Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches

Year 2023, Volume: 4 Issue: 1, 17 - 29, 26.06.2023

Yiğit Küçükçobanoğlu , Lale Aktaş

https://doi.org/10.51539/biotech.1262979

Abstract

Iron-plant interactions have crucial roles in crop production growth and development. In this study, we have analyzed the whole proteome of tomato (Solanum lycopersicum L.) plants for iron-binding proteins. A total of 213 iron-binding protein candidates were identified in the study. Out of these 213 proteins, 45 were selected for modeling and validated with a high confidence level by using different computational analyses. Results showed that Glu, Cys, Asp, and His amino acid residues were indicators of iron-binding proteins. Besides, mechanistic insights of iron-binding proteins were analyzed by molecular dynamics simulations. Simulation results proved the conformational stabilization of proteins. Validated proteins were further analyzed for subcellular localization, clustered for molecular functions and biological processes. According to the results, iron-binding proteins were mostly located in the chloroplast. Also, these proteins are involved in different molecular and biological roles ranging from oxidation-reduction processes and electron transport chain to protein repair mechanisms. This report provides structural and functional properties of iron-binding proteins for tomato proteome. The study may assist in future research on plant physiology, protein engineering, or bioengineering.

Keywords

iron - binding proteins, tomato, structural bioinformatics, functional analysis, three - dimensional modeling

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