Vloga aminokislinskega zaporedja pri strukturi proteina na primeru alfa vijačnice

Agrež, Tim-David (author), Hribar Lee, Barbara (mentor)

V procesu zvijanja protein pridobi nativno strukturo, ki mu omogoča opravljanje bioloških funkcij. Med pomembnejšimi dejavniki tega procesa je tvorba sekundarnih struktur. V nalogi sem iz objavljenih struktur iz podatkovne baze proteinskih struktur pridobil skupino struktur, iz katerih sem osamil zaporedja, ki so bila v strukturah označena kot vijačnice. Tako dobljena zaporedja sem poravnal s programom Clustal omega in pridobil pogoste vzorce, ki tvorijo vijačnice. Na koncu sem preveril, ali se dobljeni vzorci pojavijo v vijačnicah ali neurejenem delu verige tudi pri drugih proteinih in pregledal pogostost pojavnosti v vijačnicah za posamezen vzorec. Izkazalo se je, da je z izbranim pristopom možno dobiti veliko število potencialnih vzorcev, a mnogi v strukturi ne bodo nujno v obliki alfa vijačnic. Tudi za vzorce, ki kažejo nagnjenje do zvijanja v vijačnice, velja, da se tako ne zvijejo vedno in s tem sem pokazal, da proces ni tako nedvoumen, kot bi se zdelo na prvi pogled.

• Language: Slovenian
• Keywords: alfa vijačnice, struktura proteinov, aminokislinsko zaporedje
• Work type: Bachelor thesis/paper
• Typology: 2.11 - Undergraduate Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2025
• PID: 20.500.12556/RUL-172655
• COBISS.SI-ID: 256335363
• Publication date in RUL: 10.09.2025

Secondary language

• Language: English
• Title: The role of aminoacid sequence in protein structure: an example of alpha helix

Abstract

Protein molecules form their native structures which allow them to perform their function in the proces of folding. In this work a sample group of protein structures was chosen and from it sequences that formed alfa helices were isolated. Sequences were then aligned using Clustal omega and pattern sequences of the alignments were acquired. In the end the gathered pattern sequences were studied further while also looking at which parts of other sequences they were found in. In this study I managed to acquire a number of sequences that potentially signified an alpha helix fold, but many of those were not proven to fold into a helix in all structures. At the same time even the patterns that showed propensity towards a helix formation were not found in helices of other structures consistently and as such showed that secondary structure formation is not as straightforward as it may seem at first.

• Keywords: alpha helix, protein structure, aminoacid sequence