PROKOP, Martin, Jiří DAMBORSKÝ and Jaroslav KOČA. TRITON: graphic software for modelling protein mutants and calculation reaction pathways. In Materials Structure in Chemistry, Biology, Physics and Technology. vol.12, no. 1. Praha: Czech and Slovak Crystallographic Association, 2005, p. 17. ISSN 1211-5894.
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Basic information
Original name TRITON: graphic software for modelling protein mutants and calculation reaction pathways
Name in Czech TRITON: graficky program pro modelovani proteinovych mutantu a vypocet reakcnich cest
Authors PROKOP, Martin (203 Czech Republic), Jiří DAMBORSKÝ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor).
Edition vol.12, no. 1. Praha, Materials Structure in Chemistry, Biology, Physics and Technology, p. 17-17, 2005.
Publisher Czech and Slovak Crystallographic Association
Other information
Original language English
Type of outcome Proceedings paper
Field of Study 10403 Physical chemistry
Country of publisher Czech Republic
Confidentiality degree is not subject to a state or trade secret
RIV identification code RIV/00216224:14310/05:00014133
Organization unit Faculty of Science
ISSN 1211-5894
Keywords in English protein; mutant; reaction; pathway; TRITON
Tags MUTANT, pathway, PROTEIN, reaction, Triton
Changed by Changed by: Mgr. Martin Prokop, Ph.D., učo 1474. Changed: 1/4/2009 17:50.
Abstract
One of the objectives of protein engineering is to propose and construct modified enzymes with improved catalytic activity for substrate of interest. The rational engineering of an enzyme requires 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 program TRITON is a graphical tool for modelling protein mutants and assessment of their activities [1,2]. Protein mutants are modelled based on the wild type structure by homology modelling using the external program MODELLER. Enzymatic reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Activities of the mutants can be estimated by evaluation the changes in energies of the system and partial atomic charges of the active site residues during the reaction. The program TRITON offers graphical tools for preparation of input data files, for calculation and for the analysis of generated output data. Implementation ensures overall integrity of consecutive steps of the modelling of mutants and calculation of reaction pahways. The program and its methodology were proven by several studies performed on haloalkan dehalogenase enzymes [3-5]. Calculated results showed qualitative agreement with experimental data. The program TRITON can run under operating system IRIX, Linux and NetBSD. The software is available at http://ncbr.chemi.muni.cz/triton/triton.html
Abstract (in Czech)
One of the objectives of protein engineering is to propose and construct modified enzymes with improved catalytic activity for substrate of interest. The rational engineering of an enzyme requires 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 program TRITON is a graphical tool for modelling protein mutants and assessment of their activities [1,2]. Protein mutants are modelled based on the wild type structure by homology modelling using the external program MODELLER. Enzymatic reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Activities of the mutants can be estimated by evaluation the changes in energies of the system and partial atomic charges of the active site residues during the reaction. The program TRITON offers graphical tools for preparation of input data files, for calculation and for the analysis of generated output data. Implementation ensures overall integrity of consecutive steps of the modelling of mutants and calculation of reaction pahways. The program and its methodology were proven by several studies performed on haloalkan dehalogenase enzymes [3-5]. Calculated results showed qualitative agreement with experimental data. The program TRITON can run under operating system IRIX, Linux and NetBSD. The software is available at http://ncbr.chemi.muni.cz/triton/triton.html
Links
MSM0021622413, plan (intention)Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
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