2017
Understanding the molecular mechanism of substrate channeling and domain communication in protozoal bifunctional TS-DHFR
Anderson K. Understanding the molecular mechanism of substrate channeling and domain communication in protozoal bifunctional TS-DHFR. Protein Engineering Design And Selection 2017, 30: 253-261. PMID: 28338744, PMCID: PMC6438133, DOI: 10.1093/protein/gzx004.Peer-Reviewed Original ResearchConceptsBifunctional thymidylate synthase-dihydrofolate reductaseThymidylate synthase-dihydrofolate reductaseSubstrate channelingDihydrofolate reductaseN-terminal amino acid extensionAmino acid extensionDihydrofolate reductase domainThymidylate synthaseFolate metabolizing enzymesAcid extensionMonofunctional formsPolypeptide chainMutation analysisMolecular mechanismsMetabolic enzymesParasitic protozoaDNA synthesisFunctional regionsInhibitor designSpeciesEnzymeStructural similarityStructural studiesEfficient catalysisLeishmania major
2003
Detection and characterization of enzyme intermediates: utility of rapid chemical quench methodology and single enzyme turnover experiments
Anderson K. Detection and characterization of enzyme intermediates: utility of rapid chemical quench methodology and single enzyme turnover experiments. 2003, 19-48. DOI: 10.1093/oso/9780198524946.003.0002.Peer-Reviewed Original ResearchEnzyme active siteEnzyme intermediateProtein structure-function studiesSteady-state kinetic studiesStructure-function studiesTransient kinetic approachActive siteMolecule of substrateEnzyme catalysisQuenching methodologyEnzymeTurnover experimentsTransient kinetic techniquesStructure-based drug designEnzyme Transition StatesDrug designMechanistic informationKinetic techniquesSubstrate(sMillisecond time scaleProteinSitesPathwayKinetic studiesIntermediate
2002
Mechanistic Characterization of Toxoplasma gondiiThymidylate Synthase (TS-DHFR)-Dihydrofolate Reductase EVIDENCE FOR A TS INTERMEDIATE AND TS HALF-SITES REACTIVITY*
Johnson E, Hinz W, Atreya C, Maley F, Anderson K. Mechanistic Characterization of Toxoplasma gondiiThymidylate Synthase (TS-DHFR)-Dihydrofolate Reductase EVIDENCE FOR A TS INTERMEDIATE AND TS HALF-SITES REACTIVITY*. Journal Of Biological Chemistry 2002, 277: 43126-43136. PMID: 12192007, DOI: 10.1074/jbc.m206523200.Peer-Reviewed Original ResearchThe Kinetic Mechanism of the Human Bifunctional Enzyme ATIC (5-Amino-4-imidazolecarboxamide Ribonucleotide Transformylase/Inosine 5′-Monophosphate Cyclohydrolase) A SURPRISING LACK OF SUBSTRATE CHANNELING*
Bulock K, Beardsley G, Anderson K. The Kinetic Mechanism of the Human Bifunctional Enzyme ATIC (5-Amino-4-imidazolecarboxamide Ribonucleotide Transformylase/Inosine 5′-Monophosphate Cyclohydrolase) A SURPRISING LACK OF SUBSTRATE CHANNELING*. Journal Of Biological Chemistry 2002, 277: 22168-22174. PMID: 11948179, DOI: 10.1074/jbc.m111964200.Peer-Reviewed Original ResearchConceptsCyclohydrolase reactionProduction of inosine monophosphateRelease of tetrahydrofolateSteady-state kinetic techniquesStopped-flow absorbanceBifunctional enzymeActive siteBifunctional proteinSubstrate channelingInosine 5'-monophosphateCyclohydrolaseEnzymatic activityChemotherapeutic targetEnzyme reaction pathwayInosine monophosphateKinetic mechanismFormyltransferaseProteinEnzymeKinetic analysisPathwayKinetic advantageKinetic evidenceKinetic techniquesRibonucleotides
2001
Y265H Mutator Mutant of DNA Polymerase β PROPER GEOMETRIC ALIGNMENT IS CRITICAL FOR FIDELITY*
Shah A, Li S, Anderson K, Sweasy J. Y265H Mutator Mutant of DNA Polymerase β PROPER GEOMETRIC ALIGNMENT IS CRITICAL FOR FIDELITY*. Journal Of Biological Chemistry 2001, 276: 10824-10831. PMID: 11154692, DOI: 10.1074/jbc.m008680200.Peer-Reviewed Original ResearchConceptsDNA polymerase betaPolymerase betaVivo genetic screenWild-type proteinWild-type enzymeActive site residuesGenetic screenTyr-265Mutant proteinsMutator mutantsPolymerase structureProper geometric alignmentSite residuesProtein conformationNucleotidyl transferForward mutationDNA polymerasePolymerase fidelityDNTP substratesDNA synthesisProteinDeoxynucleoside triphosphatesFirst evidenceTemplate A.Enzyme
2000
An analysis of the catalytic cycle of HIV-1 reverse transcriptase: opportunities for chemotherapeutic intervention based on enzyme inhibition.
Furman P, Painter G, Anderson K. An analysis of the catalytic cycle of HIV-1 reverse transcriptase: opportunities for chemotherapeutic intervention based on enzyme inhibition. Current Pharmaceutical Design 2000, 6: 547-67. PMID: 10788596, DOI: 10.2174/1381612003400777.Peer-Reviewed Original ResearchConceptsCatalytic cycleIntrinsic binding affinityHIV-1 reverse transcriptaseCatalytic complexChemical catalysisBinding affinityCatalysisMolecular forcesReverse transcriptase inhibitorsAllosteric siteClasses of approved drugsNon-nucleoside reverse transcriptase inhibitorsTranscriptase inhibitorsNucleoside reverse transcriptase inhibitorsSite of inhibitionEnzyme inhibitionReverse transcriptaseAlternative substratesEnzyme
1999
The Catalytic Mechanism of EPSP Synthase Revisited †
Lewis J, Johnson K, Anderson K. The Catalytic Mechanism of EPSP Synthase Revisited †. Biochemistry 1999, 38: 7372-7379. PMID: 10353849, DOI: 10.1021/bi9830258.Peer-Reviewed Original ResearchMeSH Keywords3-Phosphoshikimate 1-CarboxyvinyltransferaseAlkyl and Aryl TransferasesAmino Acid SubstitutionBinding SitesCatalysisChromatography, High Pressure LiquidEscherichia coliFreezingKineticsMutagenesis, Site-DirectedNuclear Magnetic Resonance, BiomolecularPhosphoenolpyruvateProtonsSubstrate SpecificityConceptsEPSP synthaseEnzyme intermediateKinetic competenceSingle-turnover experimentsSubstrate to productSolid-state NMRSolid-state NMR studiesEnzyme assaysEnzyme reaction pathwaySDS-PAGECatalytic mechanismDegrees CSpeciesEnzymeIntermediate speciesNMR studiesSide productsCharacterized reaction productsSample preparationDisappearance of substrateSynthaseReaction productsFormation of productsBreakdown productsReaction pathways
1998
Substrate Channeling and Domain−Domain Interactions in Bifunctional Thymidylate Synthase−Dihydrofolate Reductase †
Liang P, Anderson K. Substrate Channeling and Domain−Domain Interactions in Bifunctional Thymidylate Synthase−Dihydrofolate Reductase †. Biochemistry 1998, 37: 12195-12205. PMID: 9724533, DOI: 10.1021/bi9803168.Peer-Reviewed Original ResearchConceptsDHFR active siteActive siteTS active siteCrystal structureTransient kinetic analysisEnzyme active siteBifunctional TS-DHFRProtein surfaceTS-DHFRKinetics of substrateReductase enzymeSingle polypeptide chainKinetic analysisDihydrofolateThymidylate synthasePolypeptide chainSubstrateEnzymeStructureDomain-domain interactionsSpecies of protozoaInteractionKineticsL. majorChain
1997
Pre-steady state kinetic analysis of the bifunctional human amino-imidazole carboxamide ribonucleotide formyltransferase/AMP cyclohydrolase (AICARFT/IMPCHase), a 10-formyltetrahydro-folate-requiring enzyme essential for de novo purine biosynthesis
Rayl E, Moroson B, Beardsley G, Anderson K. Pre-steady state kinetic analysis of the bifunctional human amino-imidazole carboxamide ribonucleotide formyltransferase/AMP cyclohydrolase (AICARFT/IMPCHase), a 10-formyltetrahydro-folate-requiring enzyme essential for de novo purine biosynthesis. Clinical Biochemistry 1997, 30: 275-276. DOI: 10.1016/s0009-9120(97)87769-7.Peer-Reviewed Original Research
1996
HIV-1 Reverse Transcriptase Resistance to Nonnucleoside Inhibitors †
Spence R, Anderson K, Johnson K. HIV-1 Reverse Transcriptase Resistance to Nonnucleoside Inhibitors †. Biochemistry 1996, 35: 1054-1063. PMID: 8547241, DOI: 10.1021/bi952058+.Peer-Reviewed Original ResearchConceptsMutant enzymesPre-steady-state techniquesSingle nucleotide incorporationWild-type complexMaximum incorporation rateNucleotide incorporationEnzyme complexDuplex DNAAffinity 2Cysteine mutationsTwo-step bindingWild-typeConformational changesDecreased affinityEnzymePresence of nevirapineInhibitor resistanceMutationsIncorporation rateY181C mutationWild-type RTReverse transcriptaseHIV-1NevirapineY181C
1995
Reevaluating glyphosate as a transition-state inhibitor of EPSP synthase: identification of an EPSP synthase.EPSP.glyphosate ternary complex.
Sammons R, Gruys K, Anderson K, Johnson K, Sikorski J. Reevaluating glyphosate as a transition-state inhibitor of EPSP synthase: identification of an EPSP synthase.EPSP.glyphosate ternary complex. Biochemistry 1995, 34: 6433-40. PMID: 7756274, DOI: 10.1021/bi00019a024.Peer-Reviewed Original ResearchConceptsEPSP synthaseTernary complexShikimate 3-phosphateSteady-state kineticsEnzyme active siteTransition-state analogSubstrate turnoverSynthase reactionTransition-state inhibitorsEnzymeAssociated with PEPUncompetitive inhibitorBinding resultsSynthaseActive siteFluorescence titration experimentsShikimateOxonium ionsTurnoverInteraction of glyphosateTitration experiments
1994
Detection and characterization of a phospholactoyl-enzyme adduct in the reaction catalyzed by UDP-N-acetylglucosamine enolpyruvoyl transferase, MurZ.
Brown E, Marquardt J, Lee J, Walsh C, Anderson K. Detection and characterization of a phospholactoyl-enzyme adduct in the reaction catalyzed by UDP-N-acetylglucosamine enolpyruvoyl transferase, MurZ. Biochemistry 1994, 33: 10638-45. PMID: 8075064, DOI: 10.1021/bi00201a010.Peer-Reviewed Original ResearchConceptsUDP-N-acetylglucosamineUDP-GlcNAcAbsence of UDP-GlcNAcChemical quench analysisPresence of UDP-GlcNAcSingle-turnover conditionsBinding constantsPeptidoglycan biosynthesisSolution NMRC-2Enzyme nucleophilePeptide of molecular weightStoichiometric labelingConsistent with catalysisRemoval of small moleculesE. coliAdductsSmall moleculesMurZEnzyme adductNon-covalentlySDS-PAGEM ureaLabeled peptidesEnzyme
1993
EPSP synthase inhibitor design II. The importance of the 3-phosphate group for ligand binding at the shikimate-3-phosphate site & the identification of 3-malonate ethers as novel 3-phosphate mimics.
Miller M, Anderson K, Braccolino D, Cleary D, Gruys K, Han C, Lin K, Pansegrau P, Ream J, Sammons R, Sikorski J. EPSP synthase inhibitor design II. The importance of the 3-phosphate group for ligand binding at the shikimate-3-phosphate site & the identification of 3-malonate ethers as novel 3-phosphate mimics. Bioorganic & Medicinal Chemistry Letters 1993, 3: 1435-1440. DOI: 10.1016/s0960-894x(01)80425-x.Peer-Reviewed Original Research
1991
Structure and topological symmetry of the glyphosate target 5-enolpyruvylshikimate-3-phosphate synthase: a distinctive protein fold.
Stallings W, Abdel-Meguid S, Lim L, Shieh H, Dayringer H, Leimgruber N, Stegeman R, Anderson K, Sikorski J, Padgette S, Kishore G. Structure and topological symmetry of the glyphosate target 5-enolpyruvylshikimate-3-phosphate synthase: a distinctive protein fold. Proceedings Of The National Academy Of Sciences Of The United States Of America 1991, 88: 5046-5050. PMID: 11607190, PMCID: PMC51804, DOI: 10.1073/pnas.88.11.5046.Peer-Reviewed Original ResearchThree-dimensional structureSynthesis of aromatic amino acidsProtein-folding unitTwo-domain structureBinding of substratesPolypeptide backbone chainFour-stranded sheetFolding unitsGlobular domainSequence alterationsBeta-sheetEscherichia coliElectron density mapsBroad-spectrum herbicide glyphosateAromatic amino acidsApproximate dyadAmino acidsHelixProteinActive siteLinear sequenceEnzymeSequenceCrystallographic techniquesPseudo-symmetry
1990
"Kinetic competence" of the 5-enolpyruvoylshikimate-3-phosphate synthase tetrahedral intermediate.
Anderson K, Johnson K. "Kinetic competence" of the 5-enolpyruvoylshikimate-3-phosphate synthase tetrahedral intermediate. Journal Of Biological Chemistry 1990, 265: 5567-5572. PMID: 2180929, DOI: 10.1016/s0021-9258(19)39398-6.Peer-Reviewed Original ResearchObservation by 13C NMR of the EPSP synthase tetrahedral intermediate bound to the enzyme active site.
Anderson K, Sammons R, Leo G, Sikorski J, Benesi A, Johnson K. Observation by 13C NMR of the EPSP synthase tetrahedral intermediate bound to the enzyme active site. Biochemistry 1990, 29: 1460-5. PMID: 2334707, DOI: 10.1021/bi00458a017.Peer-Reviewed Original ResearchConceptsEnzyme active siteTetrahedral intermediateFormation of pyruvateActive siteEnzyme sitesComparison of quenchingReaction of enzymeTime of incubationTetrahedral centerCompound giving riseReaction pathwaysEnzymatic hydrolysisPeak assignmentsEnzymeNMR experimentsTernary complexNMR measurementsSide productsRate of formationSpectroscopic probesLong time of incubationNMRSpeciesTriethylamineCovalent adducts
1988
A tetrahedral intermediate in the EPSP synthase reaction observed by rapid quench kinetics.
Anderson K, Sikorski J, Johnson K. A tetrahedral intermediate in the EPSP synthase reaction observed by rapid quench kinetics. Biochemistry 1988, 27: 7395-406. PMID: 3061457, DOI: 10.1021/bi00419a034.Peer-Reviewed Original ResearchConceptsPhosphoenol pyruvateBurst of product formationPre-steady-state burstQuantitation of reaction productsTransient-state kinetic analysisEnzyme-bound intermediateShikimate 3-phosphateSingle turnover experimentsPre-steady-stateSubstrate trapping experimentsRelease of substratesEquilibrium constantsSynthase reactionExcess enzymeBinding rateAbsence of phosphatePyruvateReverse reactionEnzymeTurnover experimentsEnzymatic reactionsKinetic competenceEnzyme concentrationFormation of productsConcentration of phosphateEvaluation of 5-enolpyruvoylshikimate-3-phosphate synthase substrate and inhibitor binding by stopped-flow and equilibrium fluorescence measurements.
Anderson K, Sikorski J, Johnson K. Evaluation of 5-enolpyruvoylshikimate-3-phosphate synthase substrate and inhibitor binding by stopped-flow and equilibrium fluorescence measurements. Biochemistry 1988, 27: 1604-10. PMID: 3284585, DOI: 10.1021/bi00405a032.Peer-Reviewed Original ResearchConceptsBinding of substratesBinary complexShikimate 3-phosphateStopped-flow fluorescence methodsDissociation constantFree enzymeGlyphosate bindingS3P bindingInhibitor bindingProtein fluorescenceKinetics of bindingTernary complexEnzymeStopped-flowFluorescence measurementsBindingFluorescence titrationSaturating concentrationsS3PEquilibrium fluorescence measurements