2005
TRITON: graphic software for modelling protein mutants and calculation reaction pathways
PROKOP, Martin; Jiří DAMBORSKÝ and Jaroslav KOČABasic 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; Jiří DAMBORSKÝ and Jaroslav KOČA
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
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
Marked to be transferred to RIV
Yes
RIV identification code
RIV/00216224:14310/05:00014133
Organization unit
Faculty of Science
ISSN
Keywords in English
protein; mutant; reaction; pathway; TRITON
Changed: 1/4/2009 17:50, Mgr. Martin Prokop, Ph.D.
In the original language
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
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
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