Positions

Selected Publications

Academic Article

Year Title Altmetric
2022 Application of a Novel CL7/Im7 Affinity System in Purification of Complex and Pharmaceutical Proteins.  Methods 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 Derivatives.  Journal of Natural Products.  78:2505-2509. 2015
2012 Corallopyronin a specifically targets and depletes essential obligate wolbachia endobacteria from filarial nematodes in vivo.  Journal of Infectious Diseases.  206:249-257. 2012
2012 The binding site and mechanism of the RNA polymerase inhibitor tagetitoxin: An issue open to debate.  Transcription.  3:46-50. 2012
2011 Structure and function of a membrane component SecDF that enhances protein export.  Nature.  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 Polymerase.  Journal of Molecular Biology.  401:708-725. 2010
2009 Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active site.  Journal of Biological Chemistry.  284:36711-36719. 2009
2009 Elongation by RNA polymerase: a race through roadblocks.  Current Opinion in Structural Biology.  19:691-700. 2009
2009 Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.  Nature Structural and Molecular Biology.  16:1272-1278. 2009
2009 Structural insights into mechanisms of the small RNA methyltransferase HEN1.  Nature.  461:823-827. 2009
2009 Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNA.  Molecular Cell.  34:710-721. 2009
2009 Transcription inactivation through local refolding of the RNA polymerase structure.  Nature.  457:332-335. 2009
2008 Conformational transition of Sec machinery inferred from bacterial SecYE structures.  Nature.  455:988-991. 2008
2008 X-ray structure of the complex of regulatory subunits of human DNA polymerase δ.  Cell 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 Regulation.  Journal 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.  Nature 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 factors.  EMBO Reports.  8:1038-1043. 2007
2007 Allosteric control of the RNA polymerase by the elongation factor RfaH.  Nucleic Acids Research.  35:5694-5705. 2007
2007 The transition to an elongation complex by T7 RNA polymerase is a multistep process.  Journal of Biological Chemistry.  282:22879-22886. 2007
2007 Crystal Structure of Pyruvate Dehydrogenase Phosphatase 1 and its Functional Implications.  Journal 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 Implications.  Journal of Molecular Biology.  370:407-416. 2007
2007 Structural basis for substrate loading in bacterial RNA polymerase.  Nature.  448:163-168. 2007
2007 Structural basis for transcription elongation by bacterial RNA polymerase.  Nature.  448:157-162. 2007
2007 Structural Basis for Converting a General Transcription Factor into an Operon-Specific Virulence Regulator.  Molecular Cell.  26:117-129. 2007
2006 Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head Dimer.  Journal of Molecular Biology.  364:248-258. 2006
2006 A Mechanism of Nucleotide Misincorporation during Transcription due to Template-Strand Misalignment.  Molecular 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.  Acta Crystallographica Section F: Structural Biology Communications.  62:1027-1030. 2006
2006 Elongation complexes of thermus thermophilus RNA polymerase that possess distinct translocation conformations.  Nucleic Acids Research.  34:4036-4045. 2006
2006 Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus.  Acta Crystallographica Section F: Structural Biology Communications.  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 thermophilus.  Acta Crystallographica Section F: Structural Biology Communications.  62:44-46. 2006
2006 Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus.  Acta Crystallographica Section F: Structural Biology Communications.  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 factors.  Journal of Biological Chemistry.  281:1309-1312. 2006
2005 Structural basis for transcription inhibition by tagetitoxin.  Nature Structural and Molecular Biology.  12:1086-1093. 2005
2005 Tracking RNA polymerase, one step at a time.  Cell.  123:977-979. 2005
2005 Structural basis of transcription inhibition by antibiotic streptolydigin.  Molecular Cell.  19:655-666. 2005
2005 Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.  Cell.  122:351-363. 2005
2005 Structure of Pseudomonas aeruginosa Hfq protein.  Acta crystallographica. Section D, Structural biology.  61:141-146. 2005
2004 Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase.  Journal of Biological Chemistry.  279:38087-38090. 2004
2004 RNA displacement and resolution of the transcription bubble during transcription by R7 RNA polymerase.  Molecular Cell.  15:777-788. 2004
2004 Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli.  Acta crystallographica. Section D, Structural biology.  60:1611-1613. 2004
2004 Regulation through the secondary channel - Structural framework for ppGpp-DksA synergism during transcription.  Cell.  118:297-309. 2004
2004 Structural basis for template-independent RNA polymerization.  Nature.  430:700-704. 2004
2004 Structural basis for transcription regulation by alarmone ppGpp.  Cell.  117:299-310. 2004
2004 Structural basis for substrate selection by T7 RNA polymerase.  Cell.  116:381-391. 2004
2003 Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.  Journal 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 HB8.  Acta crystallographica. Section D, Structural biology.  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 complex.  Acta crystallographica. Section D, Structural biology.  59:185-187. 2003
2003 Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase.  RNA.  9:100-111. 2003
2003 Structure of the bacterial RNA polymerase holoenzyme.  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.  48:1-8. 2003
2002 Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution.  Nature.  420:43-50. 2002
2002 Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.  Acta crystallographica. Section D, Structural biology.  58:1497-1500. 2002
2002 Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6. Å resolution.  Nature.  417:712-719. 2002
2002 An enzyme with a deep trefoil knot for the active-site architecture.  Acta crystallographica. Section D, Structural biology.  58:1129-1137. 2002
2001 Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase.  Nature Structural and Molecular Biology.  8:203-206. 2001
2001 Crucial Role of the HIGH-loop Lysine for the Catalytic Activity of Arginyl-tRNA Synthetase.  Journal 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 synthetase.  Cell.  103:793-803. 2000
1999 Crystal structures of Phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.  Journal 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 resolution.  Journal of Molecular Biology.  281:501-511. 1998
1998 Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.  Journal 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 substrate.  Science.  280:578-582. 1998
1998 Crystallization and preliminary X-ray analysis of the periplasmic receptor (PotF) of the putrescine transport system in Escherichia coli.  Acta crystallographica. Section D, Structural biology.  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 C.  Advances in Experimental Medicine and Biology.  453:157-167. 1998
1997 Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.  Nature.  389:206-211. 1997
1997 DNA-repair enzymes.  Current Opinion in Structural Biology.  7:103-109. 1997
1997 High Resolution Structure of Bacteriorhodopsin Determined by Electron Crystallography.  Photochemistry and Photobiology.  66:764-767. 1997
1996 Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli.  Journal of Biological Chemistry.  271:9519-9525. 1996
1996 Precluding uracil from DNA.  Folding & design.  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 binding.  Protein 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 recognition.  Cell.  83:773-782. 1995
1995 Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.  Science.  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 mutants.  Journal 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. coli.  Cell.  78:1063-1072. 1994
1994 Preliminary crystallographic study of Escherichia coli RuvC protein. An endonuclease specific for holliday junctions.  Journal 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 Dimer.  Annals 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′GMP.  Journal of Molecular Biology.  230:979-996. 1993
1992 The polypeptide chain fold in tyrosine phenol-lyase, a pyridoxal-5′-phosphate-dependent enzyme.  FEBS Letters.  302:256-260. 1992
1992 Tek FRODO: A new version of FRODO for Tektronix graphics stations.  Journal of Molecular Graphics and Modelling.  10:101-104. 1992

Education And Training

  • Doctorate Level Degree in Molecular Biology, 1989

    • Full Name

  • Dmitry Vassylyev