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 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 pairsOrganellesModeling the Effects of Varying the Ti Concentration on the Mechanical Properties of Cu–Ti Alloys
Fotopoulos V, O’Hern C, Shattuck M, Shluger A. Modeling the Effects of Varying the Ti Concentration on the Mechanical Properties of Cu–Ti Alloys. ACS Omega 2024, 9: 10286-10298. PMID: 38463266, PMCID: PMC10918840, DOI: 10.1021/acsomega.3c07561.Peer-Reviewed Original ResearchModified embedded atom methodDensity functional theoryInclusion of TiMolecular dynamicsTi atomsUniaxial tension deformationPolycrystalline CuDensity functional theory calculationsCu cellsPartial Shockley dislocationsMechanical propertiesGrain boundaries of CuGrain boundariesEmbedded atom methodEngineering of grain boundariesFraction of Ti atomsTensile stressLevel of local deformationLocal charge densityShockley dislocationsFunctional theoryAtom methodUniaxial tensile loadingMD simulationsInteratomic potentials
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