical Biology 2006, 10:453-454] (DOI:10.1016/j.cbpa.2006.08.019) Current Opinion in Chemical Biology. 11: 111. DOI: 10.1016/J.Cbpa.2006.11.001 |
0.486 |
|
| 2006 |
Woodside MT, Anthony PC, Behnke-Parks WM, Larizadeh K, Herschlag D, Block SM. Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science (New York, N.Y.). 314: 1001-4. PMID 17095702 DOI: 10.1126/Science.1133601 |
0.309 |
|
| 2006 |
Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. Journal of Molecular Biology. 363: 531-44. PMID 16963081 DOI: 10.1016/J.Jmb.2006.08.024 |
0.575 |
|
| 2006 |
Zalatan JG, Fenn TD, Brunger AT, Herschlag D. Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution. Biochemistry. 45: 9788-803. PMID 16893180 DOI: 10.1021/Bi060847T |
0.765 |
|
| 2006 |
Woodside MT, Behnke-Parks WM, Larizadeh K, Travers K, Herschlag D, Block SM. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proceedings of the National Academy of Sciences of the United States of America. 103: 6190-5. PMID 16606839 DOI: 10.1073/Pnas.0511048103 |
0.316 |
|
| 2006 |
Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. Plos Biology. 4: e99. PMID 16602823 DOI: 10.1371/Journal.Pbio.0040099 |
0.815 |
|
| 2006 |
Gerber AP, Luschnig S, Krasnow MA, Brown PO, Herschlag D. Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 103: 4487-92. PMID 16537387 DOI: 10.1073/Pnas.0509260103 |
0.364 |
|
| 2006 |
Zalatan JG, Herschlag D. Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis. Journal of the American Chemical Society. 128: 1293-303. PMID 16433548 DOI: 10.1021/Ja056528R |
0.741 |
|
| 2006 |
Hougland JL, Piccirilli JA, Forconi M, Lee J, Herschlag D. 6 How the Group I Intron Works: A Case Study of RNA Structure and Function Cold Spring Harbor Monograph Archive. 43: 133-205. DOI: 10.1101/087969739.43.133 |
0.781 |
|
| 2006 |
Fierke CA, Herschlag D. The wide reach of enzymology: from bioorganic chemistry to chemical biology and beyond Mechanisms Current Opinion in Chemical Biology. 10: 453-454. DOI: 10.1016/J.Cbpa.2006.08.019 |
0.492 |
|
| 2005 |
Hougland JL, Kravchuk AV, Herschlag D, Piccirilli JA. Functional identification of catalytic metal ion binding sites within RNA. Plos Biology. 3: e277. PMID 16092891 DOI: 10.1371/Journal.Pbio.0030277 |
0.66 |
|
| 2005 |
Johnson TH, Tijerina P, Chadee AB, Herschlag D, Russell R. Structural specificity conferred by a group I RNA peripheral element. Proceedings of the National Academy of Sciences of the United States of America. 102: 10176-81. PMID 16009943 DOI: 10.1073/Pnas.0501498102 |
0.423 |
|
| 2005 |
Nikolic-Hughes I, O'brien PJ, Herschlag D. Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions. Journal of the American Chemical Society. 127: 9314-5. PMID 15984827 DOI: 10.1021/Ja051603J |
0.616 |
|
| 2005 |
Das R, Travers KJ, Bai Y, Herschlag D. Determining the Mg2+ stoichiometry for folding an RNA metal ion core. Journal of the American Chemical Society. 127: 8272-3. PMID 15941246 DOI: 10.1021/Ja051422H |
0.579 |
|
| 2005 |
Forconi M, Herschlag D. Promiscuous catalysis by the tetrahymena group I ribozyme. Journal of the American Chemical Society. 127: 6160-1. PMID 15853307 DOI: 10.1021/Ja050180I |
0.787 |
|
| 2005 |
Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Rna (New York, N.Y.). 11: 344-54. PMID 15701734 DOI: 10.1261/Rna.7214405 |
0.482 |
|
| 2005 |
Bai Y, Das R, Millett IS, Herschlag D, Doniach S. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proceedings of the National Academy of Sciences of the United States of America. 102: 1035-40. PMID 15647360 DOI: 10.1073/Pnas.0404448102 |
0.682 |
|
| 2004 |
Andresen K, Das R, Park HY, Smith H, Kwok LW, Lamb JS, Kirkland EJ, Herschlag D, Finkelstein KD, Pollack L. Spatial distribution of competing ions around DNA in solution. Physical Review Letters. 93: 248103. PMID 15697865 DOI: 10.1103/Physrevlett.93.248103 |
0.495 |
|
| 2004 |
Karbstein K, Tang KH, Herschlag D. A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect. Rna (New York, N.Y.). 10: 1730-9. PMID 15496521 DOI: 10.1261/Rna.7118104 |
0.711 |
|
| 2004 |
Takamoto K, Das R, He Q, Doniach S, Brenowitz M, Herschlag D, Chance MR. Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. Journal of Molecular Biology. 343: 1195-206. PMID 15491606 DOI: 10.1016/J.Jmb.2004.08.080 |
0.715 |
|
| 2004 |
Nikolic-Hughes I, Rees DC, Herschlag D. Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer? Journal of the American Chemical Society. 126: 11814-9. PMID 15382915 DOI: 10.1021/Ja0480421 |
0.379 |
|
| 2004 |
Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. Plos Biology. 2: E79. PMID 15024427 DOI: 10.1371/Journal.Pbio.0020079 |
0.345 |
|
| 2003 |
Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proceedings of the National Academy of Sciences of the United States of America. 100: 11429-34. PMID 13679573 DOI: 10.1073/Pnas.2033246100 |
0.31 |
|
| 2003 |
Peck ML, Herschlag D. Adenosine 5'-O-(3-thio)triphosphate (ATPgammaS) is a substrate for the nucleotide hydrolysis and RNA unwinding activities of eukaryotic translation initiation factor eIF4A. Rna (New York, N.Y.). 9: 1180-7. PMID 13130132 DOI: 10.1261/Rna.2103703 |
0.779 |
|
| 2003 |
Das R, Kwok LW, Millett IS, Bai Y, Mills TT, Jacob J, Maskel GS, Seifert S, Mochrie SG, Thiyagarajan P, Doniach S, Pollack L, Herschlag D. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. Journal of Molecular Biology. 332: 311-9. PMID 12948483 DOI: 10.1016/S0022-2836(03)00854-4 |
0.693 |
|
| 2003 |
Das R, Mills TT, Kwok LW, Maskel GS, Millett IS, Doniach S, Finkelstein KD, Herschlag D, Pollack L. Counterion distribution around DNA probed by solution X-ray scattering. Physical Review Letters. 90: 188103. PMID 12786045 DOI: 10.1103/Physrevlett.90.188103 |
0.617 |
|
| 2003 |
Bartley LE, Zhuang X, Das R, Chu S, Herschlag D. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. Journal of Molecular Biology. 328: 1011-26. PMID 12729738 DOI: 10.1016/S0022-2836(03)00272-9 |
0.772 |
|
| 2003 |
Kraut DA, Carroll KS, Herschlag D. Challenges in enzyme mechanism and energetics. Annual Review of Biochemistry. 72: 517-71. PMID 12704087 DOI: 10.1146/Annurev.Biochem.72.121801.161617 |
0.734 |
|
| 2003 |
Karbstein K, Herschlag D. Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function. Proceedings of the National Academy of Sciences of the United States of America. 100: 2300-5. PMID 12591943 DOI: 10.1073/Pnas.252749799 |
0.718 |
|
| 2002 |
O'Brien PJ, Herschlag D. Alkaline Phosphatase Revisited: Hydrolysis of Alkyl Phosphates (†). Biochemistry. 41: 3207-3225. PMID 28212002 DOI: 10.1021/bi012166y |
0.573 |
|
| 2002 |
Cheng H, Nikolic-Hughes I, Wang JH, Deng H, O'Brien PJ, Wu L, Zhang ZY, Herschlag D, Callender R. Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis. Journal of the American Chemical Society. 124: 11295-306. PMID 12236744 DOI: 10.1021/Ja026481Z |
0.586 |
|
| 2002 |
Karbstein K, Carroll KS, Herschlag D. Probing the Tetrahymena group I ribozyme reaction in both directions. Biochemistry. 41: 11171-83. PMID 12220182 DOI: 10.1021/Bi0202631 |
0.72 |
|
| 2002 |
Shan SO, Herschlag D. Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis. Rna (New York, N.Y.). 8: 861-72. PMID 12166641 DOI: 10.1017/S1355838202020216 |
0.608 |
|
| 2002 |
Sorin EJ, Engelhardt MA, Herschlag D, Pande VS. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. Journal of Molecular Biology. 317: 493-506. PMID 11955005 DOI: 10.1006/Jmbi.2002.5447 |
0.378 |
|
| 2002 |
Russell R, Millett IS, Tate MW, Kwok LW, Nakatani B, Gruner SM, Mochrie SG, Pande V, Doniach S, Herschlag D, Pollack L. Rapid compaction during RNA folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 4266-71. PMID 11929997 DOI: 10.1073/Pnas.072589599 |
0.594 |
|
| 2002 |
O'Brien PJ, Herschlag D. Alkaline phosphatase revisited: hydrolysis of alkyl phosphates. Biochemistry. 41: 3207-25. PMID 11863460 DOI: 10.1021/Bi012166Y |
0.618 |
|
| 2002 |
Russell R, Zhuang X, Babcock HP, Millett IS, Doniach S, Chu S, Herschlag D. Exploring the folding landscape of a structured RNA. Proceedings of the National Academy of Sciences of the United States of America. 99: 155-60. PMID 11756689 DOI: 10.1073/Pnas.221593598 |
0.606 |
|
| 2001 |
Peluso P, Shan SO, Nock S, Herschlag D, Walter P. Role of SRP RNA in the GTPase cycles of Ffh and FtsY. Biochemistry. 40: 15224-33. PMID 11735405 DOI: 10.1021/Bi011639Y |
0.665 |
|
| 2001 |
Russell R, Herschlag D. Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. Journal of Molecular Biology. 308: 839-51. PMID 11352576 DOI: 10.1006/Jmbi.2001.4751 |
0.39 |
|
| 2001 |
O'Rear JL, Wang S, Feig AL, Beigelman L, Uhlenbeck OC, Herschlag D. Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. Rna (New York, N.Y.). 7: 537-45. PMID 11345432 DOI: 10.1017/S1355838201002461 |
0.435 |
|
| 2001 |
O'Brien PJ, Herschlag D. Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase. Biochemistry. 40: 5691-9. PMID 11341834 DOI: 10.1021/Bi0028892 |
0.597 |
|
| 2001 |
Shan S, Kravchuk AV, Piccirilli JA, Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 40: 5161-71. PMID 11318638 DOI: 10.1021/Bi002887H |
0.715 |
|
| 2001 |
Admiraal SJ, Meyer P, Schneider B, Deville-Bonne D, Janin J, Herschlag D. Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis. Biochemistry. 40: 403-13. PMID 11148034 DOI: 10.1021/Bi002472W |
0.31 |
|
| 2001 |
Ha T, Zhuang X, Babcock H, Kim H, Orr JW, Williamson JR, Bartley L, Russell R, Herschlag D, Chu S. The study of single biomolecules with fluorescence methods Springer Series in Chemical Physics. 67: 326-337. |
0.389 |
|
| 2000 |
Shan SO, Herschlag D. An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction. Rna (New York, N.Y.). 6: 795-813. PMID 10864040 DOI: 10.1017/S1355838200000649 |
0.608 |
|
| 2000 |
Zhuang X, Bartley LE, Babcock HP, Russell R, Ha T, Herschlag D, Chu S. A single-molecule study of RNA catalysis and folding. Science (New York, N.Y.). 288: 2048-51. PMID 10856219 DOI: 10.1126/Science.288.5473.2048 |
0.717 |
|
| 2000 |
Peluso P, Herschlag D, Nock S, Freymann DM, Johnson AE, Walter P. Role of 4.5S RNA in assembly of the bacterial signal recognition particle with its receptor. Science (New York, N.Y.). 288: 1640-3. PMID 10834842 DOI: 10.1126/Science.288.5471.1640 |
0.511 |
|
| 2000 |
Narlikar GJ, Bartley LE, Herschlag D. Use of duplex rigidity for stability and specificity in RNA tertiary structure. Biochemistry. 39: 6183-9. PMID 10821693 DOI: 10.1021/Bi992858A |
0.795 |
|
| 2000 |
Russell R, Millett IS, Doniach S, Herschlag D. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nature Structural Biology. 7: 367-70. PMID 10802731 DOI: 10.1038/75132 |
0.585 |
|
| 2000 |
Engelhardt MA, Doherty EA, Knitt DS, Doudna JA, Herschlag D. The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. Biochemistry. 39: 2639-51. PMID 10704214 DOI: 10.1021/Bi992313G |
0.584 |
|
| 2000 |
Yoshida A, Shan So, Herschlag D, Piccirilli JA. The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction. Chemistry & Biology. 7: 85-96. PMID 10662698 DOI: 10.1016/S1074-5521(00)00074-0 |
0.71 |
|
| 2000 |
Admiraal SJ, Herschlag D. The substrate-assisted general base catalysis model for phosphate monoester hydrolysis: Evaluation using reactivity comparisons Journal of the American Chemical Society. 122: X. DOI: 10.1021/Ja993942G |
0.346 |
|
| 2000 |
Zhuang X, Bartley L, Babcock H, Russell R, Ha T, Herschlag D, Chu S. Observing folding and catalysis of a single RNA enzyme molecule Pacific Rim Conference On Lasers and Electro-Optics, Cleo - Technical Digest. 588-589. |
0.698 |
|
| 1999 |
Lorsch JR, Herschlag D. Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro. The Embo Journal. 18: 6705-17. PMID 10581244 DOI: 10.1093/Emboj/18.23.6705 |
0.624 |
|
| 1999 |
Wang S, Karbstein K, Peracchi A, Beigelman L, Herschlag D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry. 38: 14363-78. PMID 10572011 DOI: 10.1021/Bi9913202 |
0.724 |
|
| 1999 |
Narlikar GJ, Bartley LE, Khosla M, Herschlag D. 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. Biochemistry. 38: 14192-204. PMID 10571993 DOI: 10.1021/Bi9914309 |
0.801 |
|
| 1999 |
Gerton JL, Herschlag D, Brown PO. Stereospecificity of reactions catalyzed by HIV-1 integrase Journal of Biological Chemistry. 274: 33480-33487. PMID 10559232 DOI: 10.1074/Jbc.274.47.33480 |
0.311 |
|
| 1999 |
Shan So, Yoshida A, Sun S, Piccirilli JA, Herschlag D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 96: 12299-304. PMID 10535916 DOI: 10.1073/Pnas.96.22.12299 |
0.692 |
|
| 1999 |
Russell R, Herschlag D. New pathways in folding of the Tetrahymena group I RNA enzyme Journal of Molecular Biology. 291: 1155-1167. PMID 10518951 DOI: 10.1006/Jmbi.1999.3026 |
0.39 |
|
| 1999 |
Zhang YL, Hollfelder F, Gordon SJ, Chen L, Keng YF, Wu L, Herschlag D, Zhang ZY. Impaired transition state complementarity in the hydrolysis of O- arylphosphorothioates by protein-tyrosine phosphatases Biochemistry. 38: 12111-12123. PMID 10508416 DOI: 10.1021/Bi990836I |
0.623 |
|
| 1999 |
Shan SO, Herschlag D. Hydrogen bonding in enzymatic catalysis: analysis of energetic contributions. Methods in Enzymology. 308: 246-76. PMID 10507008 DOI: 10.1016/S0076-6879(99)08013-1 |
0.6 |
|
| 1999 |
Peck ML, Herschlag D. Effects of oligonucleotide length and atomic composition on stimulation of the ATPase activity of translation initiation factor elF4A. Rna (New York, N.Y.). 5: 1210-21. PMID 10496222 DOI: 10.1017/S1355838299990817 |
0.779 |
|
| 1999 |
Shan SO, Narlikar GJ, Herschlag D. Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme. Biochemistry. 38: 10976-88. PMID 10460152 DOI: 10.1021/Bi9903897 |
0.739 |
|
| 1999 |
Shan SO, Herschlag D. 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. Biochemistry. 38: 10958-75. PMID 10460151 DOI: 10.1021/Bi990388E |
0.597 |
|
| 1999 |
Admiraal SJ, Schneider B, Meyer P, Janin J, Véron M, Deville-Bonne D, Herschlag D. Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase Biochemistry. 38: 4701-4711. PMID 10200157 DOI: 10.1021/Bi9827565 |
0.408 |
|
| 1999 |
O'Brien PJ, Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chemistry & Biology. 6: R91-R105. PMID 10099128 DOI: 10.1016/S1074-5521(99)80033-7 |
0.568 |
|
| 1999 |
Doherty EA, Herschlag D, Doudna JA. Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry. 38: 2982-90. PMID 10074350 DOI: 10.1021/Bi982113P |
0.593 |
|
| 1999 |
Russell R, Herschlag D. Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme Rna. 5: 158-166. PMID 10024168 DOI: 10.1017/S1355838299981839 |
0.412 |
|
| 1999 |
Korber P, Zander T, Herschlag D, Bardwell JCA. A new heat shock protein that binds nucleic acids Journal of Biological Chemistry. 274: 249-256. PMID 9867837 DOI: 10.1074/Jbc.274.1.249 |
0.364 |
|
| 1999 |
O'Brien PJ, Herschlag D. Does the active site arginine change the nature of the transition state for alkaline phosphatase-catalyzed phosphoryl transfer? [[11] Journal of the American Chemical Society. 121: 11022-11023. DOI: 10.1021/Ja9932582 |
0.574 |
|
| 1999 |
Admiraal SJ, Herschlag D. Catalysis of phosphoryl transfer from ATP by amine nucleophiles Journal of the American Chemical Society. 121: 5837-5845. DOI: 10.1021/Ja990903W |
0.344 |
|
| 1998 |
Peracchi A, Matulic-Adamic J, Wang S, Beigelman L, Herschlag D. Structure-function relationships in the hammerhead ribozyme probed by base rescue Rna. 4: 1332-1346. PMID 9814755 DOI: 10.1017/S1355838298980979 |
0.396 |
|
| 1998 |
Herschlag D. RNA structure: Ribozyme crevices and catalysis Nature. 395: 548-549. PMID 9783578 DOI: 10.1038/26864 |
0.381 |
|
| 1998 |
Peracchi A, Karpeisky A, Maloney L, Beigelman L, Herschlag D. A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations Biochemistry. 37: 14765-14775. PMID 9778351 DOI: 10.1021/Bi980867Y |
0.46 |
|
| 1998 |
Narlikar GJ, Herschlag D. Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction Biochemistry. 37: 9902-9911. PMID 9665695 DOI: 10.1021/Bi980495T |
0.7 |
|
| 1998 |
Lorsch JR, Herschlag D. The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry. 37: 2194-206. PMID 9485365 DOI: 10.1021/Bi9724319 |
0.674 |
|
| 1998 |
Lorsch JR, Herschlag D. The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry. 37: 2180-93. PMID 9485364 DOI: 10.1021/Bi972430G |
0.679 |
|
| 1998 |
O'Brien PJ, Herschlag D. Sulfatase activity of E. coli alkaline phosphatase demonstrates a functional link to arylsulfatases, an evolutionarily related enzyme family [10] Journal of the American Chemical Society. 120: 12369-12370. DOI: 10.1021/Ja983390M |
0.349 |
|
| 1997 |
Peracchi A, Beigelman L, Scott EC, Uhlenbeck OC, Herschlag D. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. The Journal of Biological Chemistry. 272: 26822-6. PMID 9341112 DOI: 10.1074/Jbc.272.43.26822 |
0.399 |
|
| 1997 |
Narlikar GJ, Herschlag D. Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes Annual Review of Biochemistry. 66: 19-59. PMID 9242901 DOI: 10.1146/Annurev.Biochem.66.1.19 |
0.668 |
|
| 1997 |
Hertel KJ, Peracchi A, Uhlenbeck OC, Herschlag D. Use of intrinsic binding energy for catalysis by an RNA enzyme. Proceedings of the National Academy of Sciences of the United States of America. 94: 8497-502. PMID 9238005 DOI: 10.1073/Pnas.94.16.8497 |
0.438 |
|
| 1997 |
McConnell TS, Herschlag D, Cech TR. Effects of divalent metal ions on individual steps of the Tetrahymena ribozyme reaction. Biochemistry. 36: 8293-303. PMID 9204875 DOI: 10.1021/Bi9700678 |
0.596 |
|
| 1997 |
Narlikar GJ, Khosla M, Usman N, Herschlag D. Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: Intrinsic binding energy in an RNA enzyme Biochemistry. 36: 2465-2477. PMID 9054551 DOI: 10.1021/Bi9610820 |
0.67 |
|
| 1997 |
Herschlag D, Narlikar QJ, Peracchi A, Shan S. Biological catalysis: Lessons from the comparison of RNA and protein enzymes Faseb Journal. 11: A852. |
0.528 |
|
| 1996 |
Shan SO, Herschlag D. The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis. Proceedings of the National Academy of Sciences of the United States of America. 93: 14474-9. PMID 8962076 DOI: 10.1073/Pnas.93.25.14474 |
0.574 |
|
| 1996 |
Peracchi A, Beigelman L, Usman N, Herschlag D. Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases Proceedings of the National Academy of Sciences of the United States of America. 93: 11522-11527. PMID 8876168 DOI: 10.1073/Pnas.93.21.11522 |
0.454 |
|
| 1996 |
Narlikar GJ, Herschlag D. Isolation of a local tertiary folding transition in the context of a globally folded RNA Nature Structural Biology. 3: 701-710. PMID 8756329 DOI: 10.1038/Nsb0896-701 |
0.684 |
|
| 1996 |
Maegley KA, Admiraal SJ, Herschlag D. Ras-catalyzed hydrolysis of GTP: a new perspective from model studies. Proceedings of the National Academy of Sciences of the United States of America. 93: 8160-6. PMID 8710841 DOI: 10.1073/Pnas.93.16.8160 |
0.366 |
|
| 1996 |
Mei R, Herschlag D. Mechanistic investigations of a ribozyme derived from the Tetrahymena group I intron: Insights into catalysis and the second step of self-splicing Biochemistry. 35: 5796-5809. PMID 8639540 DOI: 10.1021/Bi9527653 |
0.354 |
|
| 1996 |
Knitt DS, Herschlag D. pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa. Biochemistry. 35: 1560-70. PMID 8634287 DOI: 10.1021/Bi9521147 |
0.346 |
|
| 1996 |
Shan SO, Loh S, Herschlag D. The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis. Science (New York, N.Y.). 272: 97-101. PMID 8600542 DOI: 10.1126/Science.272.5258.97 |
0.537 |
|
| 1996 |
Shan S, Herschlag D. Energetic effects of multiple hydrogen bonds. Implications for enzymatic catalysis Journal of the American Chemical Society. 118: 5515-5518. DOI: 10.1021/Ja954205X |
0.582 |
|
| 1996 |
Hertel KJ, Herschlag D, Uhlenbeck OC. Specificity of hammerhead ribozyme cleavage. The Embo Journal. 15: 3751-3757. DOI: 10.1002/J.1460-2075.1996.Tb00745.X |
0.441 |
|
| 1995 |
Admiraal SJ, Herschlag D. Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis Chemistry & Biology. 2: 729-739. PMID 9383480 DOI: 10.1016/1074-5521(95)90101-9 |
0.403 |
|
| 1995 |
Narlikar GJ, Gopalakrishnan V, McConnell TS, Usman N, Herschlag D. Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization Proceedings of the National Academy of Sciences of the United States of America. 92: 3668-3672. PMID 7731962 DOI: 10.1073/Pnas.92.9.3668 |
0.729 |
|
| 1995 |
Hollfelder F, Herschlag D. The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphorothioates by alkaline phosphatase. Biochemistry. 34: 12255-64. PMID 7547968 DOI: 10.1021/Bi00038A021 |
0.637 |
|
| 1995 |
Herschlag D. RNA chaperones and the RNA folding problem. Journal of Biological Chemistry. 270: 20871-20874. PMID 7545662 DOI: 10.1074/Jbc.270.36.20871 |
0.419 |
|
| 1994 |
Herschlag D, Khosla M. Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step. Biochemistry. 33: 5291-5297. PMID 8172903 DOI: 10.1021/Bi00183A036 |
0.372 |
|
| 1994 |
Hertel KJ, Herschlag D, Uhlenbeck OC. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction Biochemistry. 33: 3374-3385. PMID 8136375 DOI: 10.1021/Bi00177A031 |
0.386 |
|
| 1994 |
Coetzee T, Herschlag D, Belfort M. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes & Development. 8: 1575-88. PMID 7958841 DOI: 10.1101/Gad.8.13.1575 |
0.372 |
|
| 1994 |
Knitt DS, Narlikar GJ, Herschlag D. Dissection of the role of the conserved G.U pair in group I RNA self-splicing. Biochemistry. 33: 13864-79. PMID 7947795 DOI: 10.1021/Bi00250A041 |
0.671 |
|
| 1994 |
Herschlag D, Khosla M, Tsuchihashi Z, Karpel RL. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis The Embo Journal. 13: 2913-2924. DOI: 10.1002/J.1460-2075.1994.Tb06586.X |
0.412 |
|
| 1993 |
Labow BI, Herschlag D, Jencks WP. Catalysis of the hydrolysis of phosphorylated pyridines by alkaline phosphatase has little or no dependence on the pKa of the leaving group. Biochemistry. 32: 8737-41. PMID 8395879 DOI: 10.1021/Bi00085A003 |
0.571 |
|
| 1993 |
McConnell TS, Cech TR, Herschlag D. Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding. Proceedings of the National Academy of Sciences of the United States of America. 90: 8362-6. PMID 8378306 DOI: 10.1073/Pnas.90.18.8362 |
0.566 |
|
| 1993 |
Tsuchihashi Z, Khosla M, Herschlag D. Protein enhancement of hammerhead ribozyme catalysis Science. 262: 99-102. PMID 7692597 DOI: 10.1126/Science.7692597 |
0.389 |
|
| 1993 |
Herschlag D, Eckstein F, Cech TR. The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction. Biochemistry. 32: 8312-21. PMID 7688573 DOI: 10.1021/Bi00083A035 |
0.616 |
|
| 1993 |
Herschlag D, Eckstein F, Cech TR. 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. Biochemistry. 32: 8299-311. PMID 7688572 DOI: 10.1021/Bi00083A034 |
0.646 |
|
| 1992 |
Herschlag D. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. Biochemistry. 31: 1386-1399. PMID 1736996 DOI: 10.1021/Bi00120A015 |
0.488 |
|
| 1992 |
Legault P, Herschlag D, Celander DW, Cech TR. Mutations at the guanosine-binding site of the Tetrahymena ribozyme also affect site-specific hydrolysis. Nucleic Acids Research. 20: 6613-9. PMID 1480482 DOI: 10.1093/Nar/20.24.6613 |
0.557 |
|
| 1992 |
Cech TR, Herschlag D, Piccirilli JA, Pyle AM. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. The Journal of Biological Chemistry. 267: 17479-82. PMID 1381347 |
0.733 |
|
| 1991 |
Herschlag D, Piccirilli JA, Cech TR. Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom. Biochemistry. 30: 4844-54. PMID 2036355 DOI: 10.1021/Bi00234A003 |
0.71 |
|
| 1991 |
Young B, Herschlag D, Cech TR. Mutations in a nonconserved sequence of the Tetrahymena ribozyme increase activity and specificity. Cell. 67: 1007-19. PMID 1959129 DOI: 10.1016/0092-8674(91)90373-7 |
0.598 |
|
| 1991 |
Herschlag D. Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proceedings of the National Academy of Sciences of the United States of America. 88: 6921-6925. PMID 1871108 DOI: 10.1073/Pnas.88.16.6921 |
0.413 |
|
| 1990 |
Herschlag D, Jencks WP. Catalysis of the hydrolysis of phosphorylated pyridines by Mg(OH)+: a possible model for enzymatic phosphoryl transfer. Biochemistry. 29: 5172-9. PMID 2378873 DOI: 10.1021/Bi00473A025 |
0.557 |
|
| 1990 |
Herschlag D, Cech TR. 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. Biochemistry. 29: 10172-80. PMID 2271646 DOI: 10.1021/Bi00496A004 |
0.608 |
|
| 1990 |
Herschlag D, Cech TR. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry. 29: 10159-71. PMID 2271645 DOI: 10.1021/Bi00496A003 |
0.602 |
|
| 1990 |
Herschlag D, Cech TR. DNA cleavage catalysed by the ribozyme from Tetrahymena. Nature. 344: 405-9. PMID 1690858 DOI: 10.1038/344405A0 |
0.563 |
|
| 1990 |
Herschlag D, Cech TR. Erratum: DNA cleavage catalysed by the ribozyme from Tetrahymena Nature. 344: 792-792. DOI: 10.1038/344792B0 |
0.459 |
|
| 1990 |
Herschlag D, Jencks WP. Nucleophiles of high reactivity in phosphoryl transfer reactions: α-effect compounds and fluoride ion Journal of the American Chemical Society. 112: 1951-1956. DOI: 10.1021/Ja00161A047 |
0.578 |
|
| 1990 |
Herschlag D, Jencks WP. The effects of Mg2+, hydrogen bonding, and steric factors on rate and equilibrium constants for phosphoryl transfer between Carboxylate Ions and Pyridines Journal of the American Chemical Society. 112: 1942-1950. DOI: 10.1021/Ja00161A046 |
0.586 |
|
| 1990 |
HERSCHLAG D, JENCKS WP. ChemInform Abstract: Phosphoryl Transfer to Anionic Oxygen Nucleophiles. Nature of the Transition State and Electrostatic Repulsion. Cheminform. 21. DOI: 10.1002/CHIN.199001262 |
0.448 |
|
| 1989 |
Herschlag D, Jencks WP. Phosphoryl transfer to anionic oxygen nucleophiles. Nature of the transition state and electrostatic repulsion Journal of the American Chemical Society. 111: 7587-7596. DOI: 10.1021/Ja00201A048 |
0.576 |
|
| 1989 |
Herschlag D, Jencks WP. Evidence that metaphosphate monoanion is not an intermediate in solvolysis reactions in aqueous solution Journal of the American Chemical Society. 111: 7579-7586. DOI: 10.1021/Ja00201A047 |
0.527 |
|
| 1988 |
Herschlag D. The role of induced fit and conformational changes of enzymes in specificity and catalysis Bioorganic Chemistry. 16: 62-96. DOI: 10.1016/0045-2068(88)90038-7 |
0.38 |
|
| 1987 |
Herschlag D, Jencks WP. The effect of divalent metal ions on the rate and transition-state structure of phosphoryl-transfer reactions Journal of the American Chemical Society. 109: 4665-4674. DOI: 10.1021/Ja00249A033 |
0.525 |
|
| 1987 |
HERSCHLAG D, JENCKS WP. ChemInform Abstract: The Effect of Divalent Metal Ions on the Rate and Transition-State Structure of Phosphoryl-Transfer Reactions. Cheminform. 18. DOI: 10.1002/CHIN.198746283 |
0.499 |
|
| 1987 |
HERSCHLAG D, JENCKS WP. ChemInform Abstract: Pyrophosphate Formation from Acetyl Phosphate and Orthophosphate Anions in Concentrated Aqueous Salt Solutions Does not Provide Evidence for a Metaphosphate Intermediate Cheminform. 18. DOI: 10.1002/CHIN.198717261 |
0.42 |
|
| 1986 |
Jencks WP, Haber MT, Herschlag D, Nazaretian KL. Decreasing reactivity with increasing nucleophile basicity. The effect of solvation on .beta.nuc for phosphoryl transfer to amines. Journal of the American Chemical Society. 108: 479-83. PMID 22175464 DOI: 10.1021/Ja00263A019 |
0.477 |
|
| 1986 |
Jencks WP, Haber MT, Herschlag D, Nazaretian KL. Additions and Corrections: Decreasing Reactivity with Increasing Nucleophile Basicity. The Effect of Solvation on (nuc) for Phosphoryl Transfer to Amines. Journal of the American Chemical Society. 108: 6100. PMID 22175415 DOI: 10.1021/Ja00279A603 |
0.5 |
|
| 1986 |
Herschlag D, Jencks WP. Pyrophosphate formation from acetyl phosphate and orthophosphate anions in concentrated aqueous salt solutions does not provide evidence for a metaphosphate intermediate Journal of the American Chemical Society. 108: 7938-7946. DOI: 10.1021/Ja00285A010 |
0.528 |
|
| 1986 |
Jencks WP, Haber MT, Herschlag D, Nazaretian KL. Decreasing reactivity with increasing nucleophile basicity. The effect of solvation on βnuc for phosphoryl transfer to amines Journal of the American Chemical Society. 108: 479-483. DOI: 10.1002/Chin.198623087 |
0.498 |
|
| Show low-probability matches. |
