Research Topics
| KENNETH ALLEN JOHNSONSummaryAffiliation: University of Texas Country: USA Publications
Research Grants
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Detail Information
Publications
The original Michaelis constant: translation of the 1913 Michaelis-Menten paperLeonor Michaelis
Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, The University of Texas, Austin, Texas 78735, United States
Biochemistry 50:8264-9. 2011..That constant was not the Michaelis constant, but rather V(max)/K(m), the specificity constant times the enzyme concentration (k(cat)/K(m) × E(0))...- Role of induced fit in enzyme specificity: a molecular forward/reverse switchKenneth A Johnson
Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 283:26297-301. 2008..A conformational switch may also favor release rather than reverse reaction of the product... 
Global kinetic explorer: a new computer program for dynamic simulation and fitting of kinetic dataKenneth A Johnson
KinTek Corporation, Austin, TX 78735, USA
Anal Biochem 387:20-9. 2009..This feature is critical to avoid overly complex models that are not supported by the data...- The kinetic and chemical mechanism of high-fidelity DNA polymerasesKenneth A Johnson
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, Austin, TX 78712, USA
Biochim Biophys Acta 1804:1041-8. 2010.... - FitSpace explorer: an algorithm to evaluate multidimensional parameter space in fitting kinetic dataKenneth A Johnson
KinTek Corporation, Austin, TX 78735, USA
Anal Biochem 387:30-41. 2009..In contrast, analysis of alanine racemase clearly refutes claims that global analysis of progress curves can be used to extract the free energy profiles of enzyme-catalyzed reactions... 
Novel mechanism of inhibition of HIV-1 reverse transcriptase by a new non-nucleoside analog, KM-1Louise Z Wang
Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
J Biol Chem 279:38424-32. 2004..KM-1 can bind to RT in both the absence and presence of DNA but weakens the affinity for DNA 140-fold so that it favors DNA dissociation. The data suggest that KM-1 distorts RT conformation and misaligns DNA at the active site...- High-cell density shake-flask expression and rapid purification of the large fragment of Thermus aquaticus DNA polymerase I using a new chemically and temperature inducible expression plasmid in Escherichia coliJohn W Brandis
Institute for Cell and Molecular Biology, 2500 Speedway, University of Texas at Austin, Austin, TX 78712, USA
Protein Expr Purif 63:120-7. 2009..8-L baffle-bottomed shake-flasks each holding 1.5L of culture for a final yield of approximately 33 mg per liter or 3mg of purified enzyme per gram of cells wet weight... - Incorporation and replication of 8-oxo-deoxyguanosine by the human mitochondrial DNA polymeraseJeremiah W Hanes
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
J Biol Chem 281:36241-8. 2006..These reactions are likely to play important roles in oxidative stress in mitochondria related to aging and as compounded by nucleoside analogs used to treat human immunodeficiency virus infections... - Fitting enzyme kinetic data with KinTek Global Kinetic ExplorerKenneth A Johnson
Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas, Austin, Texas, USA
Methods Enzymol 467:601-26. 2009..These concepts are illustrated by example in fitting full progress curve kinetics and in fitting the time dependence of slow-onset inhibition... - Analysis of single nucleotide incorporation reactions by capillary electrophoresisJeremiah W Hanes
Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
Anal Biochem 340:35-40. 2005..However, we also show that only select probes can be used, presumably due to unfavorable interactions between Pol gamma and certain 5' labels... - Role of histidine 932 of the human mitochondrial DNA polymerase in nucleotide discrimination and inherited diseaseDipanwita Batabyal
Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 285:34191-201. 2010..His-932 is thought to contact the β-phosphate of the incoming nucleotide, so it is perhaps surprising that H932Y appears to slow rather than accelerate pyrophosphate release... - Nucleotide-dependent conformational change governs specificity and analog discrimination by HIV reverse transcriptaseMatthew W Kellinger
Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
Proc Natl Acad Sci U S A 107:7734-9. 2010..Discrimination against 3TC-TP is based on the slower rate of incorporation due to misalignment of the substrate and/or catalytic residues... - A new paradigm for DNA polymerase specificityYu-Chih Tsai
Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas, 2500 Speedway, Austin, Texas 78712, USA
Biochemistry 45:9675-87. 2006.... - Site-specific labeling of T7 DNA polymerase with a conformationally sensitive fluorophore and its use in detecting single-nucleotide polymorphismsYu Chih Tsai
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
Anal Biochem 384:136-44. 2009..Finally, we show that the labeled enzyme can be used to identify single-nucleotide mutations in a procedure that could be automated... - Enzymatic therapeutic index of acyclovir. Viral versus human polymerase gamma specificityJeremiah W Hanes
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
J Biol Chem 282:25159-67. 2007..Mitochondrial toxicity is relatively low because acyclovir is activated only in infected cells by the promiscuous viral thymidine kinase and otherwise, mitochondrial toxicity would accumulate during long term treatment... - Fidelity of the human mitochondrial DNA polymeraseHarold R Lee
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 281:36236-40. 2006..We calculate an average fidelity of 1 error in 440,000 nucleotides... - Kinetic effects of kinesin switch I and switch II mutationsScott D Auerbach
Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 280:37061-8. 2005..These results further clarify the pathway of coupling of ATP hydrolysis to force production... - A novel mechanism of selectivity against AZT by the human mitochondrial DNA polymeraseJeremiah W Hanes
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
Nucleic Acids Res 35:6973-83. 2007..Other azido-nucleotides (AZG, AZC and AZA) and 8-oxo-7,8-dihydroguanosine-5'-triphosphate (8-oxo-dGTP) show this same phenomena... - Fidelity and processivity of reverse transcription by the human mitochondrial DNA polymeraseHarold R Lee
Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 282:31982-9. 2007..The biological and biotechnological significance of these results are discussed... - Base pair hydrogen bonds are essential for proofreading selectivity by the human mitochondrial DNA polymeraseHarold R Lee
Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
J Biol Chem 283:14411-6. 2008..The enzyme may use the alignment and prevention of fraying provided by proper hydrogen bonding and minor groove hydrogen bonding interactions as critical criteria for correct base pair recognition... - Importance of hydrogen bonding for efficiency and specificity of the human mitochondrial DNA polymeraseHarold R Lee
Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
J Biol Chem 283:14402-10. 2008..Base pair hydrogen bonding contributes at least a third of the energy underlying nucleoside incorporation efficiency and specificity... - Alternating site ATPase pathway of rat conventional kinesinScott D Auerbach
Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 280:37048-60. 2005..These studies provide a baseline set of kinetic parameters against which future studies of rat kinesin mutants may be evaluated and directly correlated with the structure of the dimeric kinesin... - Pre-steady-state kinetic analysis of cis-3-chloroacrylic acid dehalogenase: analysis and implicationsBrooklyn A Robertson
Department of Chemistry and Biochemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, USA
Biochemistry 48:11737-44. 2009..In the unliganded form, the same loop points away from the active site cavity. Similarly, substrate binding may cause this loop to close down on the active site and sequester the reaction from the external environment... - A single mutation in human mitochondrial DNA polymerase Pol gammaA affects both polymerization and proofreading activities of only the holoenzymeYoung Sam Lee
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
J Biol Chem 285:28105-16. 2010..This study provides a molecular basis for the disease symptoms exhibited by patients carrying those substitutions... - Each monomer of the dimeric accessory protein for human mitochondrial DNA polymerase has a distinct role in conferring processivityYoung Sam Lee
Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
J Biol Chem 285:1490-9. 2010..By duplicating the monomeric pol gammaB of lower eukaryotes, the dimeric mammalian proteins confer additional processivity to the holoenzyme polymerase... - Toxicity of nucleoside analogues used to treat AIDS and the selectivity of the mitochondrial DNA polymeraseHarold Lee
Institute for Cell and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 78712, USA
Biochemistry 42:14711-9. 2003..We will also discuss the promise and underlying challenges for the development of new analogues with lower toxicity... - Real-time measurement of pyrophosphate release kineticsJeremiah W Hanes
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
Anal Biochem 372:125-7. 2008 - Exonuclease removal of dideoxycytidine (zalcitabine) by the human mitochondrial DNA polymeraseJeremiah W Hanes
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
Antimicrob Agents Chemother 52:253-8. 2008.... - Study of 1-deoxy-D-xylulose-5-phosphate reductoisomerase: synthesis and evaluation of fluorinated substrate analoguesAlexander Wong
Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
Org Lett 6:3625-8. 2004..It was found that the 1-fluoro-DXP is a poor substrate, while both 3- and 4-fluoro-DXP behave as noncompetitive inhibitors... - Crystal structure of a dual activity IMPase/FBPase (AF2372) from Archaeoglobus fulgidus. The story of a mobile loopKimberly A Stieglitz
Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
J Biol Chem 277:22863-74. 2002..A direct correlation of the loop conformation with strength of Li(+) inhibition provides a useful system of classification for this extended family of enzymes... - Relationship between antiviral activity and host toxicity: comparison of the incorporation efficiencies of 2',3'-dideoxy-5-fluoro-3'-thiacytidine-triphosphate analogs by human immunodeficiency virus type 1 reverse transcriptase and human mitochondrial DNAJoy Y Feng
Gilead Sciences, Durham, North Carolina 27707, USA
Antimicrob Agents Chemother 48:1300-6. 2004..6-fold slower than the excision of dCMP. These results demonstrate that there are clear differences between HIV-1 RT and polymerase gamma in terms of preferences for substrate structure... - Characterization of novel reverse transcriptase and other RNA-associated catalytic activities by human DNA polymerase gamma: importance in mitochondrial DNA replicationEisuke Murakami
Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520 8066, USA
J Biol Chem 278:36403-9. 2003..Our finding that Pol gamma also incorporates ribonucleotide triphosphates into a DNA primer offers a plausible enzymatic pathway for the origin of the RNA-containing mtDNA genome... - Kinetic investigation of the inhibitory effect of gemcitabine on DNA polymerization catalyzed by human mitochondrial DNA polymeraseJason D Fowler
Department of Biochemistry, Ohio State Biochemistry Program, Ohio State University, Columbus, OH 43210, USA
J Biol Chem 283:15339-48. 2008..Thus, our pre-steady state kinetic studies provide direct evidence demonstrating the inhibitory effect of gemcitabine on the activity of human mitochondrial DNA polymerase... - Crystal structure of the 28 kDa glutathione S-transferase from Schistosoma haematobiumKenneth A Johnson
Department of Biochemical Sciences and Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, Rome, Italy
Biochemistry 42:10084-94. 2003..The relatively tight binding of GSH by Sh28GST explains the residually bound GSH in the crystal and supports a possible role of GSH as a tightly bound cofactor involved in the catalytic mechanism for prostaglandin D(2) synthase activity... - Proteolytic mechanism of a novel mitochondrial and chloroplastic PreP peptidasomeShashi Bhushan
Department for Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
Biol Chem 387:1087-90. 2006..The overall results support the proposed mechanism... - The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysisKenneth A Johnson
Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
EMBO J 25:1977-86. 2006..The manner in which substrates are processed inside the chamber is reminiscent of the proteasome; therefore, we refer to this protein as a peptidasome... - Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thalianaSimon T M Allard
Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:647-50. 2005..Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space... - Crystallization of Ranasmurfin, a blue-coloured protein from Polypedates leucomystaxStephen A McMahon
Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University of St Andrews Fife KY16 9RH, Scotland, UK
Acta Crystallograph Sect F Struct Biol Cryst Commun 62:1124-6. 2006..A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution... - The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesisBeverley A Yard
School of Chemistry, EaStCHEM, The University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, Scotland, UK
J Mol Biol 370:870-86. 2007..Our models provide an understanding of how these mutations may affect the activity of the enzyme... - Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferaseJaldappagari Seetharamappa
Scottish Structural Facility and Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, Scotland
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:452-6. 2007..6, b = 91.3, c = 106.0 A, alpha = beta = gamma = 90 degrees. Analysis of the systematic absences along the three principal axes indicated the space group to be P2(1)2(1)2(1). A complete data set was collected to 2.5 A resolution... - Structure of the DNA repair helicase hel308 reveals DNA binding and autoinhibitory domainsJodi D Richards
Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, Scotland
J Biol Chem 283:5118-26. 2008..These data suggest that one function of the enzyme may be in the removal of bound proteins at stalled replication forks and recombination intermediates... - Schistosoma mansoni fatty acid binding protein: specificity and functional control as revealed by crystallographic structureFrancesco Angelucci
Department of Biochemical Sciences A. Rossi Fanelli, CNR Institute of Molecular Biology and Pathology and Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
Biochemistry 43:13000-11. 2004..The binding rate constant of ligands is controlled by a slow pH dependent conformational change, which we propose to have physiological relevance... - Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricusCarmelinda Savino
Department of Biochemical Sciences and Consiglio Nazionale delle Ricerche, Institute of Molecular Biology and Pathology, University of Rome La Sapienza, P le A Moro 5, 00185 Roma, Italy
Structure 12:2001-8. 2004.... - X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1Brian G Fox
University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706, USA
Proteins 61:206-8. 2005 - Unusual chromophore and cross-links in ranasmurfin: a blue protein from the foam nests of a tropical frogMuse Oke
Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University, St Andrews, UK
Angew Chem Int Ed Engl 47:7853-6. 2008 - The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domainB Martin Hallberg
Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
J Mol Biol 360:774-87. 2006..The ribosomal protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU...
Research Grants
- MECHANISM AND FIDELITY OF DNA REPLICATIONKenneth Johnson; Fiscal Year: 2006..abstract_text> ..
- Elementary Steps in DNA PolymerizationKenneth Johnson; Fiscal Year: 2007..abstract_text> ..
- Mechanism of mitochondrial DNA replicationKENNETH ALLEN JOHNSON; Fiscal Year: 2010....
- MECHANISM AND FIDELITY OF DNA REPLICATIONKenneth Johnson; Fiscal Year: 2003..The mechanism and fidelity of the mitochondrial polymerase will be established by kinetic measurements. ..
- KINETIC ANALYSIS OF MICROTUBULE-DEPENDENT ATPASESKenneth Johnson; Fiscal Year: 2003..The combination of approaches outlined here will provide rigorous and direct information to define the structural and mechanistic basis for force production by kinesin. ..
- Nucleotide selectivity and drug resistance by HIV reverse transcriptaseKENNETH ALLEN JOHNSON; Fiscal Year: 2010....