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
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
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 ResearchMeSH KeywordsDipeptidesElectronsHydrogen BondingHydrophobic and Hydrophilic InteractionsMethionineModels, MolecularProtein ConformationProteinsConceptsSide-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
2014
Calibrated Langevin-dynamics simulations of intrinsically disordered proteins
Smith WW, Ho PY, O'Hern CS. Calibrated Langevin-dynamics simulations of intrinsically disordered proteins. Physical Review E 2014, 90: 042709. PMID: 25375525, DOI: 10.1103/physreve.90.042709.Peer-Reviewed Original ResearchPredicting 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 ResearchIntrinsic α‐helical and β‐sheet conformational preferences: A computational case study of alanine
Caballero D, Määttä J, Zhou AQ, Sammalkorpi M, O'Hern CS, Regan L. Intrinsic α‐helical and β‐sheet conformational preferences: A computational case study of alanine. Protein Science 2014, 23: 970-980. PMID: 24753338, PMCID: PMC4088981, DOI: 10.1002/pro.2481.Peer-Reviewed Original Research
2012
Calculations of the structure of basin volumes for mechanically stable packings
Ashwin SS, Blawzdziewicz J, O'Hern CS, Shattuck MD. Calculations of the structure of basin volumes for mechanically stable packings. Physical Review E 2012, 85: 061307. PMID: 23005086, DOI: 10.1103/physreve.85.061307.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationModels, ChemicalModels, MolecularMotionParticle SizeRheologyConceptsBasins of attractionMS packingsSystem size increasesFinite numberConfiguration spaceComplex geometric featuresInitial conditionsProfile functionGeometrical propertiesStable packingΓ distributionJammed systemsComputational methodsNovel computational methodSimple modelGeometric featuresFast quench ratesProbabilityComplex structureComputational model systemSmaller core volumeFrictionless particlesBasin volumeQuench rateSize increasesConstraints and vibrations in static packings of ellipsoidal particles
Schreck CF, Mailman M, Chakraborty B, O'Hern CS. Constraints and vibrations in static packings of ellipsoidal particles. Physical Review E 2012, 85: 061305. PMID: 23005084, DOI: 10.1103/physreve.85.061305.Peer-Reviewed Original ResearchConceptsStatic packingsEllipsoidal particlesFinite compressionMechanical propertiesStiffness matrixAspect ratioSpherical particlesHarmonic responseNumber of particlesAmorphous packingsParticlesAmplitude δPotential energy scalesMatrixInterparticle separationCompressionVibrationModePackingContact numberContactJammingThe Power of Hard-Sphere Models: Explaining Side-Chain Dihedral Angle Distributions of Thr and Val
Zhou AQ, O'Hern CS, Regan L. The Power of Hard-Sphere Models: Explaining Side-Chain Dihedral Angle Distributions of Thr and Val. Biophysical Journal 2012, 102: 2345-2352. PMID: 22677388, PMCID: PMC3353012, DOI: 10.1016/j.bpj.2012.01.061.Peer-Reviewed Original ResearchContact percolation transition in athermal particulate systems
Shen T, O'Hern CS, Shattuck MD. Contact percolation transition in athermal particulate systems. Physical Review E 2012, 85: 011308. PMID: 22400566, DOI: 10.1103/physreve.85.011308.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationHot TemperatureModels, ChemicalModels, MolecularPhase TransitionSurface PropertiesConceptsBidisperse particle size distributionsPercolation transitionCompression stepParticle size distributionMechanical responseSystem-spanning clusterDisplacement fieldDilute configurationsApplied stressCooperative particle motionParticle motionIsotropic compressionPercolating networkParticulate systemsElastic energyFrictionless particlesTwo-dimensional systemsUnjammed stateSize distributionDynamical matrixJammed systemsAdjacency matrixSuccessive compressionSpatial dimensionsComputer simulations
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