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
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 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 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