用机器学习工具蛋白MPNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Hsi-Wen Kao1, Wei-Lin Lu1, Meng-Ru Ho1
1Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
ACS synthetic biology
|August 9, 2023
概括
研究人员使用深度学习重新设计了ubiquitin变体 (UbVs),以增强Rsp5 E3酶活性. 三个UbV显示出低微分子结合亲和力,R4和R12增强了Rsp5功能的六倍.
科学领域:
- 生物化学 生物化学
- 结构生物学 结构生物学
- 计算生物学 计算生物学
背景情况:
- 乌比基 (Ub) 是一种关键的蛋白质,参与各种细胞过程.
- Rsp5是一种E3结合酶,在蛋白质无化中起着关键作用.
- 调节Ub相关酶的活性具有治疗意义.
研究的目的:
- 重新设计乌比奎作为Rsp5 E3结合酶的特定且功能增强的结合剂.
- 开发一种快速且具有成本效益的方法来设计功能性无处不在的变体 (UbV).
主要方法:
- 使用 ProteinMPNN 深度学习工具进行蛋白质重新设计.
- 产生了20种广泛突变的重组UbVs.
- 使用AlphaFold2.2.使用Rsp5评估蛋白质结构,热稳定性和复合形成.
- 用Rsp5.5测量了UbVs的结合亲和力和功能增强.
主要成果:
- 产生了20个折叠良好的,热稳定的UbVs.
- 使用AlphaFold2.2.使用UbVs和Rsp5之间的预测稳定复合体.
- 鉴定了三种具有较低微分子结合亲和力与RSp5.5的UbVs.
- 观察到UbVs R4和R12对Rsp5活动的六倍增强.
- 阿尔法Fold2预测了Rsp5由R4和R12激活Rsp5的全性激活.
结论:
- 深度学习可以有效地重新设计酶调节的乌比奎.
- 设计的UbV可以全性地增强像RSp5.5这样的E3酶的活性.
- 这种方法提供了一个虚拟的解决方案,用于设计功能性UbV作为Ub相关酶的调节器.
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