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
2020
Using physical features of protein core packing to distinguish real proteins from decoys
Grigas AT, Mei Z, Treado JD, Levine ZA, Regan L, O'Hern CS. Using physical features of protein core packing to distinguish real proteins from decoys. Protein Science 2020, 29: 1931-1944. PMID: 32710566, PMCID: PMC7454528, DOI: 10.1002/pro.3914.Peer-Reviewed Original ResearchConceptsProtein structureReal protein structuresProtein coreReal proteinsAmino acid sequenceProtein core packingProtein structure predictionBiennial Critical AssessmentSet of decoysAcid sequenceProtein packingHydrophobic residuesCore packingStructure Prediction competitionTarget sequenceStructure predictionDecoy structuresProteinHydrophobic coreDecoysResiduesProtein Structure Prediction competitionsKey physical featuresSequenceImportant physical features
2018
Comparing side chain packing in soluble proteins, protein‐protein interfaces, and transmembrane proteins
Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein‐protein interfaces, and transmembrane proteins. Proteins Structure Function And Bioinformatics 2018, 86: 581-591. PMID: 29427530, PMCID: PMC5912992, DOI: 10.1002/prot.25479.Peer-Reviewed Original ResearchConceptsProtein-protein interfacesClass of proteinsTransmembrane proteinSoluble proteinSolvent-inaccessible coreMembrane proteinsProtein classesCore residuesProtein-protein interactionsHigh-resolution crystal structuresHydrophobic core mutationsRelative solvent accessibilityAnalysis of mutationsSide-chain packingProtein complexesNon-core regionsSolvent accessibilityProteinSide-chain conformationsCore mutationsMutationsResiduesSide chains
2011
Revisiting the Ramachandran plot from a new angle
Zhou AQ, O'Hern CS, Regan L. Revisiting the Ramachandran plot from a new angle. Protein Science 2011, 20: 1166-1171. PMID: 21538644, PMCID: PMC3149190, DOI: 10.1002/pro.644.Peer-Reviewed Original Research
2008
Non-random-coil Behavior as a Consequence of Extensive PPII Structure in the Denatured State
Cortajarena AL, Lois G, Sherman E, O'Hern CS, Regan L, Haran G. Non-random-coil Behavior as a Consequence of Extensive PPII Structure in the Denatured State. Journal Of Molecular Biology 2008, 382: 203-212. PMID: 18644382, PMCID: PMC2603145, DOI: 10.1016/j.jmb.2008.07.005.Peer-Reviewed Original ResearchConceptsPolyproline II helical structureRandom coil polymersKinetics of foldingAggregation diseasesFluorescence correlation spectroscopyRepeat proteinsUnfolded proteinsResidual structureCoil polymersNonnative structuresSimple polymer modelIdentical domainsPolyproline IIPolypeptide chainPPII structureCorrelation spectroscopyUnfolded stateProteinHelical structureRandom-coil statisticsDenatured statePolymer modelUnforeseen potentialCoil behaviorMisfolding