Rational Redesign of Enzymes using Program TRITON


Jeřábek, P., Prokop, M., Boháč, M., Kutý, M., Koča, J., Damborský, J.


National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic


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.



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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