Daniel Herschlag: search on Z-Library

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1

Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis

Lassila, Jonathan K., Zalatan, Jesse G., Herschlag, Daniel

Journal:

Annual Review of Biochemistry

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

2

Understanding Nucleic Acid–Ion Interactions

Lipfert, Jan, Doniach, Sebastian, Das, Rhiju, Herschlag, Daniel

Journal:

Annual Review of Biochemistry

Year:

2014

Language:

english

File:

PDF, 1.58 MB

english, 2014

3

C HALLENGESIN E NZYME M ECHANISMAND E NERGETICS

Kraut, Daniel A., Carroll, Kate S., Herschlag, Daniel

Journal:

Annual Review of Biochemistry

Year:

2003

Language:

english

File:

PDF, 769 KB

english, 2003

4

ATP and MO25α Regulate the Conformational State of the STRADα Pseudokinase and Activation of the LKB1 Tumour Suppressor

Zeqiraj, Elton, Filippi, Beatrice Maria, Goldie, Simon, Navratilova, Iva, Boudeau, Jérôme, Deak, Maria, Alessi, Dario R., van Aalten, Daan M. F., Herschlag, Daniel

Journal:

Year:

2009

Language:

english

File:

PDF, 3.22 MB

english, 2009

5

From sequence to nanostructure: a critical base pair in RNA k-turns that confers folding and structural characteristics, and correlates with biological function

Huang, Lin, Shi, Xuesong, Herschlag, Daniel, Lilley, David

Journal:

Acta Crystallographica Section A Foundations and Advances

Year:

2015

File:

PDF, 382 KB

2015

6

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

Denny, Sarah Knight, Bisaria, Namita, Yesselman, Joseph David, Das, Rhiju, Herschlag, Daniel, Greenleaf, William James

Journal:

Year:

2018

Language:

english

File:

PDF, 9.33 MB

english, 2018

7

Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments

Laederach, Alain, Das, Rhiju, Vicens, Quentin, Pearlman, Samuel M, Brenowitz, Michael, Herschlag, Daniel, Altman, Russ B

Journal:

Nature Protocols

Year:

2008

Language:

english

File:

PDF, 733 KB

english, 2008

8

Isotope-Edited FTIR of Alkaline Phosphatase Resolves Paradoxical Ligand Binding Properties and Suggests a Role for Ground-State Destabilization

Andrews, Logan D., Deng, Hua, Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 3.09 MB

english, 2011

9

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry

Shi, Xuesong, Walker, Peter, Harbury, Pehr B., Herschlag, Daniel

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 4.11 MB

english, 2017

10

MECHANISTIC ASPECTS OF ENZYMATIC CATALYSIS:Lessons from Comparison of RNA and Protein Enzymes 0

Narlikar, Geeta J., Herschlag, Daniel

Journal:

Annual Review of Biochemistry

Year:

1997

Language:

english

File:

PDF, 360 KB

english, 1997

11

Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics

Merriman, Dawn K, Yuan, Jiayi, Shi, Honglue, Majumdar, Ananya, Herschlag, Daniel, Al-Hashimi, Hashim M

Journal:

Year:

2018

Language:

english

File:

PDF, 1.14 MB

english, 2018

12

The roles of structural dynamics in the cellular functions of RNAs

Ganser, Laura R., Kelly, Megan L., Herschlag, Daniel, Al-Hashimi, Hashim M.

Journal:

Nature Reviews Molecular Cell Biology

Year:

2019

Language:

english

File:

PDF, 2.06 MB

english, 2019

13

The role of the cleavage site 2′-hydroxyl in the Tetrahymena group I ribozyme reaction

Aiichiro Yoshida, Shu-ou Shan, Daniel Herschlag, Joseph A Piccirilli

Journal:

Chemistry & Biology

Year:

2000

Language:

english

File:

PDF, 288 KB

english, 2000

14

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Bai, Yu, Greenfeld, Max, Travers, Kevin J., Chu, Vincent B., Lipfert, Jan, Doniach, Sebastian, Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 177 KB

english, 2007

15

Alkaline Phosphatase Catalysis Is Ultrasensitive to Charge Sequestered between the Active Site Zinc Ions

Nikolic-Hughes, Ivana, O'Brien, Patrick J., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 39 KB

english, 2005

16

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

Herschlag, Daniel, Eckstein, Fritz, Cech, Thomas R.

Journal:

Year:

1993

Language:

english

File:

PDF, 2.58 MB

english, 1993

17

Correction to “Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase”

Schwans, Jason P., Sunden, Fanny, Gonzalez, Ana, Tsai, Yingssu, Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 529 KB

english, 2016

18

Blind Predictions of RNA/Protein Relative Binding Affinities

Kappel, Kalli, Jarmoskaite, Inga, Vaidyanathan, Pavan P., Greenleaf, William J., Herschlag, Daniel, Das, Rhiju

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 40 KB

english, 2017

19

Gold nanocrystal labels provide a sequence–to–3D structure map in SAXS reconstructions

Zettl, Thomas, Mathew, Rebecca S., Shi, Xuesong, Doniach, Sebastian, Herschlag, Daniel, Harbury, Pehr A. B., Lipfert, Jan

Journal:

Science Advances

Year:

2018

Language:

english

File:

PDF, 4.95 MB

english, 2018

20

Functional Interrelationships in the Alkaline Phosphatase Superfamily: Phosphodiesterase Activity of Escherichia coli Alkaline Phosphatase †

O'Brie, Patrick J., Herschlag, Daniel

Journal:

Year:

2001

Language:

english

File:

PDF, 92 KB

english, 2001

21

Functional Identification of Catalytic Metal Ion Binding Sites within RNA

Hougland, James L., Kravchuk, Alexander V., Herschlag, Daniel, Piccirilli, Joseph A.

Journal:

Year:

2005

Language:

english

File:

PDF, 438 KB

english, 2005

22

Optimal Legislative County Clustering in North Carolina

Carter, Daniel, Hunter, Zach, Teague, Dan, Herschlag, Gregory, Mattingly, Jonathan

Journal:

Statistics and Public Policy

Year:

2020

File:

PDF, 3.86 MB

2020

23

The Stanford Institute for Chemical Biology

Chen, James K., Du Bois, Justin, Glenn, Jeffrey, Herschlag, Daniel, Khosla, Chaitan

Journal:

ACS Chemical Biology

Year:

2013

Language:

english

File:

PDF, 158 KB

english, 2013

24

Determining the Mg 2+ Stoichiometry for Folding an RNA Metal Ion Core

Das, Rhiju, Travers, Kevin J., Bai, Yu, Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 58 KB

english, 2005

25

Chemical Rescue of Phosphoryl Transfer in a Cavity Mutant: A Cautionary Tale for Site-Directed Mutagenesis †,‡

Admiraal, Suzanne J., Meyer, Philippe, Schneider, Benoit, Deville-Bonne, Dominique, Janin, Joël, Herschlag, Daniel

Journal:

Year:

2001

Language:

english

File:

PDF, 333 KB

english, 2001

26

A Role for a Single-Stranded Junction in RNA Binding and Specificity by the Tetrahymena Group I Ribozyme

Shi, Xuesong, Solomatin, Sergey V., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 724 KB

english, 2012

27

Impaired Transition State Complementarity in the Hydrolysis of O -Arylphosphorothioates by Protein-Tyrosine Phosphatases †

Zhang, Yan-Ling, Hollfelder, Florian, Gordon, Steven J., Chen, Li, Keng, Yen-Fang, Wu, Li, Herschlag, Daniel, Zhang, Zhong-Yin

Journal:

Year:

1999

Language:

english

File:

PDF, 164 KB

english, 1999

28

Nucleophiles of high reactivity in phosphoryl transfer reactions: .alpha.-effect compounds and fluoride ion

Herschlag, Daniel, Jencks, William P.

Journal:

Journal of the American Chemical Society

Year:

1990

Language:

english

File:

PDF, 824 KB

english, 1990

29

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 Sca I Ribozyme Reveals a New Role of the G·U Pair in Self-Splicing †

Karbstein, Katrin, Lee, Jihee, Herschlag, Daniel

Journal:

Year:

2007

Language:

english

File:

PDF, 290 KB

english, 2007

30

Probing the Tetrahymena Group I Ribozyme Reaction in Both Directions †

Karbstein, Katrin, Carroll, Kate S., Herschlag, Daniel

Journal:

Year:

2002

Language:

english

File:

PDF, 159 KB

english, 2002

31

Probing the Origins of Catalytic Discrimination between Phosphate and Sulfate Monoester Hydrolysis: Comparative Analysis of Alkaline Phosphatase and Protein Tyrosine Phosphatases

Andrews, Logan D., Zalatan, Jesse G., Herschlag, Daniel

Journal:

Year:

2014

Language:

english

File:

PDF, 2.28 MB

english, 2014

32

Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein

Pinney, Margaux, Natarajan, Aditya, Yabukarski, Filip, Sanchez, David M., Liu, Fang, Liang, Ruibin, Doukov, Tzanko I., Schwans, Jason P, Martínez, Todd J., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2018

Language:

english

File:

PDF, 1.34 MB

english, 2018

33

Enhancement of RNA•Ligand Association Kinetics via an Electrostatic Anchor

Sengupta, Raghuvir N, Herschlag, Daniel

Journal:

Year:

2019

Language:

english

File:

PDF, 2.49 MB

english, 2019

34

Robust design and optimization of retroaldol enzymes

Eric A. Althoff, Ling Wang, Lin Jiang, Lars Giger, Jonathan K. Lassila, Zhizhi Wang, Matthew Smith, Sanjay Hari, Peter Kast, Daniel Herschlag, Donald Hilvert, David Baker

Journal:

Protein Science

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

35

RNA Structure, Function, and (Thermo-) Dynamics: A SAXS and Single-Molecule Perspective

Lipfert, Jan, Herschlag, Daniel, Doniach, Sebastian, Dekker, Nynke H.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 51 KB

english, 2011

36

Nanosecond Motions of the Substrate-Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling

Grant, Gian Paola G., Nguyen, Phuong, Boyd, Nathan, Herschlag, Daniel, Qin, Peter

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 56 KB

english, 2010

37

Sulfatase Activity of E. coli Alkaline Phosphatase Demonstrates a Functional Link to Arylsulfatases, an Evolutionarily Related Enzyme Family

O'Brie, Patrick J., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 49 KB

english, 1998

38

Ribozyme-catalyzed and nonenzymic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom

Herschlag, Daniel, Piccirilli, Joseph A., Cech, Thomas R.

Journal:

Year:

1991

Language:

english

File:

PDF, 1.40 MB

english, 1991

39

Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble

Bai, Yu, Chu, Vincent B., Lipfert, Jan, Pande, Vijay S., Herschlag, Daniel, Doniach, Sebastian

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 1.00 MB

english, 2008

40

Structural and Functional Comparisons of Nucleotide Pyrophosphatase/Phosphodiesterase and Alkaline Phosphatase: Implications for Mechanism and Evolution †,‡

Zalatan, Jesse G., Fenn, Timothy D., Brunger, Axel T., Herschlag, Daniel

Journal:

Year:

2006

Language:

english

File:

PDF, 511 KB

english, 2006

41

Assembly of an Exceptionally Stable RNA Tertiary Interface in a Group I Ribozyme †

Doherty, Elizabeth A., Herschlag, Daniel, Doudna, Jennifer A.

Journal:

Year:

1999

Language:

english

File:

PDF, 172 KB

english, 1999

42

Bringing Enzymology into the Genomic Era: Developing and Deploying New Tools to Quantitatively Map Functional Connections Throughout an Enzyme

Markin, Craig, Mokhtari, Daniel, Sunden, Fanny, Herschlag, Dan, Fordyce, Polly M.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 40 KB

2019

43

Structure and Function Converge To Identify a Hydrogen Bond in a Group I Ribozyme Active Site

Marcello Forconi, Raghuvir N. Sengupta, Mao-Chin Liu, Alan C. Sartorelli, Joseph A. Piccirilli, Daniel Herschlag

Journal:

Angewandte Chemie International Edition

Year:

2009

Language:

english

File:

PDF, 671 KB

english, 2009

44

Isolation of a local tertiary folding transition in the context of a globally folded RNA

Narlikar, Geeta J., Herschlag, Daniel

Journal:

Natural Structural Biology

Year:

1996

File:

PDF, 1.02 MB

1996

45

Using Unnatural Amino Acids to Probe the Energetics of Oxyanion Hole Hydrogen Bonds in the Ketosteroid Isomerase Active Site

Natarajan, Aditya, Schwans, Jason P., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2014

Language:

english

File:

PDF, 915 KB

english, 2014

46

Do Electrostatic Interactions with Positively Charged Active Site Groups Tighten the Transition State for Enzymatic Phosphoryl Transfer?

Nikolic-Hughes, Ivana, Rees, Douglas C., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 107 KB

english, 2004

47

Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site

Herschlag, Daniel, Cech, Thomas R.

Journal:

Year:

1990

Language:

english

File:

PDF, 2.17 MB

english, 1990

48

The Substrate-Assisted General Base Catalysis Model for Phosphate Monoester Hydrolysis: Evaluation Using Reactivity Comparisons

Admiraal, Suzanne J., Herschlag, Daniel

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 131 KB

english, 2000

49

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 †

Shan, Shu-ou, Herschlag, Daniel

Journal:

Year:

1999

Language:

english

File:

PDF, 355 KB

english, 1999

50

Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4–P6 RNA by smFRET

Bisaria, Namita, Herschlag, Daniel

Journal:

Biochemical Society Transactions

Year:

2015

Language:

english

File:

PDF, 564 KB

english, 2015

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