TRITON: in silico construction of protein mutants and prediction of their activities

PROKOP, Martin, Jiří DAMBORSKÝ and Jaroslav KOČA. TRITON: in silico construction of protein mutants and prediction of their activities. Bioinformatics. 2000, vol. 16, No 9, p. 845-846. ISSN 1367-4803.

Basic information

• Original name: TRITON: in silico construction of protein mutants and prediction of their activities
• Authors: PROKOP, Martin (203 Czech Republic), Jiří DAMBORSKÝ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor).
• Edition: Bioinformatics, 2000, 1367-4803.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 3.409
• RIV identification code: RIV/00216224:14310/00:00002682
• Organization unit: Faculty of Science
• UT WoS: 000165748700013
• Keywords in English: HALOALKANE DEHALOGENASE; SUBSTRATE-SPECIFICITY; CATALYTIC MECHANISM
• Tags: CATALYTIC MECHANISM, haloalkane dehalogenase, SUBSTRATE-SPECIFICITY

Abstract

Motivation: One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activities offers the possibility of process automatization. Results: The graphical program TRITON has been developed for modelling protein mutants and assessment of their activities. Protein mutants are modelled from the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of mutants activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data. Availability: The program TRITON can run under operating systems IRIX, Linux and NetBSD. The software is available at http://www.chemi.muni.cz/lbsd/triton.html.Contact: [e-mail]

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