2025
Selective Oxidation of Disparate Functional Groups Mediated by a Common Aspartic Acid-Based Peptide Catalyst Platform
Huth S, Stone E, Miller S. Selective Oxidation of Disparate Functional Groups Mediated by a Common Aspartic Acid-Based Peptide Catalyst Platform. Accounts Of Chemical Research 2025, 58: 2072-2087. PMID: 40530828, DOI: 10.1021/acs.accounts.5c00247.Peer-Reviewed Original ResearchConceptsPeptide catalystsMedicinally relevant moleculesPeptide-based catalystsBaeyer-Villiger oxidationAsp peptidesSynthetic reaction conditionsSynthetically relevant transformationsComplex natural productsNatural productsAsymmetric catalysisCatalyst platformStoichiometric oxidantOxygen atomsSelective oxidationNoncovalent interactionsReaction conditionsBioactive natural productsBioactive analoguesMolecular scaffoldsCatalystFunctional groupsDrug analoguesPeptide sequencesRelevant moleculesDrug molecules
2024
Structure and mechanism of the human CTDNEP1–NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology
Gao S, Rodríguez J, Bahmanyar S, Airola M. Structure and mechanism of the human CTDNEP1–NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321167121. PMID: 38776370, PMCID: PMC11145253, DOI: 10.1073/pnas.2321167121.Peer-Reviewed Original ResearchConceptsProtein phosphatase complexPhosphatase complexER membrane biogenesisHigh-resolution crystal structuresProtein serine/threonine phosphatasesCancer-associated mutationsDevelopment of medulloblastomaMembrane biogenesisSubstrate recognitionER expansionActive siteRegulatory subunitSubstrate peptideMammalian cellsSerine/threonine phosphataseIdentical phenotypesArg residuesMolecular detailsSubunit 1Phosphatase 1Inactivating mutationsPeptide sequencesAggressive childhood cancerMutationsPhosphatase activity
2022
Glycoproteomics
Bagdonaite I, Malaker S, Polasky D, Riley N, Schjoldager K, Vakhrushev S, Halim A, Aoki-Kinoshita K, Nesvizhskii A, Bertozzi C, Wandall H, Parker B, Thaysen-Andersen M, Scott N. Glycoproteomics. Nature Reviews Methods Primers 2022, 2: 48. DOI: 10.1038/s43586-022-00128-4.Peer-Reviewed Original ResearchGlycan structuresMass spectrometryPost-translational additionIntact glycopeptide analysisSite of modificationProtein glycosylationProtein modificationBioinformatics platformBiological processesGlycopeptide analysisMS fragmentationGlycoproteomic methodsGlycoproteomicsGlycosylationProtein isolationProteolytic digestionPeptide sequencesSystem-wide contextStudy of glycopeptidesPrimersRecent advancesExciting fieldProteinGlycansSpectrometry
2021
Multifunctional Thio-Stabilized Gold Nanoparticles for Near-Infrared Fluorescence Detection and Imaging of Activated Caspase-3.
Fan J, Cheney P, Bloch S, Xu B, Liang K, Odonkor C, Edwards W, Basak S, Mintz R, Biswas P, Achilefu S. Multifunctional Thio-Stabilized Gold Nanoparticles for Near-Infrared Fluorescence Detection and Imaging of Activated Caspase-3. Current Analytical Chemistry 2021, 17: 1182-1193. PMID: 34393690, PMCID: PMC8356907, DOI: 10.2174/1573411017999210112175743.Peer-Reviewed Original ResearchNIR fluorescent probeSpherical AuNPsGold nanoparticlesFluorescent probeAqueous mediaFluorescence enhancementDetection sensitivityNIR fluorescence enhancementTransmission electron microscopyFluorescence quenching efficiencyDye-labeled peptidesSignificant fluorescence enhancementFluorescence-quenching propertyRGD peptide sequenceActivatable NIR fluorescent probeHigh detection sensitivityFluorescence molecular probesNIR fluorescence spectroscopyMultifunctional AuNPsInfrared (NIR) fluorescent probeMultifunctional constructsNIR laser sourcePeptide sequencesOrganic dyesAuNPs
2018
Divergent Stereoselectivity in Phosphothreonine (pThr)-Catalyzed Reductive Aminations of 3‑Amidocyclohexanones
Shugrue C, Featherston AL, Lackner RM, Lin A, Miller SJ. Divergent Stereoselectivity in Phosphothreonine (pThr)-Catalyzed Reductive Aminations of 3‑Amidocyclohexanones. The Journal Of Organic Chemistry 2018, 83: 4491-4504. PMID: 29547285, PMCID: PMC5963540, DOI: 10.1021/acs.joc.8b00207.Peer-Reviewed Original ResearchConceptsReductive aminationNumerous reactive sitesPeptide catalystsParallel kinetic resolutionDFT calculationsNMR studiesReactive sitesDivergent selectivitySecondary interactionsNatural productsKinetic resolutionCatalystAminationDivergent stereoselectivitiesCatalyzed Reductive AminationPeptide sequencesSelectivityComplex substratesSubstrateDiastereoselectivityStereoselectivityProductsReactivityPhosphopeptidesPhosphothreonine
2015
Functional characterization of NAT/NCS2 proteins of Aspergillus brasiliensis reveals a genuine xanthine–uric acid transporter and an intrinsically misfolded polypeptide
Krypotou E, Scazzocchio C, Diallinas G. Functional characterization of NAT/NCS2 proteins of Aspergillus brasiliensis reveals a genuine xanthine–uric acid transporter and an intrinsically misfolded polypeptide. Fungal Genetics And Biology 2015, 75: 56-63. PMID: 25639910, DOI: 10.1016/j.fgb.2015.01.009.Peer-Reviewed Original ResearchConceptsNucleobase-ascorbate transporterUptake of purinesAcid transportAspergillus nidulansMisfolded polypeptidesER-retainedGFP tagMisfolded proteinsHeterologous expressionEvolutionary implicationsInactive proteinPutative transportersAspergillus brasiliensisFunctional characterizationTurned-overPlasma membranePeptide sequencesIn silicoProteinSubfamilyAspergillusTransport functionLow affinityHigher affinityVacuoles
2014
X‑ray Crystal Structure of Teicoplanin A2‑2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy
Han S, Le BV, Hajare HS, Baxter RH, Miller SJ. X‑ray Crystal Structure of Teicoplanin A2‑2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy. The Journal Of Organic Chemistry 2014, 79: 8550-8556. PMID: 25147913, PMCID: PMC4168787, DOI: 10.1021/jo501625f.Peer-Reviewed Original ResearchConceptsX-ray crystal structureTeicoplanin A2-2Crystal structurePeptide-based catalystsProtein ligation (IPL) techniqueCatalyst moietyPeptide catalystsComplex crystal structureMolecular arrangementN-methylimidazoleNucleophilic nitrogenObserved selectivitySugar ringCatalystPeptide sequencesT4 lysozymeDerivativesN-acetylglucosaminePhosphorylation reactionMoietyStructureSelectivityProtein strategyA2-2ComplexesMolecular Mechanism of Selective Binding of Peptides to Silicon Surface
Ramakrishnan SK, Martin M, Cloitre T, Firlej L, Gergely C. Molecular Mechanism of Selective Binding of Peptides to Silicon Surface. Journal Of Chemical Information And Modeling 2014, 54: 2117-2126. PMID: 24936969, DOI: 10.1021/ci500260v.Peer-Reviewed Original ResearchConceptsMaterial-specific peptidesAdsorption energy calculationsExtensive recent research effortsInorganic surfacesAffinity of peptidesAdsorption mechanismPeptide conformationEnergy calculationsSelective bindingMolecular interactionsAmino acidsN-type silicon semiconductorSilicon surfacePeptide sequencesConformationAcidPeptidesAffinitySurfacePhage display technologySilicon semiconductorsRecent research effortsIndividual amino acidsDisplay technologyScanning analysisDistinct BimBH3 (BimSAHB) Stapled Peptides for Structural and Cellular Studies
Bird GH, Gavathiotis E, LaBelle JL, Katz SG, Walensky LD. Distinct BimBH3 (BimSAHB) Stapled Peptides for Structural and Cellular Studies. ACS Chemical Biology 2014, 9: 831-837. PMID: 24358963, PMCID: PMC4131438, DOI: 10.1021/cb4003305.Peer-Reviewed Original Research
2012
Approaches in extracellular matrix engineering for determination of adhesion molecule mediated single cell function
Ayres-Sander C, Gonzalez A. Approaches in extracellular matrix engineering for determination of adhesion molecule mediated single cell function. Frontiers In Biology 2012, 8: 32-49. DOI: 10.1007/s11515-012-1199-x.Peer-Reviewed Original ResearchCell-ECM interactionsCell adhesion moleculeExtracellular matrixThree-dimensional matrixCellular processesNative extracellular matrixAdhesion moleculesTwo-dimensional substratesSingle cell functionCell functionCell movementECM proteinsNative proteinPeptide sequencesIntegrin expressionBioactive peptide sequencesCell functionalityMatrix engineeringProteinHuman tissuesCellsDiseased tissuesCadherinMoleculesTissue
2010
Induction of cortical endoplasmic reticulum by dimerization of a coatomer-binding peptide anchored to endoplasmic reticulum membranes
Lavieu G, Orci L, Shi L, Geiling M, Ravazzola M, Wieland F, Cosson P, Rothman JE. Induction of cortical endoplasmic reticulum by dimerization of a coatomer-binding peptide anchored to endoplasmic reticulum membranes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 6876-6881. PMID: 20351264, PMCID: PMC2872465, DOI: 10.1073/pnas.1002536107.Peer-Reviewed Original ResearchConceptsCortical endoplasmic reticulumMost animal cell typesEndoplasmic reticulumMicrotubule plus-end binding protein EB1Animal cell typesLysine-rich tailRNA interference experimentsEndoplasmic reticulum membraneCoatomer bindingSTIM proteinsMammalian cellsProtein EB1Transmembrane proteinC-terminal peptidePlasma membraneYeast cellsReticulum membraneCell typesPeptide bindsProteinPeptide sequencesIst2ReticulumInterference experimentsDimerization
2002
Synthesis and Characterization of the First Potent Inhibitor of Yapsin 1 IMPLICATIONS FOR THE STUDY OF YAPSIN-LIKE ENZYMES*
Cawley NX, Chino M, Maldonado A, Rodriguez YM, Loh YP, Ellman JA. Synthesis and Characterization of the First Potent Inhibitor of Yapsin 1 IMPLICATIONS FOR THE STUDY OF YAPSIN-LIKE ENZYMES*. Journal Of Biological Chemistry 2002, 278: 5523-5530. PMID: 12468548, DOI: 10.1074/jbc.m207230200.Peer-Reviewed Original ResearchConceptsYapsin 1Aspartyl proteaseN-terminal amino acid sequence analysisYeast expression systemAmino acid sequence analysisSecreted aspartyl proteaseAcid sequence analysisPotent peptidic inhibitorsSingle-step purificationBasic residuesExpression systemSequence analysisApparent homogeneityPeptidic inhibitorsHuman pathogensPeptide sequencesNonmammalian sourcesFirst potent inhibitorPotent inhibitorProteaseEnzymeCandida albicansSequenceInhibitorsPurification
1991
Construction and expression of transforming gene resulting from fusion of basic fibroblast growth factor gene with signal peptide sequence
Rogelj S, Stern D, Klagsbrun M. Construction and expression of transforming gene resulting from fusion of basic fibroblast growth factor gene with signal peptide sequence. Methods In Enzymology 1991, 198: 117-124. PMID: 1906971, DOI: 10.1016/0076-6879(91)98013-v.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBrainCattleCell LineCell Transformation, NeoplasticChimeraCloning, MolecularFibroblast Growth Factor 2Genes, SyntheticGenetic VectorsImmunoglobulin Heavy ChainsMiceMolecular Sequence DataProtein Sorting SignalsRecombinant Fusion ProteinsRecombinant ProteinsRestriction MappingTransfection
1988
Comparison of nonerythroid alpha-spectrin genes reveals strict homology among diverse species.
Leto T, Fortugno-Erikson D, Barton D, Yang-Feng T, Francke U, Harris A, Morrow J, Marchesi V, Benz E. Comparison of nonerythroid alpha-spectrin genes reveals strict homology among diverse species. Molecular And Cellular Biology 1988, 8: 1-9. PMID: 3336352, PMCID: PMC363070, DOI: 10.1128/mcb.8.1.1.Peer-Reviewed Original ResearchConceptsAlpha-spectrin geneErythroid alpha-spectrin geneHuman chromosome 9Alpha-spectrin chainComparison of sequencesCarboxy-terminal sequenceErythroid genesDiverse speciesExpression libraryChromosome 1Hydrophobic residuesErythroid spectrinAlpha-spectrinFilamentous proteinsFunctional sitesGenesChromosome 9Human cloneStrict homologyRepeat patternCell membraneInvariant tryptophanSpectrinPeptide sequencesCDNAComparison of Nonerythroid α-Spectrin Genes Reveals Strict Homology among Diverse Species
Leto T, Fortugno-Erikson D, Barton D, Yang-Feng T, Francke U, Harris A, Morrow J, Marchesi V, Benz E. Comparison of Nonerythroid α-Spectrin Genes Reveals Strict Homology among Diverse Species. Molecular And Cellular Biology 1988, 8: 1-9. DOI: 10.1128/mcb.8.1.1-9.1988.Peer-Reviewed Original ResearchΑ-spectrin geneHuman chromosome 9Comparison of sequencesCarboxy-terminal sequenceErythroid genesDiverse speciesSpectrin geneExpression libraryChromosome 1Hydrophobic residuesErythroid spectrinFilamentous proteinsFunctional sitesGenesChromosome 9Human cloneStrict homologyΑ-spectrinRepeat patternCell membraneInvariant tryptophanSpectrinPeptide sequencesCDNASpecies
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