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Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism

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Journal of Chemical Biology

Abstract

Kinetin, a cytokinin which promotes seed germination by inhibiting the action of abscisic acid, is an important molecule known to trigger various molecular mechanisms by interacting with an array of proteins shown from experimental observations in various model organisms. We report here the prediction of most probable protein targets of kinetin from spinach proteome using in silico approaches. Inverse docking and ligand-based similarity search was performed using kinetin as molecule. The former method prioritized six spinach proteins, whereas the latter method provided a list of protein targets retrieved from several model organisms. The most probable protein targets were selected by comparing the rank list of docking and ligand similarity methods. Both of these methods prioritized chitinase as the most probable protein target (ΔG pred = 5.064 kcal/mol) supported by the experimental structure of yeast chitinase 1 complex with kinetin (PDB: 2UY5) and Gliocladium roseum chitinase complex with 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine; 3G6M) which bears a 3D similarity of 0.43 with kinetin. An in vitro study to evaluate the effect of kinetin on spinach seed germination indicated that a very low concentration of kinetin (0.5 mg/l) did not show a significant effect compared to control in inducing seed germination process. Further, higher levels of kinetin (>0.5 mg/l) constituted an antagonist effect on spinach seed germination. It is anticipated that kinetin may have a molecular interaction with prioritized protein targets synthesized during the seed germination process and reduces growth. Thus, it appears that kinetin may not be a suitable hormone for enhancing spinach seed germination in vitro.

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Acknowledgments

Sivakumar Prasanth Kumar acknowledges support from the Department of Science and Technology, New Delhi, India, as INSPIRE Senior Research Fellowship.

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The authors declare that no competing interests exist.

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    Authors and Affiliations

    1. Department of Bioinformatics, Applied Botany Centre (ABC), Gujarat University, Ahmedabad, 380009, Gujarat, India

      Sivakumar Prasanth Kumar, Yogesh T. Jasrai & Himanshu A. Pandya

    2. Department of Botany, Gujarat University, Ahmedabad, 380009, Gujarat, India

      Vilas R. Parmar, Yogesh T. Jasrai & Himanshu A. Pandya

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    1. Sivakumar Prasanth Kumar
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    3. Yogesh T. Jasrai
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    Correspondence to Yogesh T. Jasrai.

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    Sivakumar Prasanth Kumar and Vilas R. Parmar contributed equally to this work.

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    Kumar, S.P., Parmar, V.R., Jasrai, Y.T. et al. Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism. J Chem Biol 8, 95–105 (2015). https://doi.org/10.1007/s12154-015-0135-3

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