D. Vassylyev

发表

Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution

S. Yokoyama, T. Tahirov, D. Temiakov, 2002, Nature.

Structure and function of a membrane component SecDF that enhances protein export

O. Nureki, Koreaki Ito, D. Vassylyev, 2011, Nature.

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution

S. Yokoyama, D. Vassylyev, O. Laptenko, 2002, Nature.

Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.

P. Cramer, E. Lehmann, D. Vassylyev, 2009, Molecular cell.

Structural basis for converting a general transcription factor into an operon-specific virulence regulator.

Nick V Grishin, Irina Artsimovitch, N. Grishin, 2007, Molecular cell.

Crystal Structure of Albaflavenone Monooxygenase Containing a Moonlighting Terpene Synthase Active Site*

Li Lei, Bin Zhao, S. Kelly, 2009, The Journal of Biological Chemistry.

The polypeptide chain fold in tyrosine phenol‐lyase, a pyridoxal‐5′‐phosphate‐dependent enzyme

Z. Dauter, K. Wilson, A. Antson, 1992, FEBS letters.

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.

D. Vassylyev, T. Shimizu, S. Kido, 1994 .

Structural basis for transcription inhibition by tagetitoxin

Naohiro Matsugaki, Noriyuki Igarashi, Soichi Wakatsuki, 2005, Nature Structural &Molecular Biology.

Crystal Structure and Mutational Analysis of theEscherichia coli Putrescine Receptor

D. Vassylyev, K. Morikawa, K. Kashiwagi, 1998, The Journal of Biological Chemistry.

Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications.

D. Vassylyev, Y. Devedjiev, C. Steussy, 2007, Journal of molecular biology.

Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus.

Tsuyoshi Inoue, Yusuke Mori, Hiroaki Adachi, 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8.

M. Nishiyama, S. Yokoyama, D. Vassylyev, 2003, Acta crystallographica. Section D, Biological crystallography.

Structural Basis for Double-Sieve Discrimination of L-Valine from L-Isoleucine and L-Threonine by the Complex of tRNAVal and Valyl-tRNA Synthetase

Shigeyuki Yokoyama, Osamu Nureki, O. Nureki, 2000, Cell.

DNA-repair enzymes.

D. Vassylyev, K. Morikawa, Kosuke Morikawa, 1993, Current opinion in structural biology.

The 1.8‐Å X‐ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding

Y. Matsuo, D. Vassylyev, K. Morikawa, 1996, Protein science : a publication of the Protein Society.

Interaction Between HIV-1 Nef and Calnexin: From Modeling to Small Molecule Inhibitors Reversing HIV-Induced Lipid Accumulation

M. Bukrinsky, D. Sviridov, A. Üren, 2016, Arteriosclerosis, Thrombosis and Vascular Biology.

Structural basis for template-independent RNA polymerization

O. Nureki, D. Vassylyev, R. Ishitani, 2004, Nature.

Preliminary crystallographic study of Escherichia coli RuvC protein. An endonuclease specific for Holliday junctions.

D. Vassylyev, H. Shinagawa, K. Morikawa, 1994, Journal of molecular biology.

Crystal Structure of T4 Endonuclease V: An Excision Repair Enzyme for a Pyrimidine Dimer

H. Nakamura, D. Vassylyev, K. Morikawa, 1994, Annals of the New York Academy of Sciences.

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.

D. Vassylyev, T. Shimizu, S. Kido, 1994, EMBO Journal.

Tracking RNA Polymerase, One Step at a Time

D. Vassylyev, I. Artsimovitch, 2005, Cell.

Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

Daria A. Gaykalova, D. Vassylyev, I. Artsimovitch, 2009, Nature Structural &Molecular Biology.

The carboxy‐terminal coiled‐coil of the RNA polymerase β′‐subunit is the main binding site for Gre factors

D. Vassylyev, I. Artsimovitch, M. Vassylyeva, 2007, EMBO reports.

Allosteric Modulation of the RNA Polymerase Catalytic Reaction Is an Essential Component of Transcription Control by Rifamycins

Naohiro Matsugaki, Noriyuki Igarashi, Soichi Wakatsuki, 2005, Cell.

Structural insights into mechanisms of the small RNA methyltransferase HEN1

Qixing Huang, D. Vassylyev, Jinbiao Ma, 2009, Nature.

An enzyme with a deep trefoil knot for the active-site architecture.

Shigeyuki Yokoyama, Osamu Nureki, Seiki Kuramitsu, 2002, Acta crystallographica. Section D, Biological crystallography.

Structural basis of transcription inhibition by antibiotic streptolydigin.

T. Tahirov, D. Temiakov, D. Vassylyev, 2005, Molecular cell.

Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.

D G Vassylyev, D. Vassylyev, O. Lavrik, 1999, Journal of molecular biology.

Structural basis for transcription elongation by bacterial RNA polymerase

Tahir H. Tahirov, Irina Artsimovitch, T. Tahirov, 2007, Nature.

Structural basis for substrate loading in bacterial RNA polymerase

Irina Artsimovitch, Robert Landick, Jinwei Zhang, 2007, Nature.

Structural Basis for Substrate Selection by T7 RNA Polymerase

Shigeyuki Yokoyama, Vsevolod Patlan, S. Yokoyama, 2004, Cell.

Elongation by RNA polymerase: a race through roadblocks.

D. Vassylyev, 2009, Current opinion in structural biology.

RNA displacement and resolution of the transcription bubble during transcription by T7 RNA polymerase.

W. Mcallister, D. Vassylyev, M. Jiang, 2004, Molecular cell.

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.

Melanie B. Berkmen, R. Gourse, D. Vassylyev, 2008, Journal of molecular biology.

A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment.

D. Temiakov, M. Anikin, W. Mcallister, 2006, Molecular cell.

Structural Basis for Transcription Regulation by Alarmone ppGpp

S. Yokoyama, V. Patlan, D. Vassylyev, 2004, Cell.

Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex.

S. Yokoyama, T. Tahirov, D. Temiakov, 2003, Acta crystallographica. Section D, Biological crystallography.

The binding site and mechanism of the RNA polymerase inhibitor tagetitoxin: An issue open to debate

D. Vassylyev, S. Klyuyev, 2012, Transcription.

Transcription inactivation through local refolding of the RNA polymerase structure

E. Nudler, D. Vassylyev, I. Artsimovitch, 2009, Nature.

Discrimination against Deoxyribonucleotide Substrates by Bacterial RNA Polymerase*

D. Vassylyev, I. Artsimovitch, V. Svetlov, 2004, Journal of Biological Chemistry.

Allosteric control of the RNA polymerase by the elongation factor RfaH

D. Vassylyev, I. Artsimovitch, Elena V Shabrova, 2007, Nucleic acids research.

Regulation through the RNA Polymerase Secondary Channel

J. Symerský, D. Vassylyev, I. Artsimovitch, 2006, Journal of Biological Chemistry.

Efficient, ultra-high-affinity chromatography in a one-step purification of complex proteins

Hengbin Wang, D. Vassylyev, Zhuo Zhang, 2017, Proceedings of the National Academy of Sciences.

The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase.

D. Vassylyev, R. Landick, K. S. Ha, 2010, Journal of molecular biology.

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

E. Koonin, I. Rogozin, T. Tahirov, 2008, Cell cycle.

The elongation factor RfaH and the initiation factor σ bind to the same site on the transcription elongation complex

D. Vassylyev, I. Artsimovitch, V. Svetlov, 2008, Proceedings of the National Academy of Sciences.

Merging the RNA and DNA worlds

D. Vassylyev, I. Artsimovitch, 2007, Nature Structural &Molecular Biology.

Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations

T. Tahirov, D. Temiakov, M. Anikin, 2006, Nucleic acids research.

Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.

S. Yokoyama, T. Shibata, D. Vassylyev, 2002, Acta crystallographica. Section D, Biological crystallography.

Atomic model of a pyrimidine dimer excision repair enzyme complexed with a dna substrate: Structural basis for damaged DNA recognition

Shigenori Iwai, Mariko Ariyoshi, D. Vassylyev, 1995, Cell.

Conformational transition of Sec machinery inferred from bacterial SecYE structures

Y. Sugita, O. Nureki, Koreaki Ito, 2008, Nature.

Is It Easy to Stop RNA Polymerase?

D. Vassylyev, I. Artsimovitch, 2006, Cell cycle.

Regulation through the Secondary Channel—Structural Framework for ppGpp-DksA Synergism during Transcription

Shigeyuki Yokoyama, Irina Artsimovitch, S. Yokoyama, 2004, Cell.

Crystal Structure and Mutational Analysis of theEscherichia coli Putrescine Receptor

K Morikawa, D G Vassylyev, D. Vassylyev, 1998, The Journal of Biological Chemistry.

Crystal Structure of PotD, the Primary Receptor of the Polyamine Transport System in Escherichia coli(*)

D. Vassylyev, K. Morikawa, M. Matsushima, 1996, The Journal of Biological Chemistry.

Surface of bacteriorhodopsin revealed by high-resolution electron crystallography

Akinori Kidera, Kaoru Mitsuoka, Yoshinori Fujiyoshi, 1997, Nature.

Surfaceof bacteriorhodopsin revealedbyhigh-resolution electroncrystallography

A. Kidera, Y. Fujiyoshi, A. Miyazawa, 2022 .

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 Ca(2+)-binding to troponin C.

D. Vassylyev, Y. Maéda, S. Takeda, 1998, Advances in experimental medicine and biology.

Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing

Wei Wu, Amanda E. Jones, Hengbin Wang, 2017, Proceedings of the National Academy of Sciences.

Crystal structure of troponin C in complex with troponin I fragment at 2.3-A resolution.

D G Vassylyev, D. Vassylyev, Y. Maéda, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Enzyme structure with two catalytic sites for double-sieve selection of substrate.

D G Vassylyev, O. Nureki, S. Yokoyama, 1998, Science.

Atomic structure of the RuvC resolvase: A holliday junction-specific endonuclease from E. coli

Haruki Nakamura, D. Vassylyev, H. Shinagawa, 1994, Cell.

Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.

O. Nureki, T. Kigawa, S. Yokoyama, 1995, Science.

Corallopyronin A specifically targets and depletes essential obligate Wolbachia endobacteria from filarial nematodes in vivo.

A. Hoerauf, D. Vassylyev, T. Schäberle, 2012, The Journal of infectious diseases.

endobacteria from filarial nematodes in vivo

A. Hoerauf, D. Vassylyev, T. Schäberle, 2012 .

Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.

J. Symerský, D. Vassylyev, 2007, Journal of molecular biology.

Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.

M. Nishiyama, S. Yokoyama, D. Vassylyev, 2003, Journal of molecular biology.

The crystal structure of the ttCsaA protein: an export‐related chaperone from Thermus thermophilus

S. Yokoyama, T. Shibata, D. Vassylyev, 2001, The EMBO journal.

Precluding uracil from DNA.

D. Vassylyev, K. Morikawa, 1996, Structure.

Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.

Shigeyuki Yokoyama, Osamu Nureki, O. Nureki, 2003, RNA.

Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilus.

D. Vassylyev, I. Artsimovitch, A. Perederina, 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding

Shigeyuki Yokoyama, Osamu Nureki, O. Nureki, 2003, The EMBO journal.

Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA.

D. Vassylyev, I. Artsimovitch, Y. Devedjiev, 2006, Acta Crystallographica. Section F : Structural Biology and Crystallization Communications.

Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus.

S. Yokoyama, Koreaki Ito, T. Tahirov, 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli.

Shigeyuki Yokoyama, Irina Artsimovitch, S. Yokoyama, 2004, Acta crystallographica. Section D, Biological crystallography.

Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.

D. Vassylyev, K. Morikawa, E. Ohtsuka, 1994, Journal of molecular biology.

A structural basis for transition-state stabilization in antibody-catalyzed hydrolysis: crystal structures of an abzyme at 1. 8 A resolution.

K Morikawa, D G Vassylyev, D. Vassylyev, 1998, Journal of molecular biology.

DNA-repair enzymes

D. Vassylyev, K. Morikawa, 1993 .

Insights into Structure-Activity Relationships of Bacterial RNA Polymerase Inhibiting Corallopyronin Derivatives.

A. Hoerauf, D. Vassylyev, T. Stehle, 2015, Journal of natural products.

Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer.

Koreaki Ito, T. Tahirov, D. Vassylyev, 2006, Journal of molecular biology.

Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase

Shigeyuki Yokoyama, Osamu Nureki, O. Nureki, 2001, Nature Structural Biology.

Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2'GMP.

K Morikawa, D G Vassylyev, D. Vassylyev, 1993, Journal of molecular biology.

The Transition to an Elongation Complex by T7 RNA Polymerase Is a Multistep Process*

M. Anikin, W. Mcallister, D. Vassylyev, 2007, Journal of Biological Chemistry.

Structure of Pseudomonas aeruginosa Hfq protein.

S. Yokoyama, G. Kachalova, D. Vassylyev, 2005, Acta crystallographica. Section D, Biological crystallography.

Crucial Role of the HIGH-loop Lysine for the Catalytic Activity of Arginyl-tRNA Synthetase*

O. Nureki, S. Yokoyama, D. Moras, 2001, The Journal of Biological Chemistry.

Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.

S. Yokoyama, T. Shibata, D. Vassylyev, 2002 .

Structure of the EMAPII domain of human aminoacyl‐tRNA synthetase complex reveals evolutionary dimer mimicry

J. Cherfils, M. Mirande, S. Yokoyama, 2001, The EMBO journal.

Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases.

O. Nureki, S. Yokoyama, D. Vassylyev, 2001, Cold Spring Harbor symposia on quantitative biology.

Functional Structures of Class-I Aminoacyl-tRNA Synthetases

O. Nureki, S. Yokoyama, D. Moras, 1999 .