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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
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.

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Year 2023, Volume: 4 Issue: 1, 17 - 29, 26.06.2023
https://doi.org/10.51539/biotech.1262979

Abstract

References

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  • Hase T, Schürmann P, Knaff DB (2006) The interaction of ferredoxin with ferredoxin-dependent enzymes In: Photosystem I , pp 477–498. Springer.
  • Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL (2012) MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics 28:1278–1279.
  • Houston NL, Fan C, Xiang Q-Y, Schulze J-M, Jung R, Boston RS (2005) Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. Plant Physiol 137:762–778.
  • Hu X, Dong Q, Yang J, Zhang Y (2016) Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. Bioinformatics 32:3260–3269.
  • Hu X, Shelver WH (2003) Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction. J Mol Graph Model 22:115–126.
  • Jahns P, Graf M, Munekage Y, Shikanai T (2002) Single point mutation in the Rieske iron–sulfur subunit of cytochrome b6/f leads to an altered pH dependence of plastoquinol oxidation in Arabidopsis. FEBS Lett 519:99–102.
  • Jin S, Hu Y, Fu H, Jiang S, Xiong Y, Qiao H, Zhang W, Gong Y, Wu Y (2021) Identification and characterization of the succinate dehydrogenase complex iron sulfur subunit B gene in the Oriental River Prawn, Macrobrachium nipponense. Front Genet 12.
  • Johnson DC, Dean DR, Smith AD, Johnson MK (2005) Structure, function, and formation of biological iron-sulfur clusters. Annu Rev Biochem 74:247.
  • Kannan L, Wheeler WC (2012) Maximum parsimony on phylogenetic networks. Algorithms for Molecular Biology 7:1–10.
  • Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858.
  • Kolaczkowski B, Thornton JW (2004) Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980–984.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547.
  • Kurisu G, Kusunoki M, Katoh E, Yamazaki T, Teshima K, Onda Y, Kimata-Ariga Y, Hase T (2001) Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP+ reductase. Nat Struct Biol 8:117–121.
  • Li Q, Li Y, Li X, Chen S (2021) Identification of Genes Involved in Fe–S Cluster Biosynthesis of Nitrogenase in Paenibacillus polymyxa WLY78. Int J Mol Sci 22:3771.
  • Lin Y-F, Cheng C-W, Shih C-S, Hwang J-K, Yu C-S, Lu C-H (2016) MIB: metal ion-binding site prediction and docking server. J Chem Inf Model 56:2287–2291.
  • Litomska A, Ishida K, Dunbar KL, Boettger M, Coyne S, Hertweck C (2018) Enzymatic thioamide formation in a bacterial antimetabolite pathway. Angewandte Chemie International Edition 57:11574–11578.
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There are 88 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Research Articles
Authors

Yiğit Küçükçobanoğlu 0000-0002-9856-5506

Lale Aktaş 0000-0003-0815-8470

Publication Date June 26, 2023
Acceptance Date June 9, 2023
Published in Issue Year 2023 Volume: 4 Issue: 1

Cite

APA Küçükçobanoğlu, Y., & Aktaş, L. (2023). Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches. Bulletin of Biotechnology, 4(1), 17-29. https://doi.org/10.51539/biotech.1262979
AMA Küçükçobanoğlu Y, Aktaş L. Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches. Bull. Biotechnol. June 2023;4(1):17-29. doi:10.51539/biotech.1262979
Chicago Küçükçobanoğlu, Yiğit, and Lale Aktaş. “Functional and Structural Identification of Iron-Binding Proteins on Tomato (Solanum Lycopersicum L.) Proteome via in Silico Approaches”. Bulletin of Biotechnology 4, no. 1 (June 2023): 17-29. https://doi.org/10.51539/biotech.1262979.
EndNote Küçükçobanoğlu Y, Aktaş L (June 1, 2023) Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches. Bulletin of Biotechnology 4 1 17–29.
IEEE Y. Küçükçobanoğlu and L. Aktaş, “Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches”, Bull. Biotechnol., vol. 4, no. 1, pp. 17–29, 2023, doi: 10.51539/biotech.1262979.
ISNAD Küçükçobanoğlu, Yiğit - Aktaş, Lale. “Functional and Structural Identification of Iron-Binding Proteins on Tomato (Solanum Lycopersicum L.) Proteome via in Silico Approaches”. Bulletin of Biotechnology 4/1 (June 2023), 17-29. https://doi.org/10.51539/biotech.1262979.
JAMA Küçükçobanoğlu Y, Aktaş L. Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches. Bull. Biotechnol. 2023;4:17–29.
MLA Küçükçobanoğlu, Yiğit and Lale Aktaş. “Functional and Structural Identification of Iron-Binding Proteins on Tomato (Solanum Lycopersicum L.) Proteome via in Silico Approaches”. Bulletin of Biotechnology, vol. 4, no. 1, 2023, pp. 17-29, doi:10.51539/biotech.1262979.
Vancouver Küçükçobanoğlu Y, Aktaş L. Functional and structural identification of iron-binding proteins on tomato (Solanum lycopersicum L.) proteome via in silico approaches. Bull. Biotechnol. 2023;4(1):17-29.