Faculty & Staff
- 1988 M. S., Charles University, Prague
- 1993 Ph.D., Charles University, Prague
- 1995-2001 Postdoctoral Fellow, University of Southern California
- 2001-2002 Research Assistant Professor, University of Southern California
The research in my lab focuses on the development and applications of modern computational methods to important problems in biochemistry and enzymology. For example, we are investigating the source of the remarkable accuracy with which DNA polymerases copy our genetic information. The accuracy (fidelity) of DNA replication is an important issue in the development of cancer and hereditary diseases. The replication fidelity that is needed to maintain healthy populations can be best appreciated if one realizes that there are about one billion base pairs (letters of the genetic alphabet) in our genome. When a cell divides, all these base pairs must be copied without mistakes to constitute a genome of the new cell. Thus, the human DNA polymerases must make less than one mistake per one billion of copied bases. The energetics of the formation of the Watson-Crick hydrogen bonds between the complementary DNA bases in aqueous solution is not sufficient to explain such enormous fidelity. Our calculations search for the free energy sources of the DNA replication fidelity in binding of nucleotide triphosphate substrates (dNTPs) to DNA polymerases. In addition, we were able to simulate the actual chemical step-the formation of the phosphodiester bond in the active site of the enzyme. The analysis of the chemistry for the right and wrong nucleotides provides additional informations about the mechanisms and fidelity of DNA polymerases. Recently, a new class of DNA polymerases, the so called 'error-prone' polymerases, have been discovered both in bacterial and human cells. These new polymerases play an important role in the DNA repair, cancer, and they are also implicated in the differentiation of lymphocytes (hypermutation). Thus, the investigation of high-fidelity and error-prone DNA polymerases will remain the subject of our research also in future. An integral part of our research are theoretical studies of simple model reactions in aqueous solution using program ChemSol:
Program ChemSol is designed for the calculations of solvation free energies using the Langevin Dipoles (LD) solvation model, in which the solvent is approximated by polarizable dipoles fixed on a cubic grid. The implementation and parameterization for aqueous solution were described in the paper " Langevin Dipoles Model for Ab Initio Calculations of Chemical Processes in Solution : Parameterization and Application to Hydration Free Energies of Neutral and Ionic Solutes, and Conformational Analysis in Aqueous Solution(1) The ChemSol 1.0 and 1.1 programs (download ChemSol 1.1) were used in studies of the chemical reactivity (2-4), binding (5), and conformational flexibility (6) in aqueous solution. The extension of the predictive capabilities of the LD model to hydration entropies has been implemented in the 2.0 and 2.1 versions of the program(7) (download ChemSol 2.1).
(1) Florián, J.; Warshel, A. J. Phys. Chem. B 1997, 101 , 5583.
(2) Florián, J.; Warshel, A. J. Am. Chem. Soc. 1997, 119, 5473 .
(3) Florián, J.; Warshel, A. J. Phys. Chem. B 1998, 102 , 719 .
(4) Florián, J.; Åqvist, J.; Warshel, A. J. Am. Chem. Soc. 1 998, 120, 11524 .
(5) Florián, J.; Sponer, J.; Warshel, A. J. Phys. Chem. B 1999 , 103, 884 .
(6) Florián, J.; Strajbl, M.; Warshel, A. J. Am. Chem. Soc. 1998, 120, 7959.
(7) Florián, J.; Warshel, A. J. Phys. Chem. B 1999, 103, 10282.
Computer Simulations of Protein Functions: Searching For the Molecular Origin of the Replication Fidelity of DNA Polymerases, J. Florián, M. F. Goodman and A. Warshel, Proc. Natl. Acad. Sci. USA 102, 6819 - 6824 (2005)
Molecular Dynamics Free Energy Simulations of the Binding Contribution to the Fidelity of T7 DNA Polymerase, J. Florián, A. Warshel and M. F. Goodman, J. Phys. Chem. B 106, 5754-5760 (2002)
Comment on Molecular Mechanics for Chemical Reactions, J. Florián,J. Phys. Chem. A 106, 5046 - 5047 (2002).
Remarkable Catalytic Enhancement of Orotidine 5'-monophosphate Decarboxylase Is Due To Transition State Stabilization Rather Than To Ground State Destabilization, A. Warshel, M. Strajbl, J. Villa, J. Florián, Biochemistry 39, 14728 - 14738 (2000).
Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine-Thymine, Adenine-Cytosine and Adenine-Difluorotoluene Mismatches, J. Florián, M. F. Goodman and A. Warshel, J. Phys. Chem. B 104, 10092 - 10099 (2000).
Q-Chem 2.0: A High-performance Ab Initio Electronic Structure Program Package, J. Kong, C. A. White, A. I. Krylov, D. Sherrill, R. D. Adamson, T. R. Furlani, M. S. Lee, A. M. Lee, S. R. Gwaltney, T. R. Adams, C. Ochsenfeld, A. T. B. Gilbert, G. S. Kedziora, V. A. Rassolov, D. R. Maurice, N. Nair, Y. Shao, N. A. Besley, P. E. Maslen, J. P. Dombroski, H. Daschel, W. Zhang, P. P. Korambath, J. Baker, E. F. C. Byrd, T. V. Voorhis, M. Oumi, S. Hirata, C.-P. Hsu, N. Ishikawa, J. Florián, A. Warshel, B. G. Johnson, P. M. W. Gill, M. Head-Gordon, J. A. Pople, J. Comput. Chem. 21, 1532 - 1548 (2000).
see also Complete List of Publications