2024
Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis
Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321510121. PMID: 38635633, PMCID: PMC11046580, DOI: 10.1073/pnas.2321510121.Peer-Reviewed Original ResearchConceptsLPS synthesisTetratricopeptide repeatCytoplasmic domainLevels of lipopolysaccharideCryo-EM structureGram-negative bacteriaLipopolysaccharide synthesisProtease FtsHRubredoxin domainLpxC activityTransmembrane helicesIn vivo analysisLpxCPseudomonas aeruginosaEnzymatic activityLapBFtsHAllosteric effectsYciMDual functionIn vitroTetratricopeptideAdaptorMotifDeacetylase
2023
Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention
Krimmer S, Bertoletti N, Suzuki Y, Katic L, Mohanty J, Shu S, Lee S, Lax I, Mi W, Schlessinger J. Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2300054120. PMID: 36943885, PMCID: PMC10068818, DOI: 10.1073/pnas.2300054120.Peer-Reviewed Original ResearchConceptsOncogenic KIT mutantsStem cell factorKIT mutantsHomotypic contactsCryo-EM analysisUnexpected structural plasticityLigand stem cell factorElectron microscopy structural analysisReceptor tyrosine kinase KITOncogenic mutantsHematopoietic stem cellsKIT dimerizationTyrosine kinase KITD5 regionPlasma membraneMutational analysisMutantsExtracellular domainGerm cellsHuman cancersSomatic gainCell factorStructural plasticityStem cellsKinase KITSeparating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient Centrifugation
Shu S, Mi W. Separating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient Centrifugation. Bio-protocol 2023, 13: e4638. PMID: 36968434, PMCID: PMC10031520, DOI: 10.21769/bioprotoc.4638.Peer-Reviewed Original ResearchInner membraneOuter membraneGram-negative bacteriaPeptidoglycan cell wallEscherichia coliMembrane protein purificationTotal cell membranesSucrose gradient centrifugationMembrane proteinsCell wallProtein structureFunctional studiesProtein purificationTotal membranesCell membraneSucrose gradientsBiochemical proceduresGradient centrifugationProteinMembraneColiBacteriaGradient ultracentrifugationLipidsUltracentrifugation method
2022
Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli
Shu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nature Communications 2022, 13: 4576. PMID: 35931690, PMCID: PMC9356133, DOI: 10.1038/s41467-022-32277-1.Peer-Reviewed Original ResearchConceptsRegulatory mechanismsAnti-adaptor proteinsFirst committed stepMost Gram-negative bacteriaEssential glycolipidEssential membraneGram-negative bacteriaTransmembrane helicesAdaptor proteinCommitted stepCytoplasmic domainFtsHLPS synthesisAnalysis unravelsLipopolysaccharide synthesisLapBEscherichia coliE. coliPermeability barrierProtein levelsLpxCProtease activityProteinColiYejM
2020
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex
Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA. Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 2020, 368 PMID: 32327568, PMCID: PMC7380553, DOI: 10.1126/science.aaz2449.Peer-Reviewed Original ResearchMeSH KeywordsCarrier ProteinsCryoelectron MicroscopyEndoplasmic ReticulumEndoplasmic Reticulum-Associated DegradationMembrane GlycoproteinsMembrane ProteinsMolecular Dynamics SimulationMultiprotein ComplexesProtein DomainsProtein FoldingProteolysisSaccharomyces cerevisiae ProteinsUbiquitin-Protein LigasesConceptsHrd1 complexLuminal endoplasmic reticulum proteinsCryo-electron microscopy analysisHrd1 ubiquitin ligaseEndoplasmic reticulum proteinER membraneUbiquitin ligaseProtein degradationStructural basisReticulum proteinsPolypeptide loopMembrane regionsLateral gateLuminal binding sitesBinding sitesLuminal cavityForm twoYos9RetrotranslocationERADMicroscopy analysisSubcomplexLigaseHRD1Proteasome
2018
DNA melting initiates the RAG catalytic pathway
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H. DNA melting initiates the RAG catalytic pathway. Nature Structural & Molecular Biology 2018, 25: 732-742. PMID: 30061602, PMCID: PMC6080600, DOI: 10.1038/s41594-018-0098-5.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA meltingCryo-EM structureBase-specific contactsSignal sequenceDNA transpositionSubstrate bindingRetroviral integrationRAG endonucleaseDimer openingTerminal sequenceGTG sequenceDNA cleavageScissile phosphateDNAUniversal mechanismPiston-like movementSequenceActive siteHeptamerRetrotransposonsCatalytic pathwayTransposonComplexesEndonuclease
2017
Structural basis of MsbA-mediated lipopolysaccharide transport
Mi W, Li Y, Yoon SH, Ernst RK, Walz T, Liao M. Structural basis of MsbA-mediated lipopolysaccharide transport. Nature 2017, 549: 233-237. PMID: 28869968, PMCID: PMC5759761, DOI: 10.1038/nature23649.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine DiphosphateATP-Binding Cassette TransportersBacterial ProteinsBiological TransportCell MembraneCryoelectron MicroscopyEscherichia coliHydrophobic and Hydrophilic InteractionsLipid BilayersLipopolysaccharidesModels, MolecularNanostructuresPeriplasmProtein BindingProtein DomainsConceptsPeriplasmic leafletStructural basisSingle-particle cryo-electron microscopyCryo-electron microscopyÅ resolution structureLipid flippasesGram-negative bacteriaLipopolysaccharide transportTransmembrane domainInner membraneCytoplasmic leafletMsbAOuter membraneCell envelopeResolution structureCassette transportersADP-vanadateStructural mechanismsConformational transitionLPS recognitionFunctional stateFlippasesMsbA.Hydrophobic interactionsMembraneCryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3
Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature 2017, 548: 352-355. PMID: 28682307, PMCID: PMC5736104, DOI: 10.1038/nature23314.Peer-Reviewed Original Research
2015
Single-particle electron microscopy in the study of membrane protein structure
De Zorzi R, Mi W, Liao M, Walz T. Single-particle electron microscopy in the study of membrane protein structure. Microscopy 2015, 65: 81-96. PMID: 26470917, PMCID: PMC4749050, DOI: 10.1093/jmicro/dfv058.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsSingle-particle electron microscopyMembrane protein structuresMembrane proteinsProtein structureAtomic modelElectron microscopyMore membrane proteinsUnprecedented qualityTransient receptor potential (TRP) channel familyDevice cameraChannel familyProteinStructure refinementMicroscopyStructureEnhanced potentialMinor roleCrystalsTechnical advancesTechnical limitationsGreat advantageShort orderFamily
2010
Crystallization and preliminary X‐ray analysis of tubulin‐folding cofactor A from Arabidopsis thaliana
Lu L, Nan J, Mi W, Wei C, Li L, Li Y. Crystallization and preliminary X‐ray analysis of tubulin‐folding cofactor A from Arabidopsis thaliana. Acta Crystallographica Section F: Structural Biology Communications 2010, 66: 954-956. PMID: 20693679, PMCID: PMC2917302, DOI: 10.1107/s1744309110023900.Peer-Reviewed Original Research
2009
CLIC2-RyR1 Interaction and Structural Characterization by Cryo-electron Microscopy
Meng X, Wang G, Viero C, Wang Q, Mi W, Su XD, Wagenknecht T, Williams AJ, Liu Z, Yin CC. CLIC2-RyR1 Interaction and Structural Characterization by Cryo-electron Microscopy. Journal Of Molecular Biology 2009, 387: 320-334. PMID: 19356589, PMCID: PMC2667806, DOI: 10.1016/j.jmb.2009.01.059.Peer-Reviewed Original ResearchConceptsCryo-electron microscopyChannel activitySkeletal ryanodine receptorsAffinity of ryanodineSkeletal sarcoplasmic reticulum vesiclesSmall proteinsClamp regionConformational changesPhysiological functionsDomain 5Closed stateSingle-channel recordingsStructural familyRyR1 channelsRyanodine receptorSkeletal muscleRyR1VesiclesOpen probabilityRyR channelsChannel 2Channel recordingsEfflux rateSarcoplasmic reticulum vesiclesReticulum vesicles
2008
5,5′-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2
Mi W, Li L, Su XD. 5,5′-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2. Biochemical And Biophysical Research Communications 2008, 368: 919-922. PMID: 18280248, DOI: 10.1016/j.bbrc.2008.02.021.Peer-Reviewed Original ResearchThe crystal structure of human chloride intracellular channel protein 2: A disulfide bond with functional implications
Mi W, Liang Y, Li L, Su X. The crystal structure of human chloride intracellular channel protein 2: A disulfide bond with functional implications. Proteins Structure Function And Bioinformatics 2008, 71: 509-513. PMID: 18186468, DOI: 10.1002/prot.21922.Peer-Reviewed Original Research
2005
Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutans
Zhou Y, Mi W, Li L, Zhang X, Liang Y, Su X, Wei S. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutans. Biochimica Et Biophysica Acta 2005, 1764: 324-326. PMID: 16427820, DOI: 10.1016/j.bbapap.2005.11.022.Peer-Reviewed Original Research