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1

Structural basis of substrate specificity in the serine proteases

John J. Perona, Charles S. Craik

Journal:

Protein Science

Year:

1995

Language:

english

File:

PDF, 21.23 MB

english, 1995

2

High-throughput ethomics in large groups of Drosophila

Branson, Kristin, Robie, Alice A, Bender, John, Perona, Pietro, Dickinson, Michael H

Journal:

Year:

2009

Language:

english

File:

PDF, 1.86 MB

english, 2009

3

Structural origins of substrate discrimination in trypsin and chymotrypsin

Perona, John J., Hedstrom, Lizbeth, Rutter, William J., Fletterick, Robert J.

Journal:

Year:

1995

Language:

english

File:

PDF, 5.16 MB

english, 1995

4

Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position

Rodriguez-Hernandez, Annia, Spears, Jessica L., Gaston, Kirk W., Limbach, Patrick A., Gamper, Howard, Hou, Ya-Ming, Kaiser, Rob, Agris, Paul F., Perona, John J.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 2.80 MB

english, 2013

5

Exploring writhe in supercoiled minicircle DNA

Fogg, Jonathan M, Kolmakova, Natalia, Rees, Ian, Magonov, Sergei, Hansma, Helen, Perona, John J, Zechiedrich, E Lynn

Journal:

Journal of Physics Condensed Matter

Year:

2006

Language:

english

File:

PDF, 840 KB

english, 2006

6

10.1038/6707

Perona, John J., Martin, Amy M., Sam, My D., Reich, Norbert O.

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 875 KB

english, 1999

7

10.1038/86149

Horton, Nancy C., Perona, John J.

Journal:

Natural Structural Biology

Year:

2001

Language:

english

File:

PDF, 761 KB

english, 2001

8

Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation

Horton, Nancy C., Dorner, Lydia F., Perona, John J.

Journal:

Natural Structural Biology

Year:

2001

Language:

english

File:

PDF, 2.38 MB

english, 2001

9

Shape-selective RNA recognition by cysteinyl-tRNA synthetase

Hauenstein, Scott, Zhang, Chun-Mei, Hou, Ya-Ming, Perona, John J

Journal:

Nature Structural and Molecular Biology

Year:

2004

Language:

english

File:

PDF, 982 KB

english, 2004

10

Linking Energy Production and Protein Synthesis in Hydrogenotrophic Methanogens

Oza, Javin P., Sowers, Kevin R., Perona, John J.

Journal:

Year:

2012

Language:

english

File:

PDF, 4.32 MB

english, 2012

11

Architectural Underpinnings of the Genetic Code for Glutamine†

Corigliano, Eleonora M., Perona, John J.

Journal:

Year:

2009

Language:

english

File:

PDF, 9.06 MB

english, 2009

12

Stereochemical mechanisms of tRNA methyltransferases

Ya-Ming Hou, John J. Perona

Journal:

Year:

2010

Language:

english

File:

PDF, 380 KB

english, 2010

13

Two-Step Pathway to Aminoacylated tRNA

Journal:

Year:

2005

Language:

english

File:

PDF, 46 KB

english, 2005

14

Heat Maps for Intramolecular Communication in an RNP Enzyme Encoding Glutamine

Annia Rodríguez-Hernández, John J. Perona

Journal:

Year:

2011

Language:

english

File:

PDF, 1.46 MB

english, 2011

15

tRNA-Dependent Active Site Assembly in a Class I Aminoacyl-tRNA Synthetase

Luke D Sherlin, John J Perona

Journal:

Year:

2003

Language:

english

File:

PDF, 978 KB

english, 2003

16

Relocating a Negative Charge in the Binding Pocket of Trypsin

John J. Perona, Christopher A. Tsu, Mary E. McGrath, Charles S. Craik, Robert J. Fletterick

Journal:

Journal of Molecular Biology

Year:

1993

File:

PDF, 941 KB

1993

17

Crystal Structure of Rat Anionic Trypsin Complexed with the Protein Inhibitors APPI and BPTI

John J. Perona, Christopher A. Tsu, Charles S. Craik, Robert J. Fletterick

Journal:

Journal of Molecular Biology

Year:

1993

File:

PDF, 956 KB

1993

18

Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis

John J. Perona, Amy M. Martin

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 1.31 MB

english, 1997

19

Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT)

Nancy C Horton, John J Perona

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 461 KB

english, 1998

20

Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases

Luke D Sherlin, Timothy L Bullock, Kate Juliet Newberry, Richard S.A Lipman, Ya-Ming Hou, Barbro Beijer, Brian S Sproat, John J Perona

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 1013 KB

english, 2000

21

Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site

My D. Sam, Nancy C. Horton, T.Amar Nissan, John J. Perona

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 353 KB

english, 2001

22

Non-cognate Enzyme–DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC

David A. Hiller, Amy M. Rodriguez, John J. Perona

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 601 KB

english, 2005

23

Distinct Kinetic Mechanisms of the Two Classes of Aminoacyl-tRNA Synthetases

Chun-Mei Zhang, John J. Perona, Kang Ryu, Christopher Francklyn, Ya-Ming Hou

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 578 KB

english, 2006

24

Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI

Ben Youngblood, Fa-Kuen Shieh, Stephanie De Los Rios, John J. Perona, Norbert O. Reich

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 879 KB

english, 2006

25

Structure of the Escherichia coli Leucine-responsive Regulatory Protein Lrp Reveals a Novel Octameric Assembly

Stephanie de los Rios, John J. Perona

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 2.14 MB

english, 2007

26

Kinetic Quality Control of Anticodon Recognition by a Eukaryotic Aminoacyl-tRNA Synthetase

Cuiping Liu, Howard Gamper, Svetlana Shtivelband, Scott Hauenstein, John J. Perona, Ya-Ming Hou

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.51 MB

english, 2007

27

The Energetic Contribution of Induced Electrostatic Asymmetry to DNA Bending by a Site-Specific Protein

Stephen P. Hancock, David A. Hiller, John J. Perona, Linda Jen-Jacobson

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.60 MB

english, 2011

28

Two-Step Aminoacylation of tRNA without Channeling in Archaea

Hari Bhaskaran, John J. Perona

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

29

Erratum to “Two-Step Aminoacylation of tRNA without Channeling in Archaea” [J. Mol. Biol. 411/4 (2011) 854–869]

Hari Bhaskaran, John J. Perona

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 254 KB

english, 2011

30

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases

Christopher S. Francklyn, Eric A. First, John J. Perona, Ya-Ming Hou

Journal:

Year:

2008

Language:

english

File:

PDF, 1.00 MB

english, 2008

31

Zinc-mediated Amino Acid Discrimination in Cysteinyl-tRNA Synthetase

Chun-Mei Zhang, Thomas Christian, Kate J. Newberry, John J. Perona, Ya-Ming Hou

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 929 KB

english, 2003

32

Amino Acid Discrimination by a Class I Aminoacyl-tRNA Synthetase Specified by Negative Determinants

Timothy L. Bullock, Nathan Uter, T. Amar Nissan, John J. Perona

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 2.33 MB

english, 2003

33

Type II restriction endonucleases

Journal:

Year:

2002

Language:

english

File:

PDF, 190 KB

english, 2002

34

Amino Acid Discrimination by a Highly Differentiated Metal Center of an Aminoacyl-tRNA Synthetase †

Zhang, Chun-Mei, Perona, John J., Hou, Ya-Ming

Journal:

Year:

2003

Language:

english

File:

PDF, 159 KB

english, 2003

35

Active-Site Assembly in Glutaminyl-tRNA Synthetase by tRNA-Mediated Induced Fit †

Uter, Nathan T., Perona, John J.

Journal:

Year:

2006

Language:

english

File:

PDF, 424 KB

english, 2006

36

Synthesis of Glu-tRNA Gln by Engineered and Natural Aminoacyl-tRNA Synthetases

Rodríguez-Hernández, Annia, Bhaskaran, Hari, Hadd, Andrew, Perona, John J.

Journal:

Year:

2010

Language:

english

File:

PDF, 4.28 MB

english, 2010

37

Structural Diversity and Protein Engineering of the Aminoacyl-tRNA Synthetases

Perona, John J., Hadd, Andrew

Journal:

Year:

2012

Language:

english

File:

PDF, 2.26 MB

english, 2012

38

Indirect Readout of tRNA for Aminoacylation †

Perona, John J., Hou, Ya-Ming

Journal:

Year:

2007

Language:

english

File:

PDF, 908 KB

english, 2007

39

10.1016/S0016-5107(84)72438-2

Perona, John J., Swanson, Robert, Steitz, Thomas A., Söll, Dieter

Journal:

Gastrointestinal Endoscopy

Year:

1984

Language:

english

File:

PDF, 783 KB

english, 1984

40

Overproduction and purification of Escherichia coli tRNAGln2 and its use in crystallization of the glutaminyl-tRNA synthetase-tRNAGln complex

Perona, John J., Swanson, Robert, Steitz, Thomas A., Söll, Dieter

Journal:

Journal of Molecular Biology

Year:

1988

Language:

english

File:

PDF, 2.73 MB

english, 1988

41

Crystallization of RNA-protein complexes

Perona, John J.

Journal:

Year:

1990

Language:

english

File:

PDF, 941 KB

english, 1990

42

A genetic selection elucidates structural determinants of arginine versus lysine specificity in trypsin

Perona, John J., Evnin, Luke B., Craik, Charles S.

Journal:

Year:

1993

Language:

english

File:

PDF, 875 KB

english, 1993

43

Metal Ion-Mediated Substrate-Assisted Catalysis in Type II Restriction Endonucleases

Nancy C. Horton, Kate Juliet Newberry and John J. Perona

Journal:

Proceedings of the National Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 1.67 MB

english, 1998

44

Automated image-based tracking and its application in ecology

Dell, Anthony I., Bender, John A., Branson, Kristin, Couzin, Iain D., de Polavieja, Gonzalo G., Noldus, Lucas P.J.J., Pérez-Escudero, Alfonso, Perona, Pietro, Straw, Andrew D., Wikelski, Martin, Brose

Journal:

Trends in Ecology & Evolution

Year:

2014

Language:

english

File:

PDF, 2.31 MB

english, 2014

45

Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermodynamic Stability

Bhaskaran, Hari, Taniguchi, Takaaki, Suzuki, Takeo, Suzuki, Tsutomu, Perona, John J.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.59 MB

english, 2014

46

10.1038/75910

Perona, John J., Bullock, Timothy L., Sherlin, Luke D.

Journal:

Natural Structural Biology

Year:

2000

Language:

english

File:

PDF, 647 KB

english, 2000

47

Crystal Structure of an Ecotin−Collagenase Complex Suggests a Model for Recognition and Cleavage of the Collagen Triple Helix †

Perona, John J., Tsu, Christopher A., Craik, Charles S., Fletterick, Robert J.

Journal:

Year:

1997

Language:

english

File:

PDF, 488 KB

english, 1997

48

Mn 2+ -dependent Catalysis by Restriction Enzymes: Pre-Steady-State Analysis of Eco RV Endonuclease Reveals Burst Kinetics and the Origins of Reduced Activity

Sam, My D., Perona, John J.

Journal:

Journal of the American Chemical Society

Year:

1999

Language:

english

File:

PDF, 86 KB

english, 1999

49

Divalent Metal Dependence of Site-Specific DNA Binding by Eco RV Endonuclease †

Martin, Amy M., Horton, Nancy C., Lusetti, Shelley, Reich, Norbert O., Perona, John J.

Journal:

Year:

1999

Language:

english

File:

PDF, 133 KB

english, 1999

50

Positively Charged C-Terminal Subdomains of EcoRV Endonuclease: Contributions to DNA Binding, Bending, and Cleavage †

Hiller, David A., Perona, John J.

Journal:

Year:

2006

Language:

english

File:

PDF, 566 KB

english, 2006