Razvoj računalnih programa za automatsko pronalaženje modela i domena neribosomalnih peptid sinteza

master's thesis

• Title (english): Development of computer programs to automatically find modules and domains of non-robosomal peptide synthetases
• Author: Vilson Široka
• Mentor: Daslav Hranueli (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2005-11-29, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Neribosomalno sintetizirani peptidi su sekundarni mikrobni metaboliti, koji predstavljaju veliku i raznovrsnu skupinu biološki aktivnih prirodnih spojeva. Njihov biosintetski put započinje uzastopnom kondenzacijom jednostavnih građevnih jedinica (aminokiselina), te dovodi do izgradnje peptidnih lanaca određenih dužina katalitičkim djelovanjem sintetaza neribosomalnih peptida (NRPS). Znanstvenici su do sada klonirali i sekvencirali vrlo velik broj NRPS-a, no njihove funkcionalnosti i krajnji proizvodi većinom nisu poznati. Sekvenciranje svih tih genskih nakupina ukazuje na mogućnost modeliranja procesa rekombinacije između modularnih sintetaza u uvjetima in silico. To bi pružilo mogućnost predviđanja kemijskih struktura novonastalih supstancija. U ovom je diplomskom radu, za potrebe tog projekta, izrađen novi računalni program, kojem je svrha analiza i detaljno opisivanje nedovoljno opisanih NRPS sustava. Izrađeni računalni program popunjava bazu podataka VCL sekvencijama DNA i proteina modula i domena iz prethodno nedovoljno detaljno opisanih NRPS sustava.

Abstract (english)

Nonribosomal peptides are secondary microbial metabolites which represent large and divers group of biologically active natural products. Their biosynthesis begins with a consecutive condensation of simple building block monomers – aminoacides - (a series of cycles) and leads to construction of peptide chains with defined length by catalytic activity of nonribosomal polypeptide synthetases (NRPS). So far scientists have cloned and sequenced a large number of NRPSs, but their functionalities and final products are mostly unknown. Sequencing of these gene clusters revealed the possibility of modelling the recombination process between modular synthetases in in silico. It would allow the prediction of chemical structure of novel compounds. In this diploma work, a new computer program has been constructed in order to assist the developed project, with a purpose of analysis and annotation of insufficiently described NRPS systems. The constructed computer program add DNA and protein sequences of modules and domains from mentioned NRPS systems into the VCL database.

• Keywords: baze podataka EMBL i VCL; računalni jezik PERL i projekt BioPerl; neribosomalni peptidi; moduli i domene
• Keywords (english): EMBL and VCL databases; computer language PERL and project BioPerl; non-ribosomal peptides; modules and domains
• Language: croatian
• URN:NBN: urn:nbn:hr:159:707675
• Study programme: Title: Biotechnology; specializations in: Biochemical Engineering; Course: Biochemical Engineering; Study programme type: university; Study level: graduate; Academic / professional title: diplomirani inženjer biotehnologije; smjer biokemijsko inženjerstvo (diplomirani inženjer biotehnologije; smjer biokemijsko inženjerstvo)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Repository: Repository of the Faculty of Food Technology and Biotechnology
• Created on: 2017-09-11 10:28:03