2005
TRITON: graphic software for modelling protein mutants and calculation reaction pathways
PROKOP, Martin, Jiří DAMBORSKÝ a Jaroslav KOČAZákladní údaje
Originální název
TRITON: graphic software for modelling protein mutants and calculation reaction pathways
Název česky
TRITON: graficky program pro modelovani proteinovych mutantu a vypocet reakcnich cest
Autoři
PROKOP, Martin (203 Česká republika), Jiří DAMBORSKÝ (203 Česká republika) a Jaroslav KOČA (203 Česká republika, garant)
Vydání
vol.12, no. 1. Praha, Materials Structure in Chemistry, Biology, Physics and Technology, s. 17-17, 2005
Nakladatel
Czech and Slovak Crystallographic Association
Další údaje
Jazyk
angličtina
Typ výsledku
Stať ve sborníku
Obor
10403 Physical chemistry
Stát vydavatele
Česká republika
Utajení
není předmětem státního či obchodního tajemství
Kód RIV
RIV/00216224:14310/05:00014133
Organizační jednotka
Přírodovědecká fakulta
ISSN
Klíčová slova anglicky
protein; mutant; reaction; pathway; TRITON
Změněno: 1. 4. 2009 17:50, Mgr. Martin Prokop, Ph.D.
V originále
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
Česky
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
Návaznosti
| MSM0021622413, záměr |
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