2024
Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for Pneumocystis jirovecii pneumonia in HIV-infected patients
Chen Q, Chen X, Mo P, Chen L, Du Q, Hu W, Jiang Q, Zhang Z, Zhang Y, Guo Q, Xiong Y, Deng L. Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for Pneumocystis jirovecii pneumonia in HIV-infected patients. Frontiers In Microbiology 2024, 15: 1421660. PMID: 39372273, PMCID: PMC11449763, DOI: 10.3389/fmicb.2024.1421660.Peer-Reviewed Original ResearchPneumocystis jirovecii pneumoniaMetagenomic next-generation sequencingBronchoalveolar lavage fluidHuman immunodeficiency virusReal-time polymerase chain reactionHIV-infected patientsSerum BDGPolymerase chain reactionCo-pathogensPJP patientsP. jiroveciiBronchoalveolar lavage fluid metagenomic next-generation sequencingDiagnostic performance of metagenomic next-generation sequencingDiagnostic value of bronchoalveolar lavage fluidSpecificity of metagenomic next-generation sequencingDiagnosis of Pneumocystis jirovecii pneumoniaAntimicrobial treatmentPerformance of metagenomic next-generation sequencingDose of trimethoprim-sulfamethoxazolePneumocystis jirovecii pneumonia patientDiagnostic valueNext-generation sequencingModification of antimicrobial treatmentMetagenomic next-generation sequencing resultsClinical final diagnosisHIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration
Jang S, Bedwell G, Singh S, Yu H, Arnarson B, Singh P, Radhakrishnan R, Douglas A, Ingram Z, Freniere C, Akkermans O, Sarafianos S, Ambrose Z, Xiong Y, Anekal P, Llopis P, KewalRamani V, Francis A, Engelman A. HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration. Nucleic Acids Research 2024, 52: 11060-11082. PMID: 39258548, PMCID: PMC11472059, DOI: 10.1093/nar/gkae769.Peer-Reviewed Original ResearchConceptsHIV-1 infectionHIV-1Viral DNA integrationCPSF6 knockout cellsActivity in vitroHIV-1 pathogenesisHIV-1 integrationDNA integrityLiquid-liquid phase separationViral infectionNuclear specklesInfectionCapsids in vitroCPSF6NS depletionNuclear entryCapsid bindingCapsid-binding proteinKnockout cellsBinding proteinSR proteinsNuclear rimCo-aggregationDisordered regionsStructural insights into PPP2R5A degradation by HIV-1 Vif
Hu Y, Delviks-Frankenberry K, Wu C, Arizaga F, Pathak V, Xiong Y. Structural insights into PPP2R5A degradation by HIV-1 Vif. Nature Structural & Molecular Biology 2024, 31: 1492-1501. PMID: 38789685, DOI: 10.1038/s41594-024-01314-6.Peer-Reviewed Original ResearchHost-virus protein interactionsCullin RING E3 ubiquitin ligasesInduced G2/M cell cycle arrestSets of proteinsG2/M cell cycle arrestSubstrate-binding siteCryogenic-electron microscopy structuresProtein phosphatase 2ADegradation-independent mechanismCell cycle arrestUbiquitin ligaseProtein interactionsPhosphatase 2AAntiviral proteinCycle arrestDegradation-dependentA-resolutionHIV-1 VifPPP2R5AStructural insightsDiverse interactionsProteinCellular studiesPhosphatase activityPotential target
2023
Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi–Goutières syndrome SAMHD1 dNTPase ortholog
Maehigashi T, Lim C, Wade L, Bowen N, Knecht K, Alvarez N, Kelly W, Schinazi R, Kim D, Xiong Y, Kim B. Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi–Goutières syndrome SAMHD1 dNTPase ortholog. Journal Of Biological Chemistry 2023, 299: 105148. PMID: 37567474, PMCID: PMC10485159, DOI: 10.1016/j.jbc.2023.105148.Peer-Reviewed Original ResearchSterile alpha motif (SAM) domainMotif domainHistidine-aspartate domain-containing protein 1Allosteric regulatory mechanismsDomain-containing protein 1Cellular dNTP levelsStriking conservationCaenorhabditis elegansBiochemical functionsDevelopmental roleGene knockdownRegulatory mechanismsDevelopmental defectsHuman monocytic cell lineDNTP levelsMonocytic cell lineMouse SAMHD1Aicardi-Goutières syndromeProtein 1OrthologsHIV-1 restriction factorsProteinCell linesRestriction factorsDNA building blocksFunction and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages
Ren P, Hu Y, Peng L, Yang L, Suzuki K, Fang Z, Bai M, Zhou L, Feng Y, Zou Y, Xiong Y, Chen S. Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages. Signal Transduction And Targeted Therapy 2023, 8: 281. PMID: 37518189, PMCID: PMC10387464, DOI: 10.1038/s41392-023-01509-1.Peer-Reviewed Original ResearchThe capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores
Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick R, Levintov L, Xiong Q, Wu C, Devarkar S, Tian T, Tripler T, Hu Y, Yuan S, Temple J, Feng Q, Lusk C, Aiken C, Engelman A, Perilla J, Pathak V, Lin C, Xiong Y. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2202815120. PMID: 36943880, PMCID: PMC10068764, DOI: 10.1073/pnas.2202815120.Peer-Reviewed Original ResearchConceptsHIV-1 capsidC-terminal tail regionTriple arginine motifNuclear pore complexPhenylalanine-glycine motifsBipartite motifNuclear importPore complexNuclear poresNuclear entryNup153Capsid latticeInteraction moduleProtein latticeCA assemblyCA hexamersIntact capsidsNucleoporinsHIV-1 coreMotifCapsidTail regionIntact formInfection studiesMechanistic evidenceEnrich and switch: IP6 and maturation of HIV-1 capsid
Wu C, Xiong Y. Enrich and switch: IP6 and maturation of HIV-1 capsid. Nature Structural & Molecular Biology 2023, 30: 239-241. PMID: 36849641, PMCID: PMC10033439, DOI: 10.1038/s41594-023-00940-w.Commentaries, Editorials and LettersModeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels
Shen Q, Feng Q, Wu C, Xiong Q, Tian T, Yuan S, Shi J, Bedwell G, Yang R, Aiken C, Engelman A, Lusk C, Lin C, Xiong Y. Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nature Structural & Molecular Biology 2023, 30: 425-435. PMID: 36807645, PMCID: PMC10121901, DOI: 10.1038/s41594-023-00925-9.Peer-Reviewed Original ResearchConceptsNuclear pore complexHIV-1 nuclear entryNuclear entryNuclear importNPC central channelPore complexHost nucleusCapsid dockingVirus genomeAffinity gradientNup153Central channelMechanistic insightsMolecular interactionsCapsidNucleoporinsNup358Nup62GenomeNucleusVirusDockingVirus-1 infectionImportComplexesStructural basis for recruitment of host CypA and E3 ubiquitin ligase by maedi-visna virus Vif
Hu Y, Gudnadóttir R, Knecht K, Arizaga F, Jónsson S, Xiong Y. Structural basis for recruitment of host CypA and E3 ubiquitin ligase by maedi-visna virus Vif. Science Advances 2023, 9: eadd3422. PMID: 36638173, PMCID: PMC9839330, DOI: 10.1126/sciadv.add3422.Peer-Reviewed Original ResearchConceptsMVV VifCryo-electron microscopy structureE3 ubiquitin ligase complexLentiviral VifUbiquitin ligase complexHost cofactorsUbiquitin-proteasome pathwayDistinct interaction modesUnique structural elementsLentiviral Vif proteinsEvolutionary relationshipsMicroscopy structureLigase complexCellular proteinsE3 ubiquitinAntiviral APOBEC3Structural basisFunctional analysisMolecular mechanismsMaedi-visna virusRecruitment mechanismsVif proteinCofactorProteinCypA
2022
Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity
Shen Q, Xiong Q, Zhou K, Feng Q, Liu L, Tian T, Wu C, Xiong Y, Melia T, Lusk C, Lin C. Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity. Journal Of The American Chemical Society 2022, 145: 1292-1300. PMID: 36577119, PMCID: PMC9852090, DOI: 10.1021/jacs.2c11226.Peer-Reviewed Original ResearchConceptsExchange of macromoleculesCholesterol-rich membranesHybrid nanoporesSynthetic biologyBiophysical toolsSynthetic cellsTransmembrane channelsTransmembrane nanoporesDNA ringsProtein nanoporeCell membraneBacterial toxinsDNA origami techniqueLipid membranesAnalytical chemistryMacromolecule sizeDNA origamiMembraneProgrammable sizeNanoporesSized poresNucleoporinsAverage inner diameterCellsPneumolysin
2020
Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex
Gisriel C, Zhou K, Huang H, Debus R, Xiong Y, Brudvig G. Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex. Joule 2020, 4: 2131-2148. DOI: 10.1016/j.joule.2020.07.016.Peer-Reviewed Original ResearchOxygen-evolving complexPhotosystem II enzymeWater oxidation complexWater oxidationMetal clustersMechanism of photoactivationActive siteMonomeric photosystem IIPhotosystem IICryo-EM structureStructural rearrangementsComplexesPhotoactivationSynechocystis spPeripheral subunitsCationsComputational techniquesOxidationOverall biogenesisStructureMesophilic cyanobacteriumOxygenPCC 6803II enzymesPSII
2019
The Polar Region of the HIV-1 Envelope Protein Determines Viral Fusion and Infectivity by Stabilizing the gp120-gp41 Association
Lu W, Chen S, Yu J, Behrens R, Wiggins J, Sherer N, Liu S, Xiong Y, Xiang S, Wu L. The Polar Region of the HIV-1 Envelope Protein Determines Viral Fusion and Infectivity by Stabilizing the gp120-gp41 Association. Journal Of Virology 2019, 93: 10.1128/jvi.02128-18. PMID: 30651369, PMCID: PMC6430531, DOI: 10.1128/jvi.02128-18.Peer-Reviewed Original ResearchConceptsHIV-1 fusionHIV-1 infectivityPR mutationsHIV-1 membrane fusionViral entryHIV-1 Env precursorEnv trimersMembrane fusionHIV-1 envelope proteinHIV-1 isolatesViral fusionHIV-1 Env trimersHIV-1 EnvGp120-gp41 associationTransmembrane unitViral envelope glycoproteinsHIV-1Cell-cell fusionViral fusogenicityPolar amino acidsEnv expressionVirus bindingEnvelope glycoproteinFusion inhibitorsTarget cells
2017
Biochemical basis of how phosphoserine acidic cluster motifs interact with clathrin adaptors
Singh R, Lim C, Jia X, Suarez M, Stoneham C, Xiong Y, Guatelli J. Biochemical basis of how phosphoserine acidic cluster motifs interact with clathrin adaptors. Acta Crystallographica Section A: Foundations And Advances 2017, 73: a398-a398. DOI: 10.1107/s010876731709612x.Peer-Reviewed Original Research
2016
The Role of UAF1 in the Fanconi Anemia Pathway Regulation of Homologous Recombination-Mediated Genome Maintenance
Liang F, Longerich S, Tang C, Buzovestsky O, Xiong Y, Maranon D, Wiese C, Miller A, Sung P, Kupfer G. The Role of UAF1 in the Fanconi Anemia Pathway Regulation of Homologous Recombination-Mediated Genome Maintenance. Blood 2016, 128: 1041. DOI: 10.1182/blood.v128.22.1041.1041.Peer-Reviewed Original ResearchHomologous recombinationGenome maintenanceDNA damageFA DNA repair pathwayCancer-prone genetic diseasesFanconi anemiaDNA damage hypersensitivityFunctional synergySynaptic complex assemblyProtein complex formationRad51 presynaptic filamentD-loop reactionDNA repair functionDNA damage repairDNA binding activityCell linesFANCD2 ubiquitinationGenome stabilityComplex formationRAD51 recombinaseHuman cell linesBinds DNAPresynaptic filamentRecombinase RAD51UAF1
2014
Kill HIV by Starvation–Mechanism of Allosteric Activation of SAMHD1
Ji X, Wu Y, Yan J, Mehrens J, DeLucia M, Hao C, Gronenborn A, Skowronski J, Anh J, Xiong Y. Kill HIV by Starvation–Mechanism of Allosteric Activation of SAMHD1. Acta Crystallographica Section A: Foundations And Advances 2014, 70: c121-c121. DOI: 10.1107/s2053273314098787.Peer-Reviewed Original ResearchCellular dNTP poolsCellular dNTP levelsDNTP poolsDNTP levelsDeoxyribonucleoside triphosphate triphosphohydrolaseActive tetrameric formMammalian cellsAllosteric activationSAMHD1 functionAllosteric mechanismMajor regulatorAllosteric siteInactive dimerAllosteric bindingTetrameric formAicardi-Goutières syndromeTetrameric complexMechanistic understandingCongenital viral infectionViral reverse transcriptionMonomers/dimersSAMHD1Reverse transcriptionHIV restrictionClinical manifestations
2012
Structural insights into the function of FANCM‐mediated complexes
Saro D, Sachpatzidis A, Zheng X, Singh T, Meetei A, Xiong Y, Sung P. Structural insights into the function of FANCM‐mediated complexes. The FASEB Journal 2012, 26: 536.8-536.8. DOI: 10.1096/fasebj.26.1_supplement.536.8.Peer-Reviewed Original ResearchCore complex proteinsComplex proteinsDNA bindingDNA damage-induced monoubiquitinationFA-BRCA pathwayBranch migration activityProtein-protein interactionsDNA damage responseHigh-resolution crystal structuresResolution crystal structureChromatin localizationNovel histoneDamage responseSensitivity of cellsFANCMStructural insightsBiochemical characterizationFoci formationProteinStructural workX-ray crystallographyChromosome aberrationsMigration activityFunctional integrityComplexes
2007
Characterization of a Novel Cullin5 Binding Domain in HIV-1 Vif
Xiao Z, Xiong Y, Zhang W, Tan L, Ehrlich E, Guo D, Yu X. Characterization of a Novel Cullin5 Binding Domain in HIV-1 Vif. Journal Of Molecular Biology 2007, 373: 541-550. PMID: 17869271, DOI: 10.1016/j.jmb.2007.07.029.Peer-Reviewed Original ResearchConceptsVif functionHCCH motifA3GPotential new targetsA3G degradationE3 ubiquitin ligaseUbiquitin-proteasome machineryHIV-1 VifAnti-viral drug developmentBC boxCul5 boxUbiquitin ligaseNovel motifProteasomal degradationCys residuesNew targetsDrug developmentMotifCullin5ResiduesStructural requirementsVif
2006
Zinc chelation inhibits HIV Vif activity and liberates antiviral function of the cytidine deaminase APOBEC3G
Xiao Z, Ehrlich E, Luo K, Xiong Y, Yu X. Zinc chelation inhibits HIV Vif activity and liberates antiviral function of the cytidine deaminase APOBEC3G. The FASEB Journal 2006, 21: 217-222. PMID: 17135358, DOI: 10.1096/fj.06-6773com.Peer-Reviewed Original ResearchConceptsTetrakis (2-pyridylmethyl) ethylenediamineVif functionZinc chelationE3 ubiquitin ligaseCytidine deaminase APOBEC3GCellular antiviral proteinsLentiviral Vif proteinsAPOBEC3G degradationSubstrate receptorHIV-1 VifMembrane-permeable zinc chelatorVif actsUbiquitin ligaseProteasomal degradationNovel drug designAntiviral functionAntiviral proteinVif proteinAntiviral activityVif activityAPOBEC3GAPOBEC3 proteinsNew targetsInfectivity assaysZinc chelator
2001
X-ray analysis of an RNA tetraplex (UGGGGU)4 with divalent Sr2+ ions at subatomic resolution (0.61 Å)
Deng J, Xiong Y, Sundaralingam M. X-ray analysis of an RNA tetraplex (UGGGGU)4 with divalent Sr2+ ions at subatomic resolution (0.61 Å). Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 13665-13670. PMID: 11707581, PMCID: PMC61098, DOI: 10.1073/pnas.241374798.Peer-Reviewed Original ResearchCrystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple.
Deng J, Xiong Y, Sudarsanakumar C, Shi K, Sundaralingam M. Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple. RNA 2001, 7: 1425-31. PMID: 11680847, PMCID: PMC1370186.Peer-Reviewed Original Research