Bioinformacijska analiza heterodimerizacije človeških α-aktininov-1 in -4

Godec, Ajda (author), Pavšič, Miha (mentor)

α-Aktinini so proteini, ki sodelujejo pri povezovanju aktinskih filamentov v večdimenzionalne strukture. Na splošno so sestavljeni iz aktin-vezavne domene, osrednje paličaste domene in kalmodulinu podobne domene. Funkcionalno proteinsko enoto predstavlja antiparalelni homodimer. α-aktinin -1 in -4 sta bila dolgo časa obravnavna kot ločena homodimerna proteina, pred kratkim pa so raziskave potrdile obstoj njunih heterodimerov v rakavih celičnih linijah. Namen našega dela je bil z analizo zaporedij in modelov struktur ovrednotiti stabilnost heterodimera, tudi v luči fosforilacije aminokislinskih ostankov. Poravnava aminokislinskega zaporedja α-aktinina-2, katerega struktura je znana, z zaporedjem izooblik 1 in 4 kaže na visok delež identičnosti (za izoobliko 1 78 %, za izoobliko 4 pa 75 %), kar nam je omogočilo pripravo modelov homodimerov in heterodimera izooblik 1 in 4 z relativno visoko stopnjo zanesljivosti. Stična površina modela heterodimera so pokazali, da obsega 5.167,8 Å2, med podenotama pa prevladujejo hidrofobne interakcije, kar potrjujejo tudi rezultati analize s strežnikom InterProSurf. To dejstvo potrjuje še negativna vrednost ΔiG (-28 kcal/mol), ki predstavlja merilo za tvorbo hidrofobnih interakcij. Vrednost je bila izračunana z orodjem PDBePISA. Na osnovi podatkov strežnika InterProSurf in spletnega orodja PDBePISA predvidevamo, da je na stični površini med podenotama heterodimera vključenih 94 aminokislinskih ostankov α-aktinina-1, pri α-aktininu-4 pa 100. Preko napovedi fosforilacije s strežnikom NetPhos 3.1 za napoved fosforilacijskih mest in pa podatkovnih baz o fosforilaciji proteinov qPhos in EPSD predpostavljamo 4 (α-aktinin-1) oziroma 6 (α-aktinin-4) fosforilacijskih mest, ki se nahajajo na stični površini podenot in bi kot taka lahko potencialno imela vpliv na stabilnost heterodimera.

• Language: Slovenian
• Keywords: heterodimerizacija, α-aktinin-1, α-aktinin-4, bioinformatika, fosforilacija
• Work type: Bachelor thesis/paper
• Typology: 2.11 - Undergraduate Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2020
• PID: 20.500.12556/RUL-119673
• COBISS.SI-ID: 30763523
• Publication date in RUL: 10.09.2020

Secondary language

• Language: English
• Title: Bioinformatic analysis of heterodimer formation between α-actinin-1 and -4

Abstract

α-Actinins are proteins that are involved in the formation of multidimensional structures of actin filaments. Their general structure consists of three domains: actin-binding domain, central rod domain and calmodulin-like domain. The physiologically active form is represented by antiparallel homodimers. In general, α-actinin-1 and α-actinin-4 are considered as different homodimeric entities, but recent studies have confirmed the existence of heterodimers in cancer cell lines. The purpose of our work was to evaluate the stability of the heterodimer by analyzing sequences and structural models, also in the aspect of phosphorylation of amino acid residues. Alignment results of the sequences α-actinin-2, α-actinin-1 and α-actinin-4 have shown a high percentage of amino acid identity (for isoform 1 78.26%, for isoform 4 75.00%). This allowed us to prepare a model of homodimer and heterodimer of isoforms 1 and 4 based on the structure of α-a ctinin-2 with a relatively high degree of reliability. The analysis of the interface in the 3D structural model of the heterodimer predicted the interface of 5167.8 Å2 and ΔiG = -28 kcal/mol, which represents the tendency for hydrophobic interactions. For its interface hydrophobic interactions were predicted and confirmed by the results of the InterProSurf server. Based on the data provided by InterProSurf and PDBePISA, we determine 94 interaction amino acids in the α-actinin-1 chain and 100 interaction amino acids in the α-actinin-4 chain. Based on results provided by NetPhos 3.1 server for the prediction of phosphorylation sites and databases of protein phosphorylation - qPhos and EPSD, we assume 4 (α-actinin-1) and 6 (α-actinin-4) phosphorylation sites, respectively, located on the interface surface of the subunits and as such could potentially affect the stability of the heterodimer.

• Keywords: heterodimerization, α-actinin-1, α-actinin-4, bioinformatics, phosphorylation