J. Perona

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Structural basis of substrate specificity in the serine proteases

C. Craik, J. Perona, 1995, Protein science : a publication of the Protein Society.

Evolutionary Divergence of Substrate Specificity within the Chymotrypsin-like Serine Protease Fold*

C. Craik, J. Perona, J J Perona, 1997, The Journal of Biological Chemistry.

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

J. Perona, N. Horton, L. Dorner, 2002, Nature Structural Biology.

Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.

J. Perona, N. Horton, L. Dorner, 1999, Acta crystallographica. Section D, Biological crystallography.

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

John J. Perona, Norbert O. Reich, J. Perona, 1998, Nature Structural Biology.

Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase

Jennifer R. Wolfley, E. Phizicky, J. Luft, 2011, Nucleic acids research.

Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics.

J. Perona, Nathan T. Uter, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Kinetic Partitioning between Synthetic and Editing Pathways in Class I Aminoacyl-tRNA Synthetases Occurs at Both Pre-transfer and Post-transfer Hydrolytic Steps*

J. Perona, Nevena Cvetesic, I. Gruic‐Sovulj, 2012, The Journal of Biological Chemistry.

Two-step aminoacylation of tRNA without channeling in Archaea.

J. Perona, H. Bhaskaran, 2011, Journal of molecular biology.

Partitioning of tRNA-dependent Editing between Pre- and Post-transfer Pathways in Class I Aminoacyl-tRNA Synthetases*

J. Perona, Nevena Cvetesic, John J Perona, 2010, The Journal of Biological Chemistry.

The Homotetrameric Phosphoseryl-tRNA Synthetase from Methanosarcina mazei Exhibits Half-of-the-sites Activity*

J. Perona, Ya-Ming Hou, S. Hauenstein, 2008, Journal of Biological Chemistry.

tRNA-dependent Aminoacyl-adenylate Hydrolysis by a Nonediting Class I Aminoacyl-tRNA Synthetase*

J. Perona, T. Bullock, John J Perona, 2005, Journal of Biological Chemistry.

Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution.

T. Steitz, D. Söll, J. Perona, 1989, Science.

Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase

T. Steitz, J. Perona, M. A. Rould, 1991, Nature.

Alternative designs for construction of the class II transfer RNA tertiary core.

J. Perona, T. Nissan, 2000, RNA.

Structural basis for the broad substrate specificity of fiddler crab collagenolytic serine protease 1.

R. Fletterick, C. Craik, J. Perona, 1997, Biochemistry.

Zinc-mediated amino acid discrimination in cysteinyl-tRNA synthetase.

J. Perona, Ya-Ming Hou, K. Newberry, 2003, Journal of molecular biology.

Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study

J. Perona, N. Horton, B. Connolly, 2000 .

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.

J. Perona, N. Horton, K. Newberry, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly.

J. Perona, S. de los Rios, 2007, Journal of molecular biology.

Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.

J. Perona, D. A. Hiller, 2006, Biochemistry.

Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase M.HhaI.

J. Perona, N. Reich, F. Shieh, 2006, Journal of molecular biology.

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei*

J. Perona, S. Hauenstein, 2008, Journal of Biological Chemistry.

Synthesis of Glu-tRNAGln by engineered and natural aminoacyl- tRNA synthetases†

J. Perona, A. Hadd, H. Bhaskaran, 2011 .

Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.

J. Perona, N. Horton, N. Reich, 1999, Biochemistry.

Crystallization and preliminary diffraction analysis of Escherichia coli cysteinyl-tRNA synthetase.

J. Perona, J. Kohn, Y. Hou, 1999, Acta crystallographica. Section D, Biological crystallography.

Exploring writhe in supercoiled minicircle DNA

H. Hansma, J. Perona, E. L. Zechiedrich, 2006, Journal of physics. Condensed matter : an Institute of Physics journal.

Sulfur Assimilation and Trafficking in Methanogens

J. Perona, C. Driggers, Benjamin J. Rauch, 2018 .

Structural diversity and protein engineering of the aminoacyl-tRNA synthetases.

J. Perona, A. Hadd, 2012, Biochemistry.

Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.

J. Beechem, J. Perona, N. Reich, 2003, Biochemistry.

Improving multiple isomorphous replacement phasing by heavy-atom refinement using solvent-flattened phases.

T. Steitz, J. Perona, M. A. Rould, 1992, Acta crystallographica. Section A, Foundations of crystallography.

Crystal structures of rat anionic trypsin complexed with the protein inhibitors APPI and BPTI.

R. Fletterick, C. Craik, J. Perona, 1993, Journal of molecular biology.

Crystal structure of an ecotin-collagenase complex suggests a model for recognition and cleavage of the collagen triple helix.

R J Fletterick, R. Fletterick, C. Craik, 1997, Biochemistry.

Type II restriction endonucleases.

J. Perona, 2002, Methods.

Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position.

J. Perona, R. Kaiser, P. Limbach, 2013, Journal of molecular biology.

The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein.

J. Perona, D. A. Hiller, S. P. Hancock, 2011, Journal of molecular biology.

Stereochemical mechanisms of tRNA methyltransferases

J. Perona, Ya-Ming Hou, 2010, FEBS letters.

Linking energy production and protein synthesis in hydrogenotrophic methanogens.

J. Perona, K. Sowers, J. Oza, 2012, Biochemistry.

Promiscuity of methionine salvage pathway enzymes in Methanocaldococcus jannaschii.

Robert H. White, J. Perona, K. Harich, 2018, Microbiology.

Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein

J. Perona, Benjamin J. Rauch, 2016, Journal of bacteriology.

Novel proteins for homocysteine biosynthesis in anaerobic microorganisms

J. Perona, Benjamin J. Rauch, A. Gustafson, 2014, Molecular microbiology.

Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14

J. Perona, N. Reich, P. Limbach, 2011, Nucleic acids research.

Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.

O. Uhlenbeck, S. Scaringe, J. Perona, 2001, RNA.

Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase.

J. Perona, H. Gamper, Cuiping Liu, 2007, Journal of molecular biology.

Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase.

T. Steitz, J. Perona, J J Perona, 1993, Biochemistry.

Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.

C. Francklyn, J. Perona, Ya-Ming Hou, 2002, RNA.

The substrate specificity of Uca pugilator collagenolytic serine protease 1 correlates with the bovine type I collagen cleavage sites.

C. Turck, C. Craik, J. Perona, 1994, The Journal of biological chemistry.

A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases.

T. Steitz, J. Risler, J. Perona, 1995, Biochimie.

Overproduction and purification of Escherichia coli tRNA(2Gln) and its use in crystallization of the glutaminyl-tRNA synthetase-tRNA(Gln) complex.

T. Steitz, R. Swanson, D. Söll, 1988, Journal of molecular biology.

Recognition of Flanking DNA Sequences by EcoRV Endonuclease Involves Alternative Patterns of Water-mediated Contacts*

J. Perona, N. Horton, N C Horton, 1998, The Journal of Biological Chemistry.

Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermodynamic Stability

Tsutomu Suzuki, J. Perona, Takeo Suzuki, 2014, Biochemistry.

An engineered class I transfer RNA with a class II tertiary fold.

J. Perona, T. Nissan, B. Oliphant, 1999, RNA.

Crystallization of RNA-protein complexes

J. Perona, 1990 .

Converting trypsin to chymotrypsin: residue 172 is a substrate specificity determinant.

W. Rutter, L. Hedstrom, J. Perona, 1994, Biochemistry.

Engineered metal regulation of trypsin specificity.

R J Fletterick, R. Fletterick, C. Craik, 1995, Biochemistry.

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

C. Craik, J. Perona, L. B. Evnin, 1993, Gene.

Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.

J. Perona, A. Rodríguez-Hernández, 2011, Structure.

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

J. Perona, N. Horton, N C Horton, 1998, Journal of molecular biology.

Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases.

C. Francklyn, J. Perona, Ya-Ming Hou, 2006, Journal of molecular biology.

Locating the catalytic water molecule in serine proteases.

R. Fletterick, C. Craik, J. Perona, 1993, Science.

Crystallographic snapshots along a protein-induced DNA-bending pathway.

J. Perona, N. Horton, N C Horton, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Amino Acid-dependent Transfer RNA Affinity in a Class I Aminoacyl-tRNA Synthetase*

J. Perona, Nathan T. Uter, I. Gruic‐Sovulj, 2005, Journal of Biological Chemistry.

Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants.

J. Perona, T. Bullock, Nathan T. Uter, 2003, Journal of molecular biology.

Improved Incorporation of Noncanonical Amino Acids by an Engineered tRNA(Tyr) Suppressor.

J. Perona, Joseph J. Porter, R. Mehl, 2016, Biochemistry.

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases.

C. Francklyn, J. Perona, Ya-Ming Hou, 2008, Methods.

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

J. Perona, B. Sproat, T. Bullock, 2000, Journal of molecular biology.

Tertiary core rearrangements in a tight binding transfer RNA aptamer.

J. Perona, T. Bullock, L. Sherlin, 2000 .

Tertiary core rearrangements in a tight binding transfer RNA aptamer

John J. Perona, J. Perona, T. Bullock, 2000, Nature Structural Biology.

Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP at 2.8 Å Resolution

T. Steitz, D. Söll, J. Perona, 2020, Structural Insights into Gene Expression and Protein Synthesis.

Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC.

J. Perona, D. A. Hiller, A. M. Rodriguez, 2005, Journal of molecular biology.

Shape-selective RNA recognition by cysteinyl-tRNA synthetase

J. Perona, Ya-Ming Hou, John J Perona, 2004, Nature Structural &Molecular Biology.

Active-site assembly in glutaminyl-tRNA synthetase by tRNA-mediated induced fit.

J. Perona, Nathan T. Uter, 2006, Biochemistry.

Kinetics of tRNA Folding Monitored by Aminoacylation

J. Perona, H. Bhaskaran, A. Rodríguez-Hernández, 2012, RNA.

tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase.

J. Perona, L. Sherlin, 2003, Structure.

Making the most of metal ions

J. Perona, N. Horton, 2001, Nature Structural Biology.

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

J. Perona, N. Horton, M. D. Sam, 2001, Journal of molecular biology.

Synthetic and editing mechanisms of aminoacyl-tRNA synthetases.

J. Perona, I. Gruic‐Sovulj, 2014, Topics in current chemistry.

Coevolution of specificity determinants in eukaryotic glutamyl- and glutaminyl-tRNA synthetases.

J. Perona, A. Hadd, 2014, Journal of molecular biology.

T. Steitz, J. Risler, J. Perona, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.

J. Perona, M. D. Sam, 1999, Biochemistry.

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

J. Perona, J J Perona, Amy M. Martin, 1997, Journal of molecular biology.

Structural origins of substrate discrimination in trypsin and chymotrypsin.

W. Rutter, R. Fletterick, L. Hedstrom, 1995, Biochemistry.

Exogenous acetate reconstitutes the enzymatic activity of trypsin Asp189Ser.

W. Rutter, R. Fletterick, C. Craik, 1994, Biochemistry.

Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection.

J. Perona, J. Saven, C. Driggers, 2017, Organic & biomolecular chemistry.

Indirect readout of tRNA for aminoacylation.

J. Perona, Ya-Ming Hou, 2007, Biochemistry.

DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites.

J. Perona, N. Horton, 2004, Biochemistry.

Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.

J. Perona, N. Horton, J. Kohn, 2002, Biochemistry.

Determinants for tRNA-Dependent Pretransfer Editing in the Synthetic Site of Isoleucyl-tRNA Synthetase

J. Perona, I. Gruic‐Sovulj, M. Dulic, 2014, Biochemistry.

Crystal structure of a reverse polymerase

J. Perona, J. Oza, 2010, Proceedings of the National Academy of Sciences.

Generating Efficient Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetases for Structurally Diverse Non-Canonical Amino Acids.

P. Karplus, J. Perona, R. Mehl, 2022, ACS chemical biology.

Architectural underpinnings of the genetic code for glutamine.

J. Perona, E. M. Corigliano, 2009, Biochemistry.

A rationally engineered misacylating aminoacyl-tRNA synthetase

J. Perona, T. Bullock, A. Rodríguez-Hernández, 2008, Proceedings of the National Academy of Sciences.

Relocating a negative charge in the binding pocket of trypsin.

R J Fletterick, R. Fletterick, C. Craik, 1994, Journal of molecular biology.

Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes.

T. Steitz, R. Swanson, D. Söll, 1989, Science.

Synthesis of Glu-tRNA(Gln) by engineered and natural aminoacyl-tRNA synthetases.

J. Perona, A. Hadd, H. Bhaskaran, 2010, Biochemistry.

Structural origins of amino acid selection without editing by cysteinyl‐tRNA synthetase

J. Perona, Ya-Ming Hou, K. Newberry, 2002, The EMBO journal.

Persulfide Formation Mediates Cysteine and Homocysteine Biosynthesis in Methanosarcina acetivorans.

J. Perona, L. David, John E. Klimek, 2017, Biochemistry.

Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity.

P. Karplus, J. Perona, R. Mehl, 2022, ACS chemical biology.

Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5.

J. Perona, Cuiping Liu, Ya-Ming Hou, 2010, RNA.

Recoding Aminoacyl-tRNA Synthetases for Synthetic Biology by Rational Protein-RNA Engineering

J. Perona, A. Hadd, 2014, ACS chemical biology.