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; Martin PROKOP and Jaroslav KOČA

Edition

Trends in Biochemical Sciences, 2001

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Other information

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

References:

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

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Abstract

In the original language

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.

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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