Ivan B Lomakin, PhD
Research Scientist in DermatologyCards
Appointments
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
Yale School of Medicine
Department of Dermatology, Seamco Bldg, 464 Congress Ave.
New Haven, CT 06519
United States
Appointments
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
Yale School of Medicine
Department of Dermatology, Seamco Bldg, 464 Congress Ave.
New Haven, CT 06519
United States
Appointments
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
Yale School of Medicine
Department of Dermatology, Seamco Bldg, 464 Congress Ave.
New Haven, CT 06519
United States
About
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Titles
Research Scientist in Dermatology
Affiliated Faculty, Yale Institute for Global Health
Biography
Trained in the laboratory of Nobel Laureate Dr. Thomas A. Steitz, my work has ranged from solving the crystal structure of yeast fatty acid synthase (Cell, 2007) to elucidating the mechanisms of eukaryotic translation initiation (Nature, 2013). Currently at the Bunick Lab in Yale's Department of Dermatology, I apply cryo-EM and X-ray crystallography to medically relevant questions — including uncovering the dual-inhibition mechanism of narrow-spectrum tetracycline class antibiotic sarecycline against Cutibacterium acnes (Nucleic Acids Research, 2023), advancing our understanding of intermediate filament assembly in skin biology (Nat Struct Mol Biol., 2024), and contributing to SARS-CoV-2 research (Molecular Cell, 2020).
Appointments
Education & Training
- PhD
- Institute of Genetics and Selection of Industrial Microorganisms (1993)
- MSc
- Moscow Engineering Physics Institute (1986)
Research
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Overview
Trained in the laboratory of Nobel Laureate Dr. Thomas A. Steitz, my work has ranged from solving the crystal structure of yeast fatty acid synthase (Cell, 2007) to elucidating the mechanisms of eukaryotic translation initiation (Nature, 2013). Currently at the Bunick Lab in Yale's Department of Dermatology, I apply cryo-EM and X-ray crystallography to medically relevant questions — including uncovering the dual-inhibition mechanism of narrow-spectrum tetracycline class antibiotic sarecycline against Cutibacterium acnes (Nucleic Acids Research, 2023), advancing our understanding of intermediate filament assembly in skin biology (Nat Struct Mol Biol., 2024), and contributing to SARS-CoV-2 research (Molecular Cell, 2020).
Medical Research Interests
Public Health Interests
ORCID
0000-0001-6528-5068- View Lab Website
Christopher G Bunick' lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Christopher Bunick, MD, PhD
Swapnil Chandrakant Devarkar
Minh Ho
Keith Choate, MD, PhD
Ryland Mortlock
Sidi Chen, PhD
Protein Biosynthesis
Crystallography, X-Ray
Cryoelectron Microscopy
Protein Synthesis Inhibitors
Acne Vulgaris
Publications
Featured Publications
Sarecycline 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsHuman keratin 1/10‐1B tetramer structures reveal a knob‐pocket mechanism in intermediate filament assembly
Eldirany SA, Ho M, Hinbest AJ, Lomakin IB, Bunick CG. Human keratin 1/10‐1B tetramer structures reveal a knob‐pocket mechanism in intermediate filament assembly. The EMBO Journal 2019, 38: embj2018100741. PMID: 31036554, PMCID: PMC6545558, DOI: 10.15252/embj.2018100741.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAmino Acid SubstitutionCircular DichroismCrystallography, X-RayCytoskeletonDynamic Light ScatteringHumansHydrophobic and Hydrophilic InteractionsIntermediate Filament ProteinsKeratin-1Keratin-10Models, MolecularMutation, MissenseProtein FoldingProtein Interaction Domains and MotifsProtein MultimerizationProtein Structure, QuaternaryProtein Structure, SecondarySkin DiseasesConceptsFilament assemblyN-terminal hydrophobic pocketIntermediate filament assemblyTetramer assemblyÅ structureÅ resolutionCircular dichroism measurementsTetramer formationAssembly mechanismHydrophobic faceHydrophobic pocketSecondary structureOctamer structureEpidermolytic palmoplantar keratodermaKeratin filamentsIntermediate filamentsMutationsPathogenic mutationsTetramer structureDichroism measurementsAtomic resolutionAssemblyBiochemical determinantsKeratin 1/10TetramerAntimicrobial peptides targeting bacterial ribosome
Lomakin IB, Gagnon MG, Steitz TA. Antimicrobial peptides targeting bacterial ribosome. Oncotarget 2015, 6: 18744-18745. PMID: 26300053, PMCID: PMC4662452, DOI: 10.18632/oncotarget.5114.Peer-Reviewed Original ResearchCitationsAltmetricMeSH KeywordsPosition of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing
Unbehaun A, Marintchev A, Lomakin IB, Didenko T, Wagner G, Hellen C, Pestova TV. Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. The EMBO Journal 2007, 26: 3109-3123. PMID: 17568775, PMCID: PMC1914099, DOI: 10.1038/sj.emboj.7601751.Peer-Reviewed Original ResearchCitationsAltmetricThe Crystal Structure of Yeast Fatty Acid Synthase, a Cellular Machine with Eight Active Sites Working Together
Lomakin IB, Xiong Y, Steitz TA. The Crystal Structure of Yeast Fatty Acid Synthase, a Cellular Machine with Eight Active Sites Working Together. Cell 2007, 129: 319-332. PMID: 17448991, DOI: 10.1016/j.cell.2007.03.013.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCatalytic siteCrystal structureAcyl carrier proteinPantetheine armActive siteCatalytic centerMacromolecular assembliesYeast fatty acid synthaseReaction chamberKetoacyl synthase domainWhole metabolic pathwaysTwo-dimensional diffusionAssemblyCarrier proteinSynthesisStructureComplexesCellular machinesMultiple stepsAcidSitesShellSubstrateInsight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1
Wang J, Sachpatzidis A, Christian TD, Lomakin IB, Garen A, Konigsberg WH. Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1. Biochemistry 2022, 61: 1723-1734. PMID: 35998361, DOI: 10.1021/acs.biochem.2c00192.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsRNA recognition motifSplicing factorsRNA bindingÅ resolution crystal structureTranscript 1DNA-binding domainRNA-binding pocketTumor suppression mechanismNew regulatory mechanismTumor suppressor proteinResolution crystal structureMurine virusesAcid proteinSuppressor proteinRecognition motifLung adenocarcinoma transcript 1Gene expressionRegulatory mechanismsApo structureRNA virusesHuman diseasesRNABinding pocketsHuman metastasesPositive cooperativityRecent insight into intermediate filament structure
Eldirany SA, Lomakin IB, Ho M, Bunick CG. Recent insight into intermediate filament structure. Current Opinion In Cell Biology 2020, 68: 132-143. PMID: 33190098, PMCID: PMC7925366, DOI: 10.1016/j.ceb.2020.10.001.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsIntermediate filamentsAssembly mechanismVariable N-terminalMultiple cellular processesCentral rod domainIntermediate filament structureCoil 1BCellular processesStudy of keratinsTail domainFilament assemblyRod domainC-terminalN-terminalElectrostatic surfacePathologic mutationsKey playersFilament structureRecent insightsComplex formationProteinHuman tissuesGlial fibrillary acidic proteinAcidic proteinDomainNonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA
Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Molecular Cell 2020, 80: 1055-1066.e6. PMID: 33188728, PMCID: PMC7833686, DOI: 10.1016/j.molcel.2020.10.034.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsInternal ribosome entry site RNANonstructural protein 1Host protein synthesis machineryMRNA entry channelProtein synthesis machineryCryo-EM structureProtein 1Major pathogenicity factorsDifferential expression analysisMRNA-seq dataCellular transcriptomePreinitiation complexSynthesis machineryHuman lung originTranslation inhibitionPathogenicity factorsExpression analysisSite RNAHost viabilityNSP1Protein synthesisEntry channelViral proteinsUnknown mechanismViral RNACoronavirus Nsp1: Immune Response Suppression and Protein Expression Inhibition
Yuan S, Balaji S, Lomakin IB, Xiong Y. Coronavirus Nsp1: Immune Response Suppression and Protein Expression Inhibition. Frontiers In Microbiology 2021, 12: 752214. PMID: 34659188, PMCID: PMC8512706, DOI: 10.3389/fmicb.2021.752214.Peer-Reviewed Original ResearchCitationsAltmetricConceptsImmune responseImmune response suppressionSARS-CoV-2Nonstructural protein 1Host protein expressionMillions of deathsVaccine developmentProtein expressionProtein 1Causative agentViral RNAExpression inhibitionExpression levelsCOVID-19 pandemicMultiple mechanismsPublic healthViral proteinsGene expression levelsResponse suppressionCoronavirusHost cellsInhibitionCurrent dataGlobal gene expression levelsProtein synthesisPhysical Association of Eukaryotic Initiation Factor 4G (eIF4G) with eIF4A Strongly Enhances Binding of eIF4G to the Internal Ribosomal Entry Site of Encephalomyocarditis Virus and Is Required for Internal Initiation of Translation
Lomakin I, Hellen C, Pestova T. Physical Association of Eukaryotic Initiation Factor 4G (eIF4G) with eIF4A Strongly Enhances Binding of eIF4G to the Internal Ribosomal Entry Site of Encephalomyocarditis Virus and Is Required for Internal Initiation of Translation. Molecular And Cellular Biology 2000, 20: 6019-6029. PMID: 10913184, PMCID: PMC86078, DOI: 10.1128/mcb.20.16.6019-6029.2000.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsInternal ribosomal entry siteEMCV internal ribosomal entry siteEIF4GAdditional amino-terminal sequenceEukaryotic initiation factor 4GRNA recognition motifEukaryotic initiation factor 4GIInternal ribosomal entryEntry siteComplex formationBeta-globin mRNAAmino-terminal sequenceEncephalomyocarditis virus internal ribosomal entry siteRibosomal entryRecognition motifLike domainMutational analysisPhysical associationInternal initiationHigh-affinity bindingBinding fragmentSpecific interactionsRNASimilar affinitySpecific high-affinity binding
Academic Achievements & Community Involvement
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Honors
honor Special Award for High-Impact Science
01/08/1993International AwardInternational Science FoundationDetailsRussia
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- Photo by Ivan Lomakin
We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, simultaneously inhibits two active sites of this bacterium’s ribosome.
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Yale School of Medicine
Department of Dermatology, Seamco Bldg, 464 Congress Ave.
New Haven, CT 06519
United States