Vizualizacija strukture proteina

master's thesis

• Title (english): Protein Structure Visualization
• Author: Toni Sente
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Marina Bagić Babac (član povjerenstva)
• Committee member: Ivica Botički (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2019-07-09, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Proteini su sastavni dio svake stanice, a sastoje se od jednog ili više lanaca aminokiselina. Prilikom njihovog proučavanja, možemo govoriti o četiri razine struktura: primarnoj, sekundarnoj, tercijarnoj te kvartarnoj. Niz aminokiselina kao takav, bez proučavanja međusobne interakcije unutar proteina, čini primarnu strukturu. Sekundarnu strukturu proteina čine nekoliko različitih tvorevina koje nastaju na jednom lancu od kojih su najvažnije α-zavojnice i β-lanci. Tercijarna struktura opisuje funkciju jednog lanca uz prisustvo sekundarnih struktura, dok proteini koji imaju više od jednog lanca imaju i kvartarnu strukturu koja proučava međusobni utjecaj tih lanaca.
U sklopu ovog rada razvijen je alat ProteinVisualizer čija je svrha generiranje i prikazivanje strukture proteina. Program pri pokretanju izvlači podatke o proteinu koji su zapisani u ulaznoj PDB datoteci. Za osnovu modela, kreira se krivulju koja prolazi kroz središnji atom ugljika (Cα) svake aminokiseline. Korištenjem te krivulje, te uz pomoć linearne algebre, generira se cijev, koja predstavlja okosnicu proteina, i vrpce, kojima se najčešće predstavljaju α-zavojnice i β-lanci. Konačno, spajanjem svih tih generiranih struktura, dobije se kompletan model proteina.
Rezultati koje alat generira usporedivi su s rezultatima drugih popularnih alata za vizualizaciju, što u konačnici potvrđuje ispravnost ovog postupka.

Abstract (english)

Proteins are part of every cell and they consist of one or more chains of amino acid residues. In protein analysis, there are four levels of protein structure: primary, secondary, tertiary and quaternary. Plain sequence of amino acids residues in a polypeptide chain forms primary structure. Secondary structure refers to local folded structures in a single chain, among which are the most important α-helices and β-sheets. Tertiary structure represents function of a single chain in presence of secondary structures, while interaction between multiple polypeptide chains forms a quaternary structure.
In this thesis, ProteinVisualizer software has been developed which can generate and visualize protein structure,. Program starts by parsing information about protein model from PDB file. For the model basis, curve that goes through central carbon atom (Cα) of every amino acid residue is created. By using this curve, and with help of linear algebra, tube that represents protein wireframe, but also the ribbons that represents α-helices and β-sheets, can be generated. Finally, by combining all these structures, complete protein model is created.
Results of the developed program are comparable to results of other popular tools for protein visualization, which, in the end, confirms correctness of this procedure.

• Keywords: protein; vizualizacija; struktura proteina; PDB; krivulje; Catmull-Rom; modeliranje; makromolekule; okosnica proteina; α-zavojnice; β-lanci; DirectX
• Keywords (english): protein; visualization; protein structure; PDB; curves; Catmull-Rom; modeling; macromolecules; protein wireframe; α-helix; β-sheets; DirectX
• Language: croatian
• URN:NBN: urn:nbn:hr:168:898917
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2020-01-07 21:56:51