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 acidsAmino
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 featuresAnalyses of protein cores reveal fundamental differences between solution and crystal structures
Mei Z, Treado JD, Grigas AT, Levine ZA, Regan L, O'Hern CS. Analyses of protein cores reveal fundamental differences between solution and crystal structures. Proteins Structure Function And Bioinformatics 2020, 88: 1154-1161. PMID: 32105366, PMCID: PMC7415476, DOI: 10.1002/prot.25884.Peer-Reviewed Original ResearchConceptsProtein structureX-ray crystallographyProtein coreHigh-quality protein structuresCore amino acidsSide-chain dihedral anglesNMR structureCore residuesAmino acidsCrystal structureStructural differencesCrystallographyNMR spectroscopyResiduesSquare deviationPacking-generation protocolsFundamental differencesPhysical basisContrast
2019
Void distributions reveal structural link between jammed packings and protein cores
Treado JD, Mei Z, Regan L, O'Hern CS. Void distributions reveal structural link between jammed packings and protein cores. Physical Review E 2019, 99: 022416. PMID: 30934238, PMCID: PMC6902428, DOI: 10.1103/physreve.99.022416.Peer-Reviewed Original Research
2018
A threonine zipper that mediates protein–protein interactions: Structure and prediction
Oi C, Treado JD, Levine ZA, Lim CS, Knecht KM, Xiong Y, O'Hern CS, Regan L. A threonine zipper that mediates protein–protein interactions: Structure and prediction. Protein Science 2018, 27: 1969-1977. PMID: 30198622, PMCID: PMC6201716, DOI: 10.1002/pro.3505.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProtein-protein interfacesZipper structureBeta-barrel proteinsIntermonomer hydrogen bondsBarrel proteinsThr residueSide-chain dihedral anglesBiotechnological applicationsProtein interfacesMolecular dynamics simulationsDihedral angleSide-chain conformationsThrH-bondingHydrogen bondsChain conformationMD simulationsSteric constraintsDrug discoveryDynamics simulationsResidues
2016
Understanding the physical basis for the side‐chain conformational preferences of methionine
Virrueta A, O'Hern CS, Regan L. Understanding the physical basis for the side‐chain conformational preferences of methionine. Proteins Structure Function And Bioinformatics 2016, 84: 900-911. PMID: 26917446, DOI: 10.1002/prot.25026.Peer-Reviewed Original ResearchConceptsSide-chain dihedral angle distributionsAmino acidsHigh-resolution protein crystal structuresProtein-protein interfacesMet side chainsStructure of MetProtein crystal structuresVersatile amino acidDihedral angle distributionsProtein structureProtein coreIleSide chainsLeuValPheAcidThrObserved distributionCrystal structureMetSMethionineSerTyrSelenomethionineRandom close packing in protein cores
Gaines JC, Smith WW, Regan L, O'Hern CS. Random close packing in protein cores. Physical Review E 2016, 93: 032415. PMID: 27078398, DOI: 10.1103/physreve.93.032415.Peer-Reviewed Original Research
2015
Equilibrium transitions between side‐chain conformations in leucine and isoleucine
Caballero D, Smith WW, O'Hern CS, Regan L. Equilibrium transitions between side‐chain conformations in leucine and isoleucine. Proteins Structure Function And Bioinformatics 2015, 83: 1488-1499. PMID: 26018846, DOI: 10.1002/prot.24837.Peer-Reviewed Original Research
2014
Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models
Zhou AQ, O'Hern CS, Regan L. Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models. Proteins Structure Function And Bioinformatics 2014, 82: 2574-2584. PMID: 24912976, DOI: 10.1002/prot.24621.Peer-Reviewed Original Research
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