2024
Practical Guide for Implementing Cryogenic Electron Microscopy Structure Determination in Dermatology Research
Lomakin I, Devarkar S, Freniere C, Bunick C. Practical Guide for Implementing Cryogenic Electron Microscopy Structure Determination in Dermatology Research. Journal Of Investigative Dermatology 2024, 145: 22-31. PMID: 39601740, PMCID: PMC11748023, DOI: 10.1016/j.jid.2024.10.594.Peer-Reviewed Original Research
2022
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 2022, 19: 1109-1115. PMID: 36038728, DOI: 10.1038/s41592-022-01585-1.Peer-Reviewed Original ResearchConceptsStructure comparisonStructural biology studiesStructure alignmentDNA dockingMacromolecular complexesBiology studiesMultiple structure alignmentNucleic acidsDifferent moleculesRNAProteinFundamental importanceDNAComplex structureDockingUniversal protocolAlignmentExtensive optimizationFunctionComplexes
2021
Single-molecule manipulation of macromolecules on GUV or SUV membranes using optical tweezers
Wang Y, Kumar A, Jin H, Zhang Y. Single-molecule manipulation of macromolecules on GUV or SUV membranes using optical tweezers. Biophysical Journal 2021, 120: 5454-5465. PMID: 34813728, PMCID: PMC8715244, DOI: 10.1016/j.bpj.2021.11.2884.Peer-Reviewed Original ResearchMeSH KeywordsMacromolecular SubstancesMembrane ProteinsMembranesOptical TweezersUnilamellar LiposomesConceptsOptical tweezersOptical trappingSingle-molecule manipulation studiesMembrane protein dynamicsMembrane proteinsSingle-molecule manipulationMembrane tensionTweezersHigh membrane tensionProtein conformational changesModel membranesMembrane bindingProtein dynamicsC2AB domainConformational changesManipulation studiesSUV membranesReversible foldingSmall unilamellar vesiclesGUVsTrappingDNA hairpinsUnilamellar vesiclesProteinMembraneIdentification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps
Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps. Acta Crystallographica Section D, Structural Biology 2021, 77: 534-539. PMID: 33825713, PMCID: PMC8025889, DOI: 10.1107/s2059798321001893.Peer-Reviewed Original ResearchMeSH KeywordsCryoelectron MicroscopyCrystallography, X-RayHumansIonsMacromolecular SubstancesModels, MolecularNucleotidesRibosomes
2020
Contribution of macromolecules to brain 1H MR spectra: Experts' consensus recommendations
Cudalbu C, Behar KL, Bhattacharyya PK, Bogner W, Borbath T, de Graaf R, Gruetter R, Henning A, Juchem C, Kreis R, Lee P, Lei H, Marjańska M, Mekle R, Murali‐Manohar S, Považan M, Rackayová V, Simicic D, Slotboom J, Soher BJ, Starčuk Z, Starčuková J, Tkáč I, Williams S, Wilson M, Wright AM, Xin L, Mlynárik V. Contribution of macromolecules to brain 1H MR spectra: Experts' consensus recommendations. NMR In Biomedicine 2020, 34: e4393. PMID: 33236818, PMCID: PMC10072289, DOI: 10.1002/nbm.4393.Peer-Reviewed Original ResearchSystems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing
Rukhlenko O, Kholodenko B, Kolch W. Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing. Current Opinion In Structural Biology 2020, 67: 61-68. PMID: 33126139, PMCID: PMC8062579, DOI: 10.1016/j.sbi.2020.09.007.Peer-Reviewed Original ResearchMeSH KeywordsHumansMacromolecular SubstancesMAP Kinase Signaling SystemNeoplasmsSignal TransductionSystems BiologyConceptsProtein assembliesProtein complex dynamicsDynamic protein assembliesMacromolecular protein assembliesSignal transduction networksSystems biology approachMEK-ERK pathwayProtein complexesTransduction networksCellular processesBiology approachMolecular machinesRAS-RAFOncogenic mutationsStructural studiesDrug resistanceTemporal dynamicsAssemblyRecent progressTumorigenesisMutationsPicture highlightsFine tuningPathwayDynamic processTrends in Therapeutic Conjugates: Bench to Clinic
Rudra A, Li J, Shakur R, Bhagchandani S, Langer R. Trends in Therapeutic Conjugates: Bench to Clinic. Bioconjugate Chemistry 2020, 31: 462-473. PMID: 31990184, DOI: 10.1021/acs.bioconjchem.9b00828.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDrug TherapyHumansMacromolecular SubstancesMolecular Targeted TherapyPeptide HormonesPharmaceutical PreparationsTranslational Research, Biomedical
2019
Synaptic vesicle fusion: today and beyond
Brose N, Brunger A, Cafiso D, Chapman ER, Diao J, Hughson FM, Jackson MB, Jahn R, Lindau M, Ma C, Rizo J, Shin YK, Söllner TH, Tamm L, Yoon TY, Zhang Y. Synaptic vesicle fusion: today and beyond. Nature Structural & Molecular Biology 2019, 26: 663-668. PMID: 31384060, DOI: 10.1038/s41594-019-0277-z.Peer-Reviewed Original ResearchAnimalsCalciumCryoelectron MicroscopyEndocytosisExocytosisHumansMacromolecular SubstancesMembrane FusionMembrane LipidsMembrane ProteinsNerve Tissue ProteinsNeurophysiologyNeurotransmitter AgentsOptical TweezersProtein Interaction MappingSingle Molecule ImagingSNARE ProteinsSynaptic TransmissionSynaptic Vesicles
2018
Cell Volume Controls Protein Stability and Compactness of the Unfolded State
Wang Y, Sukenik S, Davis CM, Gruebele M. Cell Volume Controls Protein Stability and Compactness of the Unfolded State. The Journal Of Physical Chemistry B 2018, 122: 11762-11770. PMID: 30289261, DOI: 10.1021/acs.jpcb.8b08216.Peer-Reviewed Original ResearchMeSH KeywordsCalibrationCell Line, TumorCell SizeFluorescence Resonance Energy TransferHumansMacromolecular SubstancesOsmotic PressureProtein StabilityProtein UnfoldingProteinsTemperature
2017
Determination of chemical identity and occupancy from experimental density maps
Wang J. Determination of chemical identity and occupancy from experimental density maps. Protein Science 2017, 27: 411-420. PMID: 29027293, PMCID: PMC5775170, DOI: 10.1002/pro.3325.Peer-Reviewed Original ResearchConceptsCharge densityFourier transformElectrostatic potentialExperimental charge densitySolvent moleculesAtomic B-factorsElectron densityBasic electronic propertiesESP mapsProtein α-helixChemical identityActive siteElectronic propertiesLarge macromolecular complexesExperimental density mapsDensity mapsMoleculesVitreous iceMacromolecular complexesΑ-helixSmall protein subunitESP valuesTransformStructure factorSupercomplexesVisualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow
Ghim M, Alpresa P, Yang S, Braakman S, Gray S, Sherwin S, van Reeuwijk M, Weinberg P. Visualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow. AJP Heart And Circulatory Physiology 2017, 313: h959-h973. PMID: 28754719, PMCID: PMC5792200, DOI: 10.1152/ajpheart.00218.2017.Peer-Reviewed Original ResearchConceptsShear stressDifferent flow profilesType of flowTransverse stressesNumerical simulationsFlow profileFluid mechanical forcesShear profileShear vectorSolute transportTwo-pore theoryStatic conditionsFlowMacromolecule transportMechanical forcesTransportStressMicrovessel wallShearOrbital shakerStress metricsLong axisTracer distributionSimulationsExperimental charge density from electron microscopic maps
Wang J. Experimental charge density from electron microscopic maps. Protein Science 2017, 26: 1619-1626. PMID: 28543856, PMCID: PMC5521614, DOI: 10.1002/pro.3198.Peer-Reviewed Original Research
2016
FIRT: Filtered iterative reconstruction technique with information restoration
Chen Y, Zhang Y, Zhang K, Deng Y, Wang S, Zhang F, Sun F. FIRT: Filtered iterative reconstruction technique with information restoration. Journal Of Structural Biology 2016, 195: 49-61. PMID: 27134004, DOI: 10.1016/j.jsb.2016.04.015.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArtifactsCoat Protein Complex IDiffusionElectron Microscope TomographyImage Processing, Computer-AssistedLiverMacromolecular SubstancesRatsConceptsAlgebra reconstruction techniqueElectron tomographyLimited angular samplingBack-projection methodIterative image reconstruction algorithmImage reconstruction algorithmTomography applicationsBiological specimenIterative reconstruction techniqueAngular regionReconstruction techniqueRay artifactsExperimental dataAngular samplingReconstruction algorithmSmooth natureStructural detailsSub-volume averagingFilter techniqueData publication with the structural biology data grid supports live analysis
Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Christopher Fromme J, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P. Data publication with the structural biology data grid supports live analysis. Nature Communications 2016, 7: 10882. PMID: 26947396, PMCID: PMC4786681, DOI: 10.1038/ncomms10882.Peer-Reviewed Original ResearchMeSH KeywordsCrystallography, X-RayDatabases, GeneticInternetMacromolecular SubstancesPublicationsSoftwareConceptsData gridData publicationData setsGlobal data accessPrimary experimental data setsBiomedical data setsData accessExperimental data setsImage dataDissemination systemPilot collectionProcessing methodsGridSetData analysisAccessParadigm shiftDynamic bodyScientific publicationsSBDGServicesInformationCrystallographic data sets
2015
SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction
Dvornek NC, Sigworth FJ, Tagare HD. SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction. Journal Of Structural Biology 2015, 190: 200-214. PMID: 25839831, PMCID: PMC4453989, DOI: 10.1016/j.jsb.2015.03.009.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsCryoelectron MicroscopyImage Processing, Computer-AssistedLikelihood FunctionsMacromolecular SubstancesModels, MolecularModels, Theoretical
2014
Function and dynamics of macromolecular complexes explored by integrative structural and computational biology
Purdy M, Bennett B, McIntire W, Khan A, Kasson P, Yeager M. Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Current Opinion In Structural Biology 2014, 27: 138-148. PMID: 25238653, PMCID: PMC6387792, DOI: 10.1016/j.sbi.2014.08.006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsComputational BiologyHumansMacromolecular SubstancesProtein Structure, SecondaryProtein Structure, TertiaryRibosomesConceptsMacromolecular complexesX-ray crystallographyIntegrative structural biologyG protein complexProtein complexesStructural biologyMD simulationsMicrosecond MD simulationsFunctional dynamicsX-ray crystallographic dataMolecular dynamics simulationsComputational biologyBiologyNew insightsBiological systemsCrystallographic dataUnprecedented synergyDynamics simulationsCrystallographyComplexesFunctional propertiesRibosomesTransmembraneGPCRsAdrenergic receptors
2013
Spatial and numerical regulation of flagellar biosynthesis in polarly flagellated bacteria
Kazmierczak BI, Hendrixson DR. Spatial and numerical regulation of flagellar biosynthesis in polarly flagellated bacteria. Molecular Microbiology 2013, 88: 655-663. PMID: 23600726, PMCID: PMC3654036, DOI: 10.1111/mmi.12221.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaBacterial ProteinsFlagellaGene Expression Regulation, BacterialMacromolecular SubstancesMonomeric GTP-Binding ProteinsTrans-ActivatorsConceptsPolar flagellatesFlagellar assemblyProper cell divisionRotation of flagellaFlagellar biosynthesisFlagellation patternsGram-negative bacteriaPeritrichous flagellaOrganelle numberCell divisionCell biologyFlhGFlhFBacterial speciesBacterial cellsFlagellatesFlagellaDifferent bacteriaMechanistic insightsProteinBacteriaRecent findingsSpeciesSpecific activityDistinct patterns
2010
Recent Applications of Fluorescence Recovery after Photobleaching (FRAP) to Membrane Bio-Macromolecules
Rayan G, Guet J, Taulier N, Pincet F, Urbach W. Recent Applications of Fluorescence Recovery after Photobleaching (FRAP) to Membrane Bio-Macromolecules. Sensors 2010, 10: 5927-5948. PMID: 22219695, PMCID: PMC3247740, DOI: 10.3390/s100605927.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsFluorescence Recovery After PhotobleachingHumansMacromolecular SubstancesMembrane ProteinsMembranesModels, BiologicalModels, TheoreticalCrystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand
Cortajarena AL, Wang J, Regan L. Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand. The FEBS Journal 2010, 277: 1058-1066. PMID: 20089039, DOI: 10.1111/j.1742-4658.2009.07549.x.Peer-Reviewed Original ResearchConceptsTPR domainC-terminusKey protein-protein interactionsTetratricopeptide repeat modulesChaperone heat shock proteinProtein-protein interactionsHeat shock responseHeat shock proteinsTPR proteinsChaperone functionTPR unitsProtein domainsNew packing arrangementRepeat modulesMolecular basisPeptide ligandsShock proteinsShock responseHsp90Terminal residuesX-ray crystal structureProteinCrystal structureDomainTetratricopeptide
2009
Block-Copolymer-Based Plasmonic Nanostructures
Mistark PA, Park S, Yalcin SE, Lee DH, Yavuzcetin O, Tuominen MT, Russell TP, Achermann M. Block-Copolymer-Based Plasmonic Nanostructures. ACS Nano 2009, 3: 3987-3992. PMID: 19947582, DOI: 10.1021/nn901245w.Peer-Reviewed Original ResearchConceptsSurface plasmon polaritonsNanoparticle arraysCharacteristic surface plasmon resonanceMetal nanoparticle arraysSurface plasmon resonanceBlock copolymer templatesThin filmsVisible wavelength rangePlasmonic nanostructuresMetal nanoparticlesNanoparticle interfaceMetal thin filmsCopolymer thin filmsCopolymer templatePlasmon resonanceOptical characterizationPlasmon polaritonsWavelength rangeBlock copolymersMetal saltsMetal arraysSolvent annealingMixed solventArrayFilms
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