Swapnil Chandrakant Devarkar
Associate Research ScientistCards
About
Research
Publications
2025
Structural 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, 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 ResearchRIG-I recognizes metabolite-capped RNAs as signaling ligands
Schweibenz B, Solotchi M, Hanpude P, Devarkar S, Patel S. RIG-I recognizes metabolite-capped RNAs as signaling ligands. Nucleic Acids Research 2023, 51: 8102-8114. PMID: 37326006, PMCID: PMC10450190, DOI: 10.1093/nar/gkad518.Peer-Reviewed Original ResearchConceptsRIG-IRNA endsRIG-I signaling pathwayIn vitro transcriptionRIG-I signalingDouble-stranded RNAInnate antiviral immune responseInterferon responseReceptor RIG-ICellular signaling assaysCapped RNACellular rolesPathogenic RNAsViral genomeEndogenous mRNAReplication intermediatesM7GSignaling ligandsImmune responseInnate immune receptor RIG-ISignaling pathwayRNASignaling assaysATPase activityAntiviral immune response1041 Atomic resolution structure of the cutibacterium acnes ribosome reveals the mechanism of protein synthesis inhibition by the antibiotic sarecycline
Lomakin I, Devarkar S, Patel S, Grada A, Bunick C. 1041 Atomic resolution structure of the cutibacterium acnes ribosome reveals the mechanism of protein synthesis inhibition by the antibiotic sarecycline. Journal Of Investigative Dermatology 2023, 143: s178. DOI: 10.1016/j.jid.2023.03.1052.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 evidenceSarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism
Lomakin I, Devarkar S, Patel S, Grada A, Bunick C. Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic Acids Research 2023, 51: 2915-2930. PMID: 36864821, PMCID: PMC10085706, DOI: 10.1093/nar/gkad103.Peer-Reviewed Original Research
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