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

Journal of Chemical Biology Pub Date : 2015-05-12 eCollection Date: 2015-07-01 DOI:10.1007/s12154-015-0135-3
Sivakumar Prasanth Kumar, Vilas R Parmar, Yogesh T Jasrai, Himanshu A Pandya
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引用次数: 11

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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用计算机和体外方法预测动素蛋白靶点:以菠菜种子萌发机制为例。
动素是一种细胞分裂素,通过抑制脱落酸的作用来促进种子萌发,是一种重要的分子,已知通过与一系列蛋白质相互作用来触发各种分子机制,这是在各种模式生物中实验观察到的。我们在这里报告了利用计算机方法预测菠菜蛋白质组中最可能的动蛋白靶点。以动蛋白为分子进行逆对接和基于配体的相似性搜索。前一种方法优先考虑6种菠菜蛋白,而后一种方法提供了从几种模式生物中检索到的蛋白质靶点列表。通过对接排序和配体相似性方法的比较,选择最可能的蛋白靶点。这两种方法都优先考虑几丁质酶作为最可能的蛋白靶点(ΔG pred = 5.064 kcal/mol),酵母几丁质酶1与动蛋白配合物(PDB: 2UY5)和玫瑰红Gliocladium几丁质酶与3,7-二氢-1,3,7-三甲基- 1h -嘌呤-2,6-二酮(咖啡因;3G6M),与kinetin的3D相似性为0.43。一项评价激动素对菠菜种子萌发影响的体外研究表明,与对照相比,极低浓度(0.5 mg/l)的激动素对种子萌发的诱导作用不显著。此外,较高水平的动素(>0.5 mg/l)对菠菜种子萌发具有拮抗作用。据推测,动素可能与种子萌发过程中合成的优先蛋白目标发生分子相互作用,从而抑制生长。因此,似乎动素可能不是一个合适的激素,以提高菠菜种子在体外发芽。
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