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 silencing 2017
2017 Efficient, ultra-high-Affinity chromatography in a one-step purification of complex proteins 2017
2016 Interaction between HIV-1 nef and calnexin: From modeling to small molecule inhibitors reversing HIV-induced lipid accumulation 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 II 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 complex 2008
2007 Merging the RNA and DNA worlds 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 DNA 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 thermophilus 2006
2006 Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilus 2006
2006 Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus 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 tagetitoxin 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 binding 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 holoenzyme 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 synthetase 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 mimicry 2001
2001 The crystal structure of the ttCsaA protein: An export-related chaperone from Thermus thermophilus 2001
2001 Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases 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 resolution 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 antibody 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 symmetry 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 stations 1992

Education And Training

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

  • Dmitry Vassylyev