In silico karakterizacija metagenomskih alkan 1-monooksigenaza

master's thesis

• Title (english): In silico characterisation of metagenomic alkane 1-monooxygenases
• Author: Davor Oršolić
• Mentor: Jurica Žučko (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2015-09-28, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Cilj istraživanja bio je provesti filogenetsku analizu, funkcionalnu karakterizaciju i trodimenzionalno strukturno modeliranje hipotetskih alkan monooksigenaza iz metagenomske knjižnice sastavljene iz umjereno onečišćenog uzorka sakupljenog iz sedimenta lučnog sidrišta u Puli. Filogenetska analiza provedena je s pomoću MEGA programa, te je dala hipotetski prikaz evolucijske povezanosti između proteina. Funkcionalnom karakterizacijom putem UniProt, InterPro i CD baze podataka potvrđena je pripadnost ispitivanih proteina alkan 1-monooksigenazama, dok strukturno modeliranje s pomoću SWISS-MODEL i I-TASSER web servisa nisu dali značajne rezultate niti za jedan od proteina. Neuspjelost strukturnog modeliranja pripisana je nedostatku homolognih proteina s eksperimentalno određenom trodimenzionalnom strukturom.

Abstract (english)

Phylogenetic analysis, functional characterization and structural modeling of putative alkan monooxygenases from metagenomic library constructed from a moderately polluted sample collected from a tanker berth station in Pula was performed. Phylogenetic analysis conducted via MEGA software resulted in phylogenetic tree representing hypothesis of evolutionary relationships between proteins. Functional characterization using UniProt, InterPro and CDD search engines confirmed similarities between putative proteins and alkan 1-monooxygenases, while structural modeling via SWISS-MODEL and I-TASSER server didn't give significant results. Inefficiency of structural modeling was attributed to absence of homologous proteins with experimentally determined three-dimensional structure.

• Keywords: alkB; metagenomska knjižnica; karakterizacija; filogenetsko stablo; razgradnja alkana
• Keywords (english): alkB; metagenomic library; characterization; phylogenetic tree; alkane degradation
• Language: croatian
• URN:NBN: urn:nbn:hr:159:068577
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-04-28 12:40:09