综合计算分析SRK-SP11分子相互作用的基础自我不兼容性在Brassicaceae使用改善的结构预测的蛋白质含氨酸丰富的蛋白质
Tomoki Sawa1, Yoshitaka Moriwaki1,2, Hanting Jiang1
1Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Computational and structural biotechnology journal
|November 6, 2023
概括
改进了Brassicaceae的自我不相容性 (SI) 研究,这项研究提高了S-locus蛋白11 (SP11) 结构预测. 精选多个序列对齐 (MSA) 提高了SP11和S受体激酶 (SRK) 综合体的精度,揭示了新的结合模式.
科学领域:
- 植物生殖生物学 植物生殖生物学
- 分子遗传学 分子遗传学
- 结构生物学是结构生物学.
背景情况:
- 在布拉西卡系中,自我不相容性 (SI) 取决于S受体激酶 (SRK) 和S位点蛋白11 (SP11) 的相互作用.
- 以前的研究预测了SRK-SP11复合体,但由于SP11多态性而面临挑战.
- 对SP11结构的AlphaFold2预测显示了精度的局限性 (46%与<75 pLDDT).
研究的目的:
- 为了提高预测S位蛋白11 (SP11) 和S受体激酶 (SRK) ectodomain (eSRK) 复杂结构的准确性.
- 为了研究eSRK-SP11复合物的结合自由能量和模式,跨越不同的Brassicaceae类型.
- 提供计算洞察力,了解控制单 haplotype 特定 SI 的残留水平相互作用.
主要方法:
- 利用精选多个序列对齐 (MSA) 对于富含氨酸的蛋白质来增强SP11和eSRK-SP11结构预测.
- 采用分子动力学 (MD) 模拟来计算预测的eSRK-SP11复合体的结合自由能量.
- 分析了各种Brassicaceae类别的残留物级别的结合模式.
主要成果:
- 精选的MSA显著提高了预测SP11和eSRK-SP11复杂模型的准确性.
- 模拟MD揭示了单双类型特定的结合模式,与B. rapa*相比,一些*Arabidopsis*单双类型表现出不同的相互作用.
- 计算模型为控制SRK-SP11复合体形成的残留水平相互作用提供了详细的见解.
结论:
- 增强的结构预测方法,特别是使用精选的MSA,对于研究SP11等多态蛋白质至关重要.
- 这些发现为人们更深入地了解了Brassicaceae中单元型特异性自我不相容性的分子基础.
- 预测模型可用于促进对植物生殖机制的进一步研究.
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