TRITON: graphic software for rational engineering of enzymes

DAMBORSKÝ, Jiří, Martin PROKOP and Jaroslav KOČA. TRITON: graphic software for rational engineering of enzymes. Trends in Biochemical Sciences. 2001, vol. 28, No 1, p. 71-73.

Basic information

• Original name: TRITON: graphic software for rational engineering of enzymes
• Authors: DAMBORSKÝ, Jiří (203 Czech Republic), Martin PROKOP (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor).
• Edition: Trends in Biochemical Sciences, 2001.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: Netherlands
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• RIV identification code: RIV/00216224:14310/01:00002737
• Organization unit: Faculty of Science
• UT WoS: 000168719600019
• Keywords in English: Protein engineering; Enzyme reactions; Homology modeling
• Tags: Enzyme reactions, Homology modeling, Protein engineering

Abstract

The engineering of enzymes for improving their catalytic properties is one of the present-day challenges of biochemistry and molecular biology. 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 availability of the three-dimensional structure of the protein, preferably in the complex with the substrate, makes a significant step forward in the understanding the protein-ligand interactions. However, this is just an initial step in understanding how these interactions influence the conversion of the substrate to the product. The catalytic efficiency of enzymes is usually determined by their ability to stabilise the transition state of their reactions. Consequently, an examination of the enzyme-substrate complex, i.e. the educt structure, may not give a realistic picture about the importance of particular residues for the catalysis. Computer modelling, namely quantum mechanic calculations, which enables the modelling of biochemical reactions and the localisation of the transition state structure, may bring substantially deeper insight to the problem.

Links

• GA203/97/P149, research and development project: Name: Studium molekulárních mechanismů biodegradačních reakcí - konstrukce QSBR modelů a proteinové inženýrství dehalogenas

Investor: Czech Science Foundation, Study of the molecular mechanisms of biodegradation reactions - construction of QSBR models and protein engineering of haloalkane dehalogenases

• ME 276, research and development project: Name: Racionální re-design mikrobiálních enzymů podílejících se na degradaci toxických organických polutantů

Investor: Ministry of Education, Youth and Sports of the CR, Rational re-design of microbial enzymes involved in degradation of toxic organic pollutants.

• MSM 143100005, plan (intention): Name: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Structure-function Relationships and their role in the Metabolism