Rational Redesign of Enzymes using Program TRITON
Jeřábek, P., Prokop, M., Boháč, M., Kutý, M.,
Koča, J., Damborský, J.
Engineering of enzymes to improve their catalytic properties is one of the present-day challenges of biochemistry and molecular biology on the side of experimentalists and molecular modeling on the side of theoreticians. The rational engineering of a given enzyme requires an understanding of the structural features determining its catalytic efficiency. In particular, a protein engineer has to know which amino acid residues of the protein are involved in the catalysis and how to modify them to achieve an increased activity. The three-dimensional structure of the protein or protein-substrate complex is usually[JD1] required for protein engineering using molecular modeling.
Our laboratory has been developing program
TRITON as a graphical tool for modeling protein mutants and assessment of their
activities [1, 2]. TRITON serves as the simple and effective graphical
interface for preparation of input data for calculation and analysis of
outputs. Mutants are constructed from the wild type structure as the template
by homology modeling using program MODELLER [3]. Then the process of enzymatic
reaction taking place both in the wild type and in the mutant active site is
modeled using the semi-empirical quantum mechanical program MOPAC [4].
Semi-quantitative predictions of mutant activities are achieved by evaluating the
changes in the activation energies of the system associated with the mutation,
changes of partial atomic charges on selected atoms and electrostatic
interaction energies of the active site residues with the substrate during the
reaction. The applicability of TRITON has been extensively tested using
bacterial enzymes haloalkane dehalogenases as model systems [5-9].
TRITON
has primarily been developed for molecular biologists and biochemists,
non-specialists in computer modeling. Preparation of calculations using the
wizards implemented in the TRITON is very easy even for beginners in computer
modeling. The program TRITON can be run under operating systems IRIX, Linux and
NetBSD and is provided free of charge to the academic users. For more
information about TRITON see the web page
http://ncbr.chemi.muni.cz/triton/triton.html.
References:
1. Damborský, J., Prokop, M., and Koča, J., Trends in Biochemical Sciences 26 (2001) 71-73.
2. Prokop, M., Damborský, J., and Koča, J., Bioinformatics 16 (2000) 845-846.
3. Sali, A., Molecular
Medicine Today 1 (1995) 270-277.
4. Stewart, J. J. P., Journal
of Computer-Aided Molecular Design 4
(1990) 1-45.
5. Damborsky, J., Kutý, M., Němec, M., and Koča, J., Journal of Chemical Information and Computer
Sciences 37 (1997) 562-568.
6. Kutý, M., Damborský, J., Prokop, M., and Koča, J., Journal of Chemical Information and Computer
Sciences 38 (1998) 736-741.
7. Damborsky, J., Boháč, M., Prokop, M., Kutý, M., and Koča,
J., Protein Engineering 11 (1998) 901-907.
8. Boháč, M., Nagata, Y., Prokop, Z., Prokop, M., Monincová,
M., Koča, J., Tsuda, M., and Damborský, J., Biochemistry
41 (2002) 14272-14280.
9. Kmuníček, J., Boháč, M., Luengo, S., Gago, F., Wade, R. C.,
and Damborský, J., J Computer-Aided
Molecular Design 17 (2003)
299-311.
[JD1]pokud strukturu nemame, ale je k dispozici blizky homolog, muzeme pouzit homologni modelovani + docking