In silico characterization of the impact of mutation (LEU112PRO) on the structure and function of carotenoid cleavage dioxygenase 8 in Oryza sativa
In silico characterization of the impact of mutation (LEU112PRO) on the structure and function of carotenoid cleavage dioxygenase 8 in Oryza sativa
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DOI：
10.1016/j.phytochem.2020.112365
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发表时间：
2020-07-01
期刊：
影响因子：
3.8
通讯作者：
Behera, Lambodar
中科院分区：
文献类型：
--
作者：
Gupta, Manoj Kumar;Gouda, Gayatri;Behera, Lambodar
“类胡萝卜素裂解双加氧酶8”(CCD8)蛋白突变(p.LEU112PRO)通过与生长素和细胞分裂素的相互作用促进水稻分蘖的形成。然而，由于不存在CCD8的“三维”结构，有关其结构和功能的详细信息至今仍不清楚。因此，本研究采用计算方法，通过比较建模技术预测CCD8蛋白的三维结构，并通过分子动力学模拟研究突变(p.LEU112PRO)对其功能和结构的影响。结果表明，野生型CCD8蛋白由10个α螺旋和25个β链组成，而突变型CCD8由11个α螺旋和24个β链组成。此外，分子对接研究表明，野生型与生长素和细胞分裂素的结合亲和力比突变体更好。随后对这四个复合体分别进行的分子动力学模拟表明，野生型和突变型CCD8在与生长素结合后，其运动都会减少，这反过来会阻止生长素从芽中运输出去，增加分蘖数。然而，当细胞分裂素与野生型和突变型CCD8结合时，它分别抑制和增强CCD8的活性。由于细胞分裂素正向调节分蘖数的形成，突变体CCD8与细胞分裂素结合后活性增强可能是导致突变体分蘖数高于野生型植株的主要原因。在不久的将来，突变体CCD8与生长素和细胞分裂素一起可能被用来提高水稻的产量。
Mutation (p.LEU112PRO) in "carotenoid cleavage dioxygenase 8" (CCD8) protein increases tiller formation in rice plants by cross-talking with auxin and cytokinins. However, owing to the nonexistence of a "three-dimension" structure of CCD8, detail information about its structure and function remain elusive until date. Hence, in the present study, computational approaches were adopted to predict "three-dimensional" (3D) structure of CCD8 protein through comparative modeling techniques and to study the effect of mutation (p.LEU112PRO) on its function as well as architecture through "molecular dynamics" simulation studies. The obtained result reveals that wild-type CCD8 protein is made up of 10 alpha-helix and 25 beta-strands while mutant CCD8 is made up of 11 alpha-helix and 24 beta-strands. Further, molecular docking studies reveals that the wild-type has a better binding affinity with auxin and cytokinin in comparison to mutant. Subsequent molecular dynamics simulation of these four complexes, separately, reveals that the movement of both wild-type as well as mutant CCD8 get reduced after binding with auxin, which in turn prevent auxin transport out of the bud and increases tiller number. However, when cytokinin binds with wild-type and mutant CCD8, it inhibits and enhance CCD8 activity, respectively. As cytokinin positively regulates tiller number formation, enhance activity of mutant CCD8 after binding with cytokinin might be the main reason for more tiller number in mutant than wild-type plant. In the near future, mutant CCD8 along with auxin and cytokinin may be utilized for increasing grain yield in rice plants.