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 ResearchMeSH KeywordsCrystallizationEscherichia coliHydrogen BondingHydrophobic and Hydrophilic InteractionsMolecular Dynamics SimulationProtein BindingProtein ConformationProtein EngineeringProteinsSolventsSurface PropertiesThreonineConceptsProtein-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 simulationsResiduesComparing 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 ResearchMeSH KeywordsAmino AcidsBinding SitesDatabases, ProteinHydrophobic and Hydrophilic InteractionsMembrane ProteinsModels, MolecularMutationProtein BindingProtein Interaction MappingProtein Structure, SecondarySolubilitySurface PropertiesConceptsProtein-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 structureMetSMethionineSerTyrSelenomethionine
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 ResearchComputational BiologyHydrophobic and Hydrophilic InteractionsIsoleucineLeucineMolecular Dynamics SimulationNuclear Magnetic Resonance, BiomolecularProtein ConformationProtein FoldingProteins
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 ResearchCalibrationComputer SimulationFluorescence Resonance Energy TransferHydrophobic and Hydrophilic InteractionsIntrinsically Disordered ProteinsModels, MolecularProtein ConformationStatic ElectricityPredicting 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 ResearchMeSH KeywordsAlgorithmsAmino Acid SequenceAmino AcidsAmino Acids, AromaticAnimalsDatabases, ProteinDipeptidesHumansHydrophobic and Hydrophilic InteractionsModels, MolecularOligopeptidesProtein ConformationProtein EngineeringProteinsStereoisomerism