Dmitry Vassylyev, Ph.D.

image3731 Address: Kaul Human Genetics Building
Room 402B
720 20th Street South
Birmingham, AL 35294
(205) 975-8136
(205) 934-0758
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Publications  Collaboration  Equipment  Job

Dr. Dmitry G. Vassylyev, Professor

Masters Degree in Physics - Lomonosov Moscow State University, USSR 1984.
PhD  in Chemistry - Institute of Molecular Biology Acad. Sci. USSR (Moscow), 1989.
Postdoctoral training - Institute of Molecular Biology (Moscow) 1989-1992;
Protein Engineering Institute (Osaka, Japan) 1992-1995.
Senior Scientist - Biomolecular Engineering Research Institute (Osaka, Japan ) 1995-1996.
Senior Research Scientist - International Institute for Advanced Research (Panasonic, Kyoto, Japan) 1996-1998.
Group Leader - RIKEN Harima Institute (Harima, Japan) 1998-2005.
Professor - University of Alabama at Birmingham 2005-present.

Protein crystallography provides the most detailed and compelling account of the structure and function of biological macromolecules and leads to a better understanding of all cellular processes. Building on the experience we have accumulated during previous crystallographic studies covering a wide range of proteins, protein-ligand and protein-nucleic acid complexes from various biological pathways, since 2002 my lab focused on structural analysis of transcription, using crystallography as a tool and RNA polymerase (RNAP) as a major target. Crystallographic studies of transcription are particularly challenging, as most of the proteins from this pathway appear to be very flexible and unstable, thus being refractory to crystallizations and structure determination. Together with the ribosome, multi-subunit RNAPs are among the biggest asymmetric macromolecules studied by X-ray diffraction so far and are therefore at the cutting edge of modern protein crystallography.

The 2.6 A resolution crystal structure of a bacterial multi-subunit RNAP holoenzyme (MW ~450kDa) provided key insights into the mechanism of transcription initiation [Vassylyev et al. (2002), Nature]. The high resolution structure of the single-subunit T7 RNAP elongation complex (EC, MW ~120kDa) shed significant light on the basic principles of transcription elongation [Tahirov et al. (2002), Nature]. The atomic structure of the T7 RNAP EC with the incoming substrate analog revealed an intriguing two-step mechanism of substrate selection that might be common for all RNAPs [Temiakov et al. (2004), Cell]. The high resolution structure of a bacterial RNAP holoenzyme in complex with the "magic spot" (ppGpp) yielded a new model of transcriptional regulation during stringent control, an adaptive response of bacteria to amino acid starvation [Artsimovitch et al. (2004), Cell]. Subsequently, the crystal structure of the DksA protein, known to amplify the ppGpp effect, allowed us to propose and verify a detailed molecular mechanism for the DksA/ppGpp synergism [Perederina et al. (2004), Cell].  The structure of the Gfh1 protein that belongs to a family of the transcript cleavage Gre-factors, but possesses distinct effects on transcription revealed an unexpected structural variability of the protein that likely determines its unique functional properties [Symersky, et al. (2005), JBC].

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Bacterial RNAP is an attractive target for the design of antibiotics. First, despite the overall homology in structure and function of bacterial and eukaryotic RNAPs, each exhibits many distinct features, in particular, in the regulation of transcription. Second, consisting of over 3,000 amino acids, bacterial RNAP comprises a huge solvent-exposed surface that contains numerous cavities and channels, many of which are used for binding nucleic acids and/or transcription factors. Blocking off these cavities with a steric inhibitor may therefore result in disruption of transcription and eventually cell death. In order to utilize structure-based drug design of a novel antibiotics targeting RNAP one should understand the molecular mechanism of their action for which determination of the atomic structures of RNAP in complexes with the promising inhibitors is of central importance. To this end we have determined the high resolution crystal structures of the RNAP holoenzyme complexed with four bacteria-specific inhibitors: rifapentin and rifabutin (clinically important compounds from the rifamycin line of antibiotics) [Artsimovitch et al., (2005), Cell]., streptolydigin [Temiakov et al., (2005), Mol. Cell]., and tagetin [Vassylyev et al., (2005), Nature Struc. Mol. Biol.]. These works shed considerable light on the mechanistic aspects of the transcription regulation by these compounds thereby allowing intellectual improvement of their inhibitory properties.

 rifabutin tagetin strepto

Our studies were successful due to an integrated approach, wherein all stages of the structural analysis were carried out in a close collaboration among experts in crystallography and biochemistry. The studies extended beyond structure determinations to focused, functional analyses that tested structural predictions/implications. This collaborative framework allowed us in a relatively short time to address a number of questions concerning the fundamental principles of transcription and its regulation. At present my group is extensively collaborating with a number of well-established laboratories that specialize primarily on the biochemistry of transcription: Drs. William T. McAllister, Dmitry Temiakov, and Michael Anikin, University of Medicine and Dentistry of New Jersey; Drs. Irina Artsimovitch and Vladimir Svetlov, The Ohio State University; and Dr. Konstantin Severinov, Rutgers University.

Given the considerable progress of our collaborative work, we plan to continue and expand our efforts towards structural and functional studies of the major transcription intermediates. We will study (1) bacterial RNAP elongation complex with the bound transcription factors, substrates, and inhibitors; (2) various bacterial promoter complexes with alternative s factors and activators/repressors; (3) the T7 RNAP termination complex and other macromolecules that are critical for correctly regulated transcription. We will also utilize the already solved structures together with many structures in our pipeline in the structure-based drug design targeting bacterial RNAPs.

Mailing Address: 
Dr. Dmitry G. Vassylyev 
1530 3rd Avenue South
Birmingham, AL 35294-0005

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: (205) 975-8159
Fax: (205) 934-0758