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Modeling Protein–Protein Interaction of the KNOTTED-LIKE HOMEOBOX 3 Protein Involved in Symbiotic Nodule Development in Medicago truncatula

  • STRUCTURAL-FUNCTIONAL ANALYSIS OF BIOPOLYMERS AND THEIR COMPLEXES
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Abstract

KNOTTED-LIKE HOMEOBOX (KNOX) proteins are homeodomain containing transcription factors, and regulate many aspects of plant development through homo or heterodimerization with another group of TALE transcription factors known as BELL. In Medicago truncatula the MtKNOX3 gene is involved in nodule development. In this work, we hypothesized that MtKNOX3 involvement in the activation of cytokinin signaling during nodule development could be through heterodimerization with BELL proteins. Thereby, the expression of different BELL genes in Medicago was analyzed, and it was shown that the expression of Medtr8g078480 and Medtr8g098815 genes increases during nodule development. Besides, the Medtr8g078480 shows a co-expression pattern with MtKNOX3 at different developmental stages of nodule development. Afterward, the interaction of MtKNOX3 with the MtBELL1-2 (Medtr8g078480) protein was shown using docking, and their stability was analyzed by molecular dynamic simulation and mmpbsa methods. Moreover, the stability of MtKNOX3- Medtr8g078480 heterodimers was compared with the MtKNOX3 homodimer.

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Funding

This work was supported by ongoing institutional funding. No additional grants to carry out or direct this particular research were obtained.

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Authors and Affiliations

  1. Cell and Molecular Biology Department, Kosar University of Bojnord, 9453155168, Bojnord, Iran

    M. Azarakhsh

  2. Department of Genetics and Biotechnology, Saint Petersburg State University, 199034, St. Petersburg, Russia

    M. Lebedeva

  3. Department of Chemistry, SRM, Institute of Science and Technology, Delhi-NCR Campus, Ghaziabad, India

    V. K. Vishvakarma

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  1. M. Azarakhsh
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  2. M. Lebedeva
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Contributions

Material preparation, data collection, and analysis were performed by Mahboobeh Azarakhsh, original draft preparation: Mahboobeh Azarakhsh, review and editing, Mahboobeh Azarakhsh, Maria Lebedeva, and Vijay Vishvakarma. All authors have read and agreed to the published version of the manuscript.

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Correspondence to M. Azarakhsh.

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Azarakhsh, M., Lebedeva, M. & Vishvakarma, V.K. Modeling Protein–Protein Interaction of the KNOTTED-LIKE HOMEOBOX 3 Protein Involved in Symbiotic Nodule Development in Medicago truncatula. Mol Biol 58, 336–345 (2024). https://doi.org/10.1134/S0026893324020031

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