Swapnil Chandrakant Devarkar
Associate Research ScientistCards
About
Research
Publications
2025
Visualizing the translation landscape in human cells at high resolution
Zheng W, Zhang Y, Wang J, Wang S, Chai P, Bailey E, Zhu C, Guo W, Devarkar S, Wu S, Lin J, Zhang K, Liu J, Lomakin I, Xiong Y. Visualizing the translation landscape in human cells at high resolution. Nature Communications 2025, 16: 10757. PMID: 41315256, PMCID: PMC12663405, DOI: 10.1038/s41467-025-65795-9.Peer-Reviewed Original ResearchConceptsTranslational landscapeHuman cellsCryo-focused ion beamHigh-resolution structuresHuman 80S ribosomesSingle-particle cryo-electron microscopyCryo-EM approachCryo-electron microscopyRibosome structurePurified ribosomesConsensus structureRibosomeE siteA-resolutionIon beamCryo-EMProtein synthesisNative ribosomesStructure of macromoleculesNative environmentPolyamine bindingCycloheximideEnvironment of ionsCellsPolyaminesDistinct Target Site of Lenacapavir in Immature HIV‑1 and Concurrent Binding with the Maturation Inhibitor Bevirimat
Wu C, Meuser M, Rey J, Meshkin H, Yang R, Devarkar S, Freniere C, Shi J, Aiken C, Perilla J, Xiong Y. Distinct Target Site of Lenacapavir in Immature HIV‑1 and Concurrent Binding with the Maturation Inhibitor Bevirimat. Journal Of The American Chemical Society 2025, 147: 42685-42700. PMID: 41198571, DOI: 10.1021/jacs.5c13735.Peer-Reviewed Original ResearchMechanistic basis for a novel dual-function Gag-Pol dimerizer potentiating CARD8 inflammasome activation and clearance of HIV-infected cells
Hollander K, Devarkar S, Tang S, Tiwari R, Ma S, Lee W, Denn E, Wang Q, Spasov K, Robbins J, Frey K, Jorgensen W, Xiong Y, Shan L, Anderson K. Mechanistic basis for a novel dual-function Gag-Pol dimerizer potentiating CARD8 inflammasome activation and clearance of HIV-infected cells. Npj Drug Discovery 2025, 2: 22. PMID: 40904837, PMCID: PMC12401731, DOI: 10.1038/s44386-025-00025-2.Peer-Reviewed Original ResearchNon-nucleoside reverse transcriptase inhibitorsGag-Pol dimerizationGag-PolClearance of HIV-infected cellsLatent HIV-1 reservoirHIV-1-infected cellsHIV-1 reservoirHIV-infected cellsHIV-1 proteaseReverse transcriptase inhibitorsCatechol diethersHigh-throughput screeningCell-based high-throughput screeningTranscriptase inhibitorsDimerGag-Pol polyproteinDual-functionInflammasome activationInfected cellsCARD8Trigger pyroptosisNodal modulator (NOMO) is a force-bearing transmembrane protein required for muscle differentiation
Naughton B, Devarkar S, Todorow V, Mallik S, Oxendine S, Junnarkar S, Ren Y, Berro J, Kirstein J, Xiong Y, Schlieker C. Nodal modulator (NOMO) is a force-bearing transmembrane protein required for muscle differentiation. Journal Of Cell Biology 2025, 224: e202505010. PMID: 40663102, PMCID: PMC12262048, DOI: 10.1083/jcb.202505010.Peer-Reviewed Original ResearchConceptsER morphologyLuminal domainTransmembrane proteinsER-resident transmembrane proteinMembrane-shaping proteinsNetwork of sheetsER membrane systemIg domainsInterface mutationsConditions of mechanical strainBiological processesFunctional importanceNodal modulationMuscle differentiationProteinTension sensorMyogenesisStriated MuscleMuscle physiologyMembrane systemMechanical forcesNematode motilityMotilityMutationsNematodesStructural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase
Devarkar S, Budding C, Pathirage C, Kavoor A, Herbert C, Limbach P, Musier-Forsyth K, Xiong Y. Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase. Nucleic Acids Research 2025, 53: gkaf114. PMID: 40036503, PMCID: PMC11878792, DOI: 10.1093/nar/gkaf114.Peer-Reviewed Original ResearchConceptsTransfer ribonucleic acidHuman lysyl-tRNA synthetaseLysyl-tRNA synthetaseHigh-resolution cryo-electron microscopyPost-transcriptional modificationsCryo-electron microscopyD-loopCatalytic stepStructural basisAminoacylationCryo-EMProtein synthesisCatalytic efficiencyFunctional impactSynthetaseRibonucleic acidActive siteMachineryLysRSMetazoansMs2t6ATRNALys3Mcm5s2UR37Integral role
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 ResearchMechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin
Lomakin I, Devarkar S, Grada A, Bunick C. Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin. Journal Of Investigative Dermatology 2024, 144: 2553-2561.e3. PMID: 39122144, DOI: 10.1016/j.jid.2024.07.013.Peer-Reviewed Original ResearchNetwork of water-mediated interactionsCutibacterium acnesPeptide bond formationNascent peptideWater-mediated interactionsTranslational inhibitionAntibiotic resistanceCryogenic electron microscopyA-resolutionMechanistic basesAntibiotic-based therapiesRRNAAminoacyl groupRibosomeAcne pathogenesisAcne therapyAntibiotic stewardshipClindamycinIncreased resistanceAcne vulgarisClinical targetsAcneAntibioticsPeptideTRNA586 Molecular mechanism of protein synthesis inhibition in Cutibacterium acnes by clindamycin
Lomakin I, Devarkar S, Armillei M, Bunick C. 586 Molecular mechanism of protein synthesis inhibition in Cutibacterium acnes by clindamycin. Journal Of Investigative Dermatology 2024, 144: s102. DOI: 10.1016/j.jid.2024.06.602.Peer-Reviewed Original Research
2023
Structural basis for translation inhibition by MERS-CoV Nsp1 reveals a conserved mechanism for betacoronaviruses
Devarkar S, Vetick M, Balaji S, Lomakin I, Yang L, Jin D, Gilbert W, Chen S, Xiong Y. Structural basis for translation inhibition by MERS-CoV Nsp1 reveals a conserved mechanism for betacoronaviruses. Cell Reports 2023, 42: 113156. PMID: 37733586, PMCID: PMC12447786, DOI: 10.1016/j.celrep.2023.113156.Peer-Reviewed Original ResearchConceptsMERS-CoV nsp1Translation inhibitionRibosomal subunitΒ-CoVsModest sequence conservationMRNA entry channelEssential pathogenicity factorHost gene expressionHuman 40S ribosomal subunitSARS-CoV-2 nsp1Cryogenic electron microscopySequence conservationNon-structural protein 1Terminal domainPathogenicity factorsStructural basisGene expressionDevelopment of antiviralsNSP1Entry channelProtein 1Potential therapeutic targetSubunitsExtensive interactionsTherapeutic targetGroup II intron splicing mechanisms – ribozymes and retrotransposons
Xu L, Chung K, Liu T, Chai P, Peng J, Devarkar S, Pyle A. Group II intron splicing mechanisms – ribozymes and retrotransposons. Acta Crystallographica Section A: Foundations And Advances 2023, 79: a260-a260. DOI: 10.1107/s2053273323097395.Peer-Reviewed Original Research
Academic Achievements & Community Involvement
Get In Touch
Contacts
Mailing Address
Molecular Biophysics and Biochemistry
260 Whitney Avenue, Yale Science Building
New Haven, Connecticut 06511
United States