Effect of Soil Zinc Concentration on Plants Growth: Molecular Modelling and Docking of Interactions between Plant Proteins and Zinc Ions

Authors

  • Sadiya Alka Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medical Science, Abubakar Tafawa Balewa University, P.M.B. 0248, Bauchi, Bauchi State, Nigeria.
  • Habeebat Adekilekun Oyewusi Department of Science Laboratory Technology (Biochemistry Unit), School of Science and Computer Studies, The Federal Polytechnic, P.M.B. 5351, Ado-Ekiti, Ekiti State, Nigeria.
  • Mohammed Jibrin Ndeji Department of Microbiology, Faculty of Natural Sciences, Ibrahim Badamasi Babangida University, P.M.B. 11, Lapai, Niger State, Nigeria.
  • Ali Timothy Gandu Department of Science Laboratory Technology, Nuhu Bamalli Polytechnic, P.M.B. 1061, Zaria, Kaduna State, Nigeria.
  • Habeebulahi Ajibola Adekilekun Department of Pharmacology and Toxicology, Faculty of Medicine, Kampala International University, Western Campus, P.O. Box 71, Ishaka-Bushenyi, Uganda.
  • Zinat Suleiman Mohammed Department of Biochemistry, Faculty of Science, Bauchi State University Gadau, P.M.B. 065, Gadau, Bauchi State, Nigeria.
  • Muhammad Jamilu Dauda Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medical Science, Abubakar Tafawa Balewa University, P.M.B. 0248, Bauchi, Bauchi State, Nigeria.

DOI:

https://doi.org/10.54987/jebat.v8i1.1121

Keywords:

Soil, Zinc, Plant, Modelling, Molecular docking

Abstract

This study examines plant-soil interactions involving zinc (Zn), focusing on the physiological effects on plant development and the molecular interactions between plant proteins and metal ions. About 2 kg of soil mixed with gravel (1.5:1 v/v) were placed in pots, and seeds of sunflower (Helianthus annuus), amaranth (Amaranthus spp.), cowpea (Vigna unguiculata), and groundnut (Arachis hypogaea) were sown and irrigated for two weeks. Seedlings were treated with a 500 ppm zinc sulfate solution, and shoots, leaves, and roots were separated for length and weight measurements. Zinc concentration in digested tissues was determined using atomic absorption spectroscopy (AAS). Computational modeling and molecular docking were performed using PubChem data and structural tools such as Chimera, Phyre2, and PyMOL. The BbZIP protein structure was modeled, and active sites were predicted using COACH-D, while CAVER Web 1.0 identified quantum tunnel pathways. Phytochemical analysis revealed the presence of bioactive compounds, including flavonoids, tannins, steroids, and saponins. Treated plants exhibited reduced growth compared to the controls, with significant zinc accumulation in the soil, shoots, and roots. The highest Zn concentration (315 ppm) occurred in groundnut roots. Five major binding poses were identified, involving catalytic residues Met91, Leu92, Phe94, Ala95, Ala96, Pro210, Glu211, Ala214, Gly93, and others. Molecular docking showed a binding affinity of –3.8 kcal/mol and an inhibition constant (Ki) of 247.81 mM. The BbZIP–Zn complex was stabilized by four hydrogen bonds (Ala96, Ala290, Ser236, Leu294). Overall, this study highlights the critical role of zinc in plant stress responses and development through physiological and molecular mechanisms.

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Published

2025-07-31

How to Cite

Alka, S., Oyewusi, H. A. ., Ndeji, M. J. ., Gandu, A. T. ., Adekilekun, H. A. ., Mohammed, Z. S. ., & Dauda, M. J. . (2025). Effect of Soil Zinc Concentration on Plants Growth: Molecular Modelling and Docking of Interactions between Plant Proteins and Zinc Ions. Journal of Environmental Bioremediation and Toxicology, 8(1), 27–33. https://doi.org/10.54987/jebat.v8i1.1121

Issue

Vol. 8 No. 1 (2025)

Section

Articles

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