2025
Eukaryotic Microproteins
Jaunbocus N, Ebenki V, Su H, Slavoff S. Eukaryotic Microproteins. Annual Review Of Biochemistry 2025, 94: 1-28. PMID: 40245354, PMCID: PMC12207985, DOI: 10.1146/annurev-biochem-080124-012840.Peer-Reviewed Original ResearchRelationship between Immunogenicity and Protein Structure at Amino Acid Substitution Sites of Blood Group Antigens
Howe J, Stack G. Relationship between Immunogenicity and Protein Structure at Amino Acid Substitution Sites of Blood Group Antigens. Blood 2025 PMID: 40163810, DOI: 10.1182/blood.2024025071.Peer-Reviewed Original ResearchProtein structureAa substitutionsBlood group antigensThree-dimensional protein structuresAmino acid substitution sitesAmino acidsGroup antigensSurface-accessible loopsInvestigating protein structureStructure predictionProtein regionsB strandsTertiary structureFlexible regionsInformatics analysisAlphaFold2ProteinAminoImmunogenic antigensSitesDeterminants of immunogenicitySubstitutionPolypeptideConfidence scoresDisordered coilsAutosomal dominant SLURP1 variants cause palmoplantar keratoderma and progressive symmetric erythrokeratoderma
Jiang X, Mortlock R, Lomakin I, Zhou J, Hu R, Cossio M, Bunick C, Choate K. Autosomal dominant SLURP1 variants cause palmoplantar keratoderma and progressive symmetric erythrokeratoderma. British Journal Of Dermatology 2025, 192: 896-906. PMID: 39913669, PMCID: PMC12036768, DOI: 10.1093/bjd/ljaf049.Peer-Reviewed Original ResearchProgressive symmetric erythrokeratodermaAmino acidsGenetic variantsPathogenic variantsNF-kB signalingPalmoplantar keratodermaSpatial transcriptomicsPatient keratinocytesWhole-exome sequencingSLURP1 expressionIn silico predictionVariant consequencesSignal peptideMal de MeledaExome sequencingSecreted proteinsHealthy control cellsInnate immune activationIn silico modelsPhenotypic spectrumControl cellsConfirmed with mass spectrometryAminoAutosomal dominant transmissionTranscriptomeProtein codes promote selective subcellular compartmentalization
Kilgore H, Chinn I, Mikhael P, Mitnikov I, Van Dongen C, Zylberberg G, Afeyan L, Banani S, Wilson-Hawken S, Lee T, Barzilay R, Young R. Protein codes promote selective subcellular compartmentalization. Science 2025, 387: 1095-1101. PMID: 39913643, PMCID: PMC12034300, DOI: 10.1126/science.adq2634.Peer-Reviewed Original ResearchConceptsProtein sequencesSubcellular compartmentsDiverse subcellular compartmentsProtein language modelsAmino acid sequenceProtein codingAcid sequenceSubcellular localizationDiverse proteinsHuman proteinsSubcellular compartmentalizationFolding codePathological mutationsCompartment localizationProteinSequenceCompartmentMutationsAminoNucleolusCompartmentalizationCellsEngineering a genomically recoded organism with one stop codon
Grome M, Nguyen M, Moonan D, Mohler K, Gurara K, Wang S, Hemez C, Stenton B, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs F. Engineering a genomically recoded organism with one stop codon. Nature 2025, 639: 512-521. PMID: 39910296, PMCID: PMC11903333, DOI: 10.1038/s41586-024-08501-x.Peer-Reviewed Original Research
2024
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33: e5219. PMID: 39548730, PMCID: PMC11568256, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchConceptsForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesProteins in vivoForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesDynamics in vivoStructures in vivoInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoIdentifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33 PMID: 38800659, PMCID: PMC11118665, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoMD simulationsFRET pairsOrganelles
2023
A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations
Loney R, Delesalle V, Chaudry B, Czerpak M, Guffey A, Goubet-McCall L, McCarty M, Strine M, Tanke N, Vill A, Krukonis G. A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations. Viruses 2023, 15: 2267. PMID: 38005943, PMCID: PMC10674732, DOI: 10.3390/v15112267.Peer-Reviewed Original ResearchEpistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance
Ogbunugafor C, Guerrero R, Miller-Dickson M, Shakhnovich E, Shoulders M. Epistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance. Physical Review E 2023, 108: 054408. PMID: 38115433, PMCID: PMC10935598, DOI: 10.1103/physreve.108.054408.Peer-Reviewed Original ResearchConceptsProtein spaceAmino acid sequenceAmino acid substitutionsGenotype-phenotype mapAcid sequenceProtein variantsBacterial enzymesAcid substitutionsProtein phenotypesEngineered proteinsDHFR enzymeProteinEpistasisDrug resistanceMutationsAminoProcess of evolutionEnzymePhenotypeTraitsPleiotropySequenceVariantsBiophysical components
2014
Organosilatrane building blocks
Brennan B, Gust D, Brudvig G. Organosilatrane building blocks. Tetrahedron Letters 2014, 55: 1062-1064. DOI: 10.1016/j.tetlet.2013.12.082.Peer-Reviewed Original ResearchBoronic estersFunctional groupsSilica gel purificationFurther synthetic manipulationsAlkynyl functional groupBuilding blocksUseful building blocksPinacol boronic estersSynthetic manipulationsCoupling reactionReactive aminoEthynyl analoguesReactionEstersAnaloguesPalladiumBromoMoleculesAminoPurification
2004
Asymmetric α-Alkylation of N ‘-tert-Butanesulfinyl Amidines. Application to the Total Synthesis of (6R,7S)-7-Amino-7,8-dihydro-α-bisabolene
Kochi T, Ellman JA. Asymmetric α-Alkylation of N ‘-tert-Butanesulfinyl Amidines. Application to the Total Synthesis of (6R,7S)-7-Amino-7,8-dihydro-α-bisabolene. Journal Of The American Chemical Society 2004, 126: 15652-15653. PMID: 15571381, DOI: 10.1021/ja044753n.Peer-Reviewed Original Research
1999
Towards subunit-specific proteasome inhibitors: synthesis and evaluation of peptide α', β'-epoxyketones
Elofsson M, Splittgerber U, Myung J, Mohan R, Crews C. Towards subunit-specific proteasome inhibitors: synthesis and evaluation of peptide α', β'-epoxyketones. Cell Chemical Biology 1999, 6: 811-822. PMID: 10574782, DOI: 10.1016/s1074-5521(99)80128-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAortaCattleCell DivisionCells, CulturedChymotrypsinCysteine EndopeptidasesCysteine Proteinase InhibitorsDrug DesignEndothelium, VascularEpoxy CompoundsGlutamatesIndicators and ReagentsIrritantsKineticsMacromolecular SubstancesMiceMolecular ConformationMultienzyme ComplexesPeptidesProteasome Endopeptidase ComplexTrypsinConceptsCatalytic activityMolecular probesAcetylated peptidesExcellent selectivityPotent proteasome inhibitorVivo anti-inflammatory activityMost compoundsMajor catalytic activityChymotrypsin-like activityPeptide αAromatic amino acidsEpoxyketonesAminoP2-P4Multicatalytic protease complexPeptidesAnti-inflammatory activitySelectivityProbeLarge multicatalytic protease complexesProteasome inhibitorsAmino acidsSynthesisCompoundsComplexes
1982
[11] The identification of helical segments in the polypeptide chain of bacteriorhodopsin
Engelman D, Goldman A, Steitz T. [11] The identification of helical segments in the polypeptide chain of bacteriorhodopsin. Methods In Enzymology 1982, 88: 81-88. DOI: 10.1016/0076-6879(82)88014-2.Peer-Reviewed Original ResearchLysine amino groupsAqueous surfaceAqueous environmentAmino groupsModification of interestPurple membrane fragmentsElectron microscopyReagentsHelical segmentsMoleculesBacteriorhodopsin structureHelical regionSingle lysineSoluble enzymePolypeptide chainCyanogen bromide fragmentsDerivitizationProteolytic enzymesKind of modificationHelixMembraneMembrane fragmentsComplexesAminoModification
1978
STUDIES OF THE STRUCTURE OF THE HUMAN Ia-LIKE ANTIGEN11This research is supported by grants from the U.S. Public Health Service (AI-10736 and AI-09576).
Springer T, Kaufman J, Terhorst C, Strominger J. STUDIES OF THE STRUCTURE OF THE HUMAN Ia-LIKE ANTIGEN11This research is supported by grants from the U.S. Public Health Service (AI-10736 and AI-09576). 1978, 229-234. DOI: 10.1016/b978-0-12-483260-2.50029-x.Peer-Reviewed Original Research
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