Selected Publications

Academic Article

Year Title Altmetric
2022 Application of a Novel CL7/Im7 Affinity System in Purification of Complex and Pharmaceutical ProteinsMethods in Molecular Biology.  2466:61-82. 2022
2017 Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencingProceedings of the National Academy of Sciences of USA.  114:E7949-E7958. 2017
2017 Efficient, ultra-high-Affinity chromatography in a one-step purification of complex proteinsProceedings of the National Academy of Sciences of USA.  114:E5138-E5147. 2017
2016 Interaction between HIV-1 nef and calnexin: From modeling to small molecule inhibitors reversing HIV-induced lipid accumulationArteriosclerosis, Thrombosis and Vascular Biology.  36:1758-1771. 2016
2015 Insights into Structure-Activity Relationships of Bacterial RNA Polymerase Inhibiting Corallopyronin DerivativesJournal of Natural Products.  78:2505-2509. 2015
2012 Corallopyronin a specifically targets and depletes essential obligate wolbachia endobacteria from filarial nematodes in vivoJournal of Infectious Diseases.  206:249-257. 2012
2012 The binding site and mechanism of the RNA polymerase inhibitor tagetitoxin: An issue open to debateTranscription.  3:46-50. 2012
2011 Structure and function of a membrane component SecDF that enhances protein exportNature.  474:235-238. 2011
2010 The NusA N-Terminal Domain Is Necessary and Sufficient for Enhancement of Transcriptional Pausing via Interaction with the RNA Exit Channel of RNA PolymeraseJournal of Molecular Biology.  401:708-725. 2010
2009 Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active siteJournal of Biological Chemistry.  284:36711-36719. 2009
2009 Elongation by RNA polymerase: a race through roadblocksCurrent Opinion in Structural Biology.  19:691-700. 2009
2009 Mechanism of chromatin remodeling and recovery during passage of RNA polymerase IINature Structural and Molecular Biology.  16:1272-1278. 2009
2009 Structural insights into mechanisms of the small RNA methyltransferase HEN1Nature.  461:823-827. 2009
2009 Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNAMolecular Cell.  34:710-721. 2009
2009 Transcription inactivation through local refolding of the RNA polymerase structureNature.  457:332-335. 2009
2008 Conformational transition of Sec machinery inferred from bacterial SecYE structuresNature.  455:988-991. 2008
2008 X-ray structure of the complex of regulatory subunits of human DNA polymerase δCell Cycle.  7:3026-3036. 2008
2008 Still Looking for the Magic Spot: The Crystallographically Defined Binding Site for ppGpp on RNA Polymerase Is Unlikely to Be Responsible for rRNA Transcription RegulationJournal of Molecular Biology.  377:551-564. 2008
2008 The elongation factor RfaH and the initiation factor σ bind to the same site on the transcription elongation complexProceedings of the National Academy of Sciences of USA.  105:865-870. 2008
2007 Merging the RNA and DNA worldsNature Structural and Molecular Biology.  14:1122-1123. 2007
2007 The carboxy-terminal coiled-coil of the RNA polymerase β′-subunit is the main binding site for Gre factorsEMBO Reports.  8:1038-1043. 2007
2007 Allosteric control of the RNA polymerase by the elongation factor RfaHNucleic Acids Research.  35:5694-5705. 2007
2007 The transition to an elongation complex by T7 RNA polymerase is a multistep processJournal of Biological Chemistry.  282:22879-22886. 2007
2007 Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 and its Functional ImplicationsJournal of Molecular Biology.  370:417-426. 2007
2007 Crystal Structure of an Asymmetric Complex of Pyruvate Dehydrogenase Kinase 3 with Lipoyl Domain 2 and its Biological ImplicationsJournal of Molecular Biology.  370:407-416. 2007
2007 Structural basis for substrate loading in bacterial RNA polymeraseNature.  448:163-168. 2007
2007 Structural basis for transcription elongation by bacterial RNA polymeraseNature.  448:157-162. 2007
2007 Structural Basis for Converting a General Transcription Factor into an Operon-Specific Virulence RegulatorMolecular Cell.  26:117-129. 2007
2006 Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head DimerJournal of Molecular Biology.  364:248-258. 2006
2006 A Mechanism of Nucleotide Misincorporation during Transcription due to Template-Strand MisalignmentMolecular Cell.  24:245-255. 2006
2006 Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNAActa Crystallographica Section F: Structural Biology and Crystallization Communications Online.  62:1027-1030. 2006
2006 Elongation complexes of thermus thermophilus RNA polymerase that possess distinct translocation conformationsNucleic Acids Research.  34:4036-4045. 2006
2006 Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilusActa Crystallographica Section F: Structural Biology and Crystallization Communications Online.  62:909-912. 2006
2006 Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilusActa Crystallographica Section F: Structural Biology and Crystallization Communications Online.  62:44-46. 2006
2006 Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilusActa Crystallographica Section F: Structural Biology and Crystallization Communications Online.  62:376-380. 2006
2006 Is it easy to stop RNA polymerase?Cell Cycle.  5:399-404. 2006
2006 Regulation through the RNA polymerase secondary channel: Structural and functional variability of the coiled-coil transcription factorsJournal of Biological Chemistry.  281:1309-1312. 2006
2005 Structural basis for transcription inhibition by tagetitoxinNature Structural and Molecular Biology.  12:1086-1093. 2005
2005 Tracking RNA polymerase, one step at a timeCell.  123:977-979. 2005
2005 Structural basis of transcription inhibition by antibiotic streptolydiginMolecular Cell.  19:655-666. 2005
2005 Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycinsCell.  122:351-363. 2005
2005 Structure of Pseudomonas aeruginosa Hfq proteinActa Crystallographica Section D: Biological Crystallography.  61:141-146. 2005
2004 Discrimination against deoxyribonucleotide substrates by bacterial RNA polymeraseJournal of Biological Chemistry.  279:38087-38090. 2004
2004 RNA displacement and resolution of the transcription bubble during transcription by R7 RNA polymeraseMolecular Cell.  15:777-788. 2004
2004 Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coliActa Crystallographica Section D: Biological Crystallography.  60:1611-1613. 2004
2004 Regulation through the secondary channel - Structural framework for ppGpp-DksA synergism during transcriptionCell.  118:297-309. 2004
2004 Structural basis for template-independent RNA polymerizationNature.  430:700-704. 2004
2004 Structural basis for transcription regulation by alarmone ppGppCell.  117:299-310. 2004
2004 Structural basis for substrate selection by T7 RNA polymeraseCell.  116:381-391. 2004
2003 Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8Journal of Molecular Biology.  332:729-740. 2003
2003 Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8Acta Crystallographica Section D: Biological Crystallography.  59:1651-1652. 2003
2003 ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA bindingThe EMBO Journal.  22:676-688. 2003
2003 Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complexActa Crystallographica Section D: Biological Crystallography.  59:185-187. 2003
2003 Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetaseRNA.  9:100-111. 2003
2003 Structure of the bacterial RNA polymerase holoenzymeTanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.  48:1-8. 2003
2002 Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolutionNature.  420:43-50. 2002
2002 Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilusActa Crystallographica Section D: Biological Crystallography.  58:1497-1500. 2002
2002 Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6. Å resolutionNature.  417:712-719. 2002
2002 An enzyme with a deep trefoil knot for the active-site architectureActa Crystallographica Section D: Biological Crystallography.  58:1129-1137. 2002
2001 Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetaseNature Structural and Molecular Biology.  8:203-206. 2001
2001 Crucial Role of the HIGH-loop Lysine for the Catalytic Activity of Arginyl-tRNA SynthetaseJournal of Biological Chemistry.  276:3723-3726. 2001
2001 Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicryThe EMBO Journal.  20:570-578. 2001
2001 The crystal structure of the ttCsaA protein: An export-related chaperone from Thermus thermophilusThe EMBO Journal.  20:562-569. 2001
2001 Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetasesCold Spring Harbor Laboratory: Symposia on Quantitative Biology.  66:167-173. 2001
2000 Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetaseCell.  103:793-803. 2000
1999 Crystal structures of Phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogueJournal of Molecular Biology.  287:555-568. 1999
1998 A structural basis for transition-state stabilization in antibody-catalyzed hydrolysis: Crystal structures of an abzyme at 1.8 Å resolutionJournal of Molecular Biology.  281:501-511. 1998
1998 Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificityJournal of Biological Chemistry.  273:17604-17609. 1998
1998 Crystal structure of troponin C in complex with troponin I fragment at 2.3-Å resolutionProceedings of the National Academy of Sciences of USA.  95:4847-4852. 1998
1998 Enzyme structure with two catalytic sites for double-sieve selection of substrateScience.  280:578-582. 1998
1998 Crystallization and preliminary X-ray analysis of the periplasmic receptor (PotF) of the putrescine transport system in Escherichia coliActa Crystallographica Section D: Biological Crystallography.  54:132-134. 1998
1998 The crystal structure of troponin C in complex with N-terminal fragment of troponin I: The mechanism of how the inhibitory action of troponin I is released by Ca2+-binding to troponin CAdvances in Experimental Medicine and Biology.  453:157-167. 1998
1997 Surface of bacteriorhodopsin revealed by high-resolution electron crystallographyNature.  389:206-211. 1997
1997 DNA-repair enzymesCurrent Opinion in Structural Biology.  7:103-109. 1997
1997 High Resolution Structure of Bacteriorhodopsin Determined by Electron CrystallographyPhotochemistry and Photobiology.  66:764-767. 1997
1996 Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coliJournal of Biological Chemistry.  271:9519-9525. 1996
1996 Precluding uracil from DNAStructure.  4:1381-1385. 1996
1996 The 1.8-Å X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine bindingProtein Science.  5:1984-1990. 1996
1995 Atomic model of a pyrimidine dimer excision repair enzyme complexed with a dna substrate: Structural basis for damaged DNA recognitionCell.  83:773-782. 1995
1995 Architectures of class-defining and specific domains of glutamyl-tRNA synthetaseScience.  267:1958-1965. 1995
1995 Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: Refinement at 1.45 Å and X-ray analysis of the three active site mutantsJournal of Molecular Biology.  249:360-375. 1995
1995 Crystallization and preliminary X-ray analysis: Transition state complex of a chloramphenicol prodrug activation specific catalytic antibodyProtein and Peptide Letters: international journal for rapid publication of short papers in protein and peptide science.  1:252-255. 1995
1994 Atomic structure of the RuvC resolvase: A holliday junction-specific endonuclease from E. coliCell.  78:1063-1072. 1994
1994 Preliminary crystallographic study of Escherichia coli RuvC protein. An endonuclease specific for holliday junctionsJournal of Molecular Biology.  241:281-282. 1994
1994 Crystal structure of vitelline membrane outer layer protein I (VMO-I): A folding motif with homologous Greek key structures related by an internal three-fold symmetryThe EMBO Journal.  13:1003-1010. 1994
1994 Crystal Structure of T4 Endonuclease V: An Excision Repair Enzyme for a Pyrimidine DimerAnnals of the New York Academy of Sciences.  726:198-207. 1994
1993 Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2′GMPJournal of Molecular Biology.  230:979-996. 1993
1992 The polypeptide chain fold in tyrosine phenol-lyase, a pyridoxal-5′-phosphate-dependent enzymeFEBS Letters.  302:256-260. 1992
1992 Tek FRODO: A new version of FRODO for Tektronix graphics stationsJournal of Molecular Graphics and Modelling.  10:101-104. 1992

Education And Training

  • Doctorate Level Degree in Molecular Biology, 1989
  • Full Name

  • Dmitry Vassylyev