An in silico approach for structural and functional analysis of Heavy Metal Associated (HMA) proteins in Brassica oleracea

TitleAn in silico approach for structural and functional analysis of Heavy Metal Associated (HMA) proteins in Brassica oleracea
Publication TypeJournal Article
Year of Publication2016
JournalPeriodicals of Engineering and Natural Sciences
Volume4
Issue2
Section41
Publication Languageeng
AuthorsŠutković, J
Secondary AuthorsKekić, M
Tertiary AuthorsLjubijankić, M
Corporate AuthorsPetar Glamočlija
KeywordsHeavy metals; accumulation; transport; interactome; docking site, Protein structure prediction
Abstract

Heavy metal ATPases (HMAs) are the most important proteins involved in heavy metal accumulation process. Brassica oleracea has 5 HMA (1-5) homologues whose 3D structure has been predicted and validated in this study by different bioinformatics tools. Phylogenetic and multiple sequence alignment analyses showed high relationship between HMA2 and HMA4, while two same domains were identified in all five HMA proteins: E1-E2 ATPase and haloacid dehydrogenase (HAD) domain. Four HMA (2-5) proteins were identified to be localized in the plasma membrane, while HMA1 localization is predicted to be in plastid. Interactome analysis revealed high interaction of all HMA (1-5) proteins with many metal ion binding proteins and chaperones. Among these, interesting and strong interaction is observed between all HMA (1-5) proteins and ATX1, while HMA1, HMA2 and HMA4 have been found to strongly interact with FP3 (farnesylated protein 3) and FP6 (farnesylated protein 6) proteins. Docking site predictions and electrostatic potentials between HMA2/HMA4 and the interactome proteins were explained and discussed in this study.

DOI10.21533/pen.v4i2