2025
Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling
Li T, Stayrook S, Li W, Wang Y, Li H, Zhang J, Liu Y, Klein D. Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling. Nature Communications 2025, 16: 3580. PMID: 40234450, PMCID: PMC12000326, DOI: 10.1038/s41467-025-58828-w.Peer-Reviewed Original ResearchConceptsThrombospondin type I repeatsIsthmin-1Pre-adipocytesType I repeatsBacterial streptavidinSurface helicesI repeatsMolecular detailsDiverse functionsFunctional studiesAkt phosphorylationFunctional roleStructural plasticityInsulin-like propertiesCrystal structureAMOPGrowth factorDomainPhosphorylationApoptosisLiver steatosisProteinHelixAktStreptavidin
2022
Molecular determinants of complexin clamping and activation function
Bera M, Ramakrishnan S, Coleman J, Krishnakumar SS, Rothman JE. Molecular determinants of complexin clamping and activation function. ELife 2022, 11: e71938. PMID: 35442188, PMCID: PMC9020821, DOI: 10.7554/elife.71938.Peer-Reviewed Original ResearchConceptsSynaptotagmin-1Single-vesicle fusionAccessory helixFusion clampHelical domainMolecular detailsComplexinMutational analysisVesicle releaseFusion kineticsMolecular determinantsSpecific interactionsInhibitory functionProbability of fusionRapid CaSNAREpinsAssembly processFusionClamping functionDomainHelixVesiclesFunctionMembraneInteractionThe flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation
Tachiyama S, Chan KL, Liu X, Hathroubi S, Li W, Peterson B, Khan M, Ottemann K, Liu J, Roujeinikova A. The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2118401119. PMID: 35046042, PMCID: PMC8794807, DOI: 10.1073/pnas.2118401119.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacterial Physiological PhenomenaBacterial ProteinsFlagellaHelicobacter pyloriMembrane ProteinsModels, MolecularMolecular Motor ProteinsMultiprotein ComplexesProtein BindingProtein ConformationProtein Interaction Domains and MotifsProtein TransportStructure-Activity RelationshipConceptsStator unitsStomatin/prohibitin/flotillin/HflK/C (SPFH) domainWild-type cellsSignificant structural similarityPeriplasmic domainAssembly factorsFlagellar motorAccessory proteinsFliLLinker regionActive conformationFlagellar baseC-domainMotBStructural similarityStator assemblyProteinPutative mechanismsElectron tomography reconstructionsIntact motorCellsActivationDomainMotAHelix
2019
Electrostatic lateral interactions drive ESCRT-III heteropolymer assembly
Banjade S, Tang S, Shah Y, Emr S. Electrostatic lateral interactions drive ESCRT-III heteropolymer assembly. ELife 2019, 8: e46207. PMID: 31246173, PMCID: PMC6663469, DOI: 10.7554/elife.46207.Peer-Reviewed Original ResearchConceptsESCRT-IIIESCRT-III subunit Snf7Charge-inversion mutationsESCRT-III complexHetero-polymersVesicle biogenesisInteraction specificityElectrostatic interactionsHelixIn vivoFunctional defectsIn vitroVariable architectureAssemblyElectrostatic lateral interactionsVps24BiogenesisSnf7Lateral interactionsPolymer flexibilityMutationsA hydrophobic gate in the inner pore helix is the major determinant of inactivation in mechanosensitive Piezo channels
Zheng W, Gracheva EO, Bagriantsev SN. A hydrophobic gate in the inner pore helix is the major determinant of inactivation in mechanosensitive Piezo channels. ELife 2019, 8: e44003. PMID: 30628892, PMCID: PMC6349400, DOI: 10.7554/elife.44003.Peer-Reviewed Original ResearchConceptsPiezo channelsLining inner helixIon channelsMechanosensitive Piezo channelsInner pore helixImportance of inactivationMouse Piezo1Disease-causing mutationsHydrophobic gateInner helixPore helixPhysiological processesMechanism of inactivationStimulation triggersInactivationInactivation gatePiezo1Normal functionHelixHydrophobic barrierFast inactivationPhysical constrictionSecondary gateRate of inactivationMajor determinant
2018
Structural Basis for MARK1 Kinase Autoinhibition by Its KA1 Domain
Emptage RP, Lemmon MA, Ferguson KM, Marmorstein R. Structural Basis for MARK1 Kinase Autoinhibition by Its KA1 Domain. Structure 2018, 26: 1137-1143.e3. PMID: 30099988, PMCID: PMC6092042, DOI: 10.1016/j.str.2018.05.008.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCheckpoint Kinase 1Cloning, MolecularCrystallography, X-RayEscherichia coliGene ExpressionGenetic VectorsHumansKineticsModels, MolecularMutationPeptidesProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsProtein Serine-Threonine KinasesRecombinant ProteinsStructural Homology, ProteinSubstrate SpecificityThermodynamicsConceptsKA1 domainSer/Thr protein kinaseKinase structureRelated kinasesUBA domainKinase domainProtein kinaseStructural basisC-terminusUnexpected interfaceC-lobeKinaseΑD helixPotential new avenuesAutoinhibitoryData implicateDomain surfaceDomainNew avenuesYeastAutoinhibitionCrystal structureHelixAlzheimer's diseaseVariantsRegulation of C-C chemokine receptor 5 (CCR5) stability by Lys197 and by transmembrane protein aptamers that target it for lysosomal degradation
Petti LM, Marlatt SA, Luo Y, Scheideman EH, Shelar A, DiMaio D. Regulation of C-C chemokine receptor 5 (CCR5) stability by Lys197 and by transmembrane protein aptamers that target it for lysosomal degradation. Journal Of Biological Chemistry 2018, 293: 8787-8801. PMID: 29678881, PMCID: PMC5995508, DOI: 10.1074/jbc.ra117.001067.Peer-Reviewed Original ResearchConceptsG protein-coupled receptorsC motif chemokine receptor 5Transmembrane helicesAmino acidsProtein aptamerFifth transmembrane helixUncharged amino acidsSpecific amino acidsProtein-coupled receptorsSubstitution of LysTraptamersReceptor stabilityLysosomal degradationHomologous positionsDiverse mechanismsChemokine receptor 5Initial characterizationNew therapeutic approachesHuman T cellsStable complexesCCR5 expressionCentral roleNew insightsChemokine receptorsHelixStructural basis and energy landscape for the Ca2+ gating and calmodulation of the Kv7.2 K+ channel
Bernardo-Seisdedos G, Nuñez E, Gomis-Perez C, Malo C, Villarroel Á, Millet O. Structural basis and energy landscape for the Ca2+ gating and calmodulation of the Kv7.2 K+ channel. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: 2395-2400. PMID: 29463698, PMCID: PMC5873240, DOI: 10.1073/pnas.1800235115.Peer-Reviewed Original ResearchConceptsC-lobeKey biological signalsPrincipal molecular componentsAssociation of helicesTransmembrane regionStructural basisFunction of CaKv7.2 channelsBasal cytosolic CaConformational rearrangementsN-lobeInactive stateKey controllerMolecular componentsCytosolic CaIntracellular CaKv7.2HelixInactive channelsM-currentBiological signalsCalcification stateMillisecond timeNeuronal excitabilityPopulated excited states
2017
Mechanisms for initiating cellular DNA replication
Bleichert F, Botchan MR, Berger JM. Mechanisms for initiating cellular DNA replication. Science 2017, 355 PMID: 28209641, DOI: 10.1126/science.aah6317.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsReplicative helicasesDNA replicationRing-shaped hexameric helicasesDNA replication factoriesDNA replication initiationDomains of lifeCellular DNA replicationDNA helixReplisome assemblyReplication initiationMolecular choreographyHexameric helicasesReplication factoriesAccessory proteinsHelicasesDNA synthesisMultistep processDNAHelixReplicationProteinMechanismInitiationAssemblyLoader
2016
Data on diverse roles of helix perturbations in membrane proteins
Shelar A, Bansal M. Data on diverse roles of helix perturbations in membrane proteins. Data In Brief 2016, 9: 781-802. PMID: 27844046, PMCID: PMC5099277, DOI: 10.1016/j.dib.2016.10.023.Peer-Reviewed Original ResearchInter-helical interactionsMembrane proteinsHelix perturbationTM helicesMembrane protein familyProtein familyHydrophobic residuesDiverse rolesKinked geometryΠ-helixOligomer formationBackbone torsion anglesProteinHelixStructural variationsHelical conformationDistinct typesBilayersResiduesStrong evidenceLinear αRoleHelix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer
Shelar A, Bansal M. Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. Biochimica Et Biophysica Acta 2016, 1858: 2804-2817. PMID: 27521749, DOI: 10.1016/j.bbamem.2016.08.003.Peer-Reviewed Original ResearchConceptsInter-helical interactionsMembrane proteinsTM regionHelix perturbationTM helicesΠ-helixDistinct sequence signaturesIntegral membrane proteinsLow sequence identityHeme-copper oxidasesTransmembrane helicesProtein functionSequence signaturesSequence identityHydrophobic mismatchΑ-helixProtein chainsAmino acidsHelical fragmentsCopper oxidasesProteinHelix terminiHelixTerminusBilayersHoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix
Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA 2016, 22: 743-749. PMID: 26952103, PMCID: PMC4836648, DOI: 10.1261/rna.055707.115.Peer-Reviewed Original ResearchConceptsElectrophoretic mobility shift assaysRNA triple helicesBase triplesMetastasis-associated lung adenocarcinoma transcript 1RNA stability elementMobility shift assaysTriple helixHuman metastasis-associated lung adenocarcinoma transcript 1Small molecule bindingU base triplesNucleotide compositionCellular functionsTriple-helical stabilityShift assaysLung adenocarcinoma transcript 1Stability elementEMSA resultsBiological significanceMolecule bindingRNA catalysisHelixTranscript 1Triple helix stabilityC tripleReporter
2015
A structural model for facultative anion channels in an oligomeric membrane protein: the yeast TRK (K+) system
Pardo JP, González-Andrade M, Allen K, Kuroda T, Slayman CL, Rivetta A. A structural model for facultative anion channels in an oligomeric membrane protein: the yeast TRK (K+) system. Pflügers Archiv - European Journal Of Physiology 2015, 467: 2447-2460. PMID: 26100673, DOI: 10.1007/s00424-015-1712-6.Peer-Reviewed Original ResearchConceptsTransmembrane helicesAnion channelTrk proteinNon-animal cellsOligomeric membrane proteinsAmphipathic transmembrane helicesLigand-gated anion channelsClass of proteinsTrk transportersRCK domainsBacterial membersRegulatory domainMembrane proteinsFungal proteinsTrk systemHydrophobic gatingPrimary sequenceMembrane voltageBiological membranesProteinCytoplasmic collarFunctional processesChloride effluxHelixPathway
2014
Sequence and conformational preferences at termini of α‐helices in membrane proteins: Role of the helix environment
Shelar A, Bansal M. Sequence and conformational preferences at termini of α‐helices in membrane proteins: Role of the helix environment. Proteins Structure Function And Bioinformatics 2014, 82: 3420-3436. PMID: 25257385, DOI: 10.1002/prot.24696.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsComputational BiologyConserved SequenceDatabases, ProteinHumansHydrogen BondingHydrophobic and Hydrophilic InteractionsLipid BilayersMembrane ProteinsModels, BiologicalProtein ConformationProtein FoldingProtein StabilityProtein Structure, SecondarySoftware ValidationTerminology as TopicConceptsMembrane proteinsSequence preferenceΑ-helixC-terminusHelical membrane proteinsCommon secondary structural elementsHelix terminiStructural motifsSecondary structural elementsSecondary structure predictionRat neurotensin receptorTransmembrane helicesMembrane environmentHelix bundleSequencing studiesHelical positionsAmino acidsProteinStructure predictionTerminusMembrane coreGlobular proteinsMotifHelixConformational preferencesA PH Domain in ACAP1 Possesses Key Features of the BAR Domain in Promoting Membrane Curvature
Pang X, Fan J, Zhang Y, Zhang K, Gao B, Ma J, Li J, Deng Y, Zhou Q, Egelman EH, Hsu VW, Sun F. A PH Domain in ACAP1 Possesses Key Features of the BAR Domain in Promoting Membrane Curvature. Developmental Cell 2014, 31: 73-86. PMID: 25284369, PMCID: PMC4198613, DOI: 10.1016/j.devcel.2014.08.020.Peer-Reviewed Original ResearchStructural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix
Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nature Structural & Molecular Biology 2014, 21: 633-640. PMID: 24952594, PMCID: PMC4096706, DOI: 10.1038/nsmb.2844.Peer-Reviewed Original ResearchThe Ever Changing Moods of Calmodulin: How Structural Plasticity Entails Transductional Adaptability
Villarroel A, Taglialatela M, Bernardo-Seisdedos G, Alaimo A, Agirre J, Alberdi A, Gomis-Perez C, Soldovieri MV, Ambrosino P, Malo C, Areso P. The Ever Changing Moods of Calmodulin: How Structural Plasticity Entails Transductional Adaptability. Journal Of Molecular Biology 2014, 426: 2717-2735. PMID: 24857860, DOI: 10.1016/j.jmb.2014.05.016.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsC-lobeProtein Data Bank databaseStructure-function studiesDomain organizationProtein complexesCaM bindingHuman diseasesRole of CaMStructural plasticityGreat diversityCaM mutationsNew exciting avenuesThree-dimensional arrangementHuman pathophysiologyDiversity of targetsRemarkable varietyIndependent signalsCalmodulinDiversityExciting avenuesBindingRecent advancesTargetExceptional versatilityHelixLipidation of the LC3/GABARAP family of autophagy proteins relies on a membrane-curvature-sensing domain in Atg3
Nath S, Dancourt J, Shteyn V, Puente G, Fong WM, Nag S, Bewersdorf J, Yamamoto A, Antonny B, Melia TJ. Lipidation of the LC3/GABARAP family of autophagy proteins relies on a membrane-curvature-sensing domain in Atg3. Nature Cell Biology 2014, 16: 415-424. PMID: 24747438, PMCID: PMC4111135, DOI: 10.1038/ncb2940.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAmino Acid MotifsAnimalsApoptosis Regulatory ProteinsAutophagy-Related Protein 7Autophagy-Related Protein 8 FamilyAutophagy-Related ProteinsCell MembraneCytoskeletal ProteinsHeLa CellsHumansHydrophobic and Hydrophilic InteractionsLiposomesMembrane ProteinsMiceMice, KnockoutMicrofilament ProteinsMicrotubule-Associated ProteinsMutationPhosphatidylethanolaminesRatsSignal TransductionStress, PhysiologicalTransfectionUbiquitin-Activating EnzymesUbiquitin-Conjugating EnzymesConceptsLipid-packing defectsLC3/GABARAP familyLC3/GABARAP lipidationAmino-terminal amphipathic helixE2-like enzymeGABARAP familyAutophagic machineryIsolation membraneAmphipathic helixIntracellular membranesAutophagy proteinsRescue experimentsATG3LipidationCurved rimProteinMotifPhysiologic roleMembranePhagophoreAutophagosomesMachineryHelixEnzyme
2013
Coordination of K+ Transporters in Neurospora: TRK1 Is Scarce and Constitutive, while HAK1 Is Abundant and Highly Regulated
Rivetta A, Allen KE, Slayman CW, Slayman CL. Coordination of K+ Transporters in Neurospora: TRK1 Is Scarce and Constitutive, while HAK1 Is Abundant and Highly Regulated. MSphere 2013, 12: 684-696. PMID: 23475706, PMCID: PMC3647778, DOI: 10.1128/ec.00017-13.Peer-Reviewed Original ResearchConceptsTransmembrane helicesCarbon starvationModel organism Neurospora crassaPotassium transportersNeurospora crassaClass proteinsQuantitative Western blottingATP hydrolysisPotassium limitationTRK1Molecular machinesHAK1Trk1pWestern blottingPotassium channelsCoexpressionStarvationTransportersHelixTransporter affinityElectrophysiological characterizationExpressionMM/hCrassaNeurospora
2012
Molecular Basis for a Protein-Mediated DNA-Bridging Mechanism that Functions in Condensation of the E. coli Chromosome
Dupaigne P, Tonthat NK, Espéli O, Whitfill T, Boccard F, Schumacher MA. Molecular Basis for a Protein-Mediated DNA-Bridging Mechanism that Functions in Condensation of the E. coli Chromosome. Molecular Cell 2012, 48: 560-571. PMID: 23084832, PMCID: PMC7505563, DOI: 10.1016/j.molcel.2012.09.009.Peer-Reviewed Original ResearchConceptsMolecular basisColi chromosomeLarge chromosomal domainsDNA-binding motifE. coli chromosomeChromosomal domainsChromosome condensationGenomic packagingLoop DNAC-terminalChromosomesMacrodomainsMat sitesMatPMatP.DNAMotifHelixMutationsResiduesElectron microscopy studiesMicroscopy studiesMechanismTetramerEnterobacteria
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