Office: PHSC 130A Phone: (405) 325-1677 Email: valya@ou.edu Group Homepage Link	Valentin V. Rybenkov Associate Professor M.S.  (Moscow Institute of Physics and Technology) 1989 Ph.D. (Moscow Institute of Physics and Technology) 1992 Postdoctoral Research Assistant (University of California, Berkeley) 1993-2000 OU Junior Faculty Research Program Recipient, 2001
Division: Biochemistry Research Interests Physical chemistry and biochemistry of nucleic acids; chromatin structure and dynamics; mechanistic enzymology, especially as related to the chromatin modifying molecular motors.

Research Description

DNA exists within the cell as an elaborately folded nucleoprotein structure called the chromosome. Chromatin structure undergoes marked, tightly controlled changes during the cell cycle. Correct folding of the chromosome is essential for faithful execution of such fundamental events as chromosome replication, gene expression, or cell division. Errors in either of the processes often result in genomic instability and chromosomal alterations potentially leading to carcinogenesis or developmental defects. However a comprehensive picture of how chromosome rearrangements are achieved is still lacking.

It has become increasingly clear recently that a number of chromatin remodeling functions are carried out by ATP-dependent molecular motors, molecular machines that dedicatedly deform DNA at the expense of ATP hydrolysis. On a local level, a variety of chromatin remodeling factors act to establish the "open" chromatin conformation in a relatively short fragment of the chromosome so that to affect gene expression in specific loci. The global chromatin rearrangements, such as chromosome condensation during cell division, also appear to be mediated by the activity of the chromatin modifying molecular motors. An emerging group of DNA-dependent ATPases, the proteins of SMC (structural maintenance of chromosome) family, have been implicated in such diverse range of cellular functions as chromosome condensation, dosage compensation and DNA repair. My lab’s research is focused on the mechanism of SMC proteins.

The structure of SMC proteins befits their role in orchestrating large-scale chromatin rearrangements. They consist of two globular domains, the ATP- and DNA-binding domains, connected by two long coiled-coil regions. In solution the proteins dimerize in an anti-parallel manner to form a molecule where the two DNA binding domains can be as far as 100 nm apart. Within the cell, the SMC proteins associate with other, non-SMC proteins to form various complexes with specific cellular functions. The best biochemically characterized SMC complex is 13S condensin, a Xenopus SMC complex responsible for chromosome condensation during cell division. We recently learnt that 13S condensin compacts DNA by directly introducing global writhe into the molecule (see Fig.1, Kimura et al 1999). Most intriguingly, this activity requires hydrolysis of ATP and not merely ATP binding. This is an entirely novel kind of enzymatic activity. Whereas the proposed mechanism of SMC suggests immediate extrapolation for the in vivo activity of condensin, a number of questions remain unanswered. Does condensin compact DNA in a single scissoring motion or does it employ something like loop extrusion mechanism? What is the role of ATP in the reaction? Does condensin form a supramolecular structure on DNA? How general is the found activity of condensin among various SMC proteins? How is activity of SMCs regulated inside the cell? We are addressing these questions using MukBEF, a bacterial analog of 13S condensin, as a model protein. In addition to the more traditional biochemical and topological methods (see Rybenkov et al 1997, Kimura et al 1999, Vologodskii et al 2000 for examples) we are planning to use single molecule techniques.

In the latter approach, a microscopic bead is attached to a single DNA molecule, and both position of the bead and the force exerted on the molecule is measured in real time. This set-up offers a unique advantage in studying the “DNA motors”, since protein-induced DNA deformation can be measured directly as the shortening of the DNA molecule (Fig. 2). Furthermore, single molecule methods allow to monitor complete reaction cycle of the enzyme and to focus, if need be, on the short-lived intermediates, which may be difficult to detect by the bulk, population-averaged methods. We expect that single molecule data will complement the biochemical results and will allow to reconstruct the mechanism of MukBEF. That in turn should bring us closer to understanding how does the chromatin structure relate to its functions.

Rybenkov, V.V., Cozzarelli, N.R. and Vologodskii, A.V., "The probability of DNA knotting and the effective diameter of the DNA double helix." Proc. Natl. Acad. Sci. USA, 90, 5307-5311, 1993. 

Rybenkov, V.V., Vologodskii, A.V. and Cozzarelli, N.R., "The effect of ionic conditions on conformations of supercoiled DNA. I Sedimentation analysis." J. Mol. Biol., 267, 299-311, 1997.

Rybenkov, V.V., Vologodskii, A.V. and Cozzarelli, N.R., "The effect of ionic conditions on conformations of supercoiled DNA. II Catenation equilibrium." J. Mol. Biol., 267, 312-323, 1997.

Rybenkov, V.V., Vologodskii, A.V. and Cozzarelli, N.R., "The effect of ionic conditions on DNA helical repeat, effective diameter, and free energy of supercoiling" Nucl. Acids Res., 25, 1412-1418, 1997.

Rybenkov, V.V., Ullsperger, C. U., Vologodskii, A.V. and Cozzarelli, N.R., "Simplification of DNA topology below equilibrium values by type II topoisomerases." Science, 277, 690-693, 1997.

Alexandrov, A.I., Cozzarelli N.R., Holmes, V.F., Khodursky, A.B., Peter, B.J., Postow, L., Rybenkov, V.V. and Vologodskii, A.V. "Mechanisms of separation of the complementary strands of DNA during replication." in "Structural Biology and Functional Genomics", NATO Science Series 3 (High technology), E. Morton Bradbury and Sandor Pongor (eds), Kluwer Academic Publishers, Dordrecht, Boston, London, 1999, pp. 217-235.

Kimura, K., Rybenkov, V.V., Crisona, N., Hirano, T. and Cozzarelli, N.R. "13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation" Cell, 98 (2), 239-248, 1999.

Vologodskii, A.V., Zhang, W., Rybenkov, V.V., Podtelezhnikov, A.A., Subramanian, D., Griffith, J.D., Cozzarelli, N.R. "Mechanism of topology simplification by type II DNA topoisomerases", Proc. Natl. Acad. Sci., 98(6), 3045-3049, 2001.

Dekker, N.H., Rybenkov, V.V., Duguet, M., Cozzarelli, N.R., Bensimon, D. "The Mechanism of Type IA Topoisomerases"Proc. Natl. Acad. Sci. USA, (2002) 99(19):12126-31.

Petrushenko, Z.M., Lai, C., Rai, R., Rybenkov, V.V. "DNA reshaping by MukB: right-handed knotting, left-handed supercoiling" J. Biol. Chem., (2006) 281(8):4606-15.

Wang, Q., Mordukhova, E., Edwards A., Rybenkov, V.V. "Chromosome condensation in the absence of non-SMC subunits of MukBEF." J. Bacteriol., (2006) 188(12):4431-41.

Petrushenko, Z.M., Lai, C., Rybenkov, V.V. "Antagonistic interaction between kleisins and DNA with bacterial condensin MukB" submitted 2006.

She, W., Wang, Q., Mordukhova, E.A. and Rybenkov, V.V. "MukEF is required for stable association of MukB with the chromosome" submitted 2006