基于机制的GAP重新设计以激活瘤性RAS
Dénes Berta1, Sascha Gehrke1, Kinga Nyíri2,3
1Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom.
Journal of the American Chemical Society
|September 8, 2023
概括
但突变会导致癌症. 这项研究揭示了GTP水解机制,并设计了新的Ras-GAP突变物来恢复瘤性Ras蛋白的功能.
科学领域:
- 生物化学
- 分子生物学
- 计算化学
背景情况:
- Ras GTPases是细胞信号通路的关键调节者.
- Ras基因的突变,特别是Gly12,Gly13和Gln61,在癌症中很常见,导致GTPase活性受损.
- 了解GTP水解的机制对于开发向癌症疗法至关重要.
研究的目的:
- 阐明Ras.GAP复合物催化的GTP水解的机制.
- 使用致癌的Ras突变物 (G12D,G12C) 验证拟议的机制.
- 开发一种用于设计Ras-GAP突变的计算策略,以恢复瘤Ras的催化活性.
主要方法:
- 使用量子力学/分子力学 (QM/MM) 自由能量计算和最小化来研究反应机制.
- 通过计算激活障碍对190个Ras-GAP突变进行了计算选.
- 开发了一种机器学习模型,用于超快速选单个和双个Ras-GAP突变.
主要成果:
- 通过Ras.GAP提出了一种两步GTP水解机制,其中Gln61作为一种过渡的布伦斯特德基.
- 该机制准确地预测了G12D和G12CRas突变的催化活性丧失.
- 计算查发现了几种Ras-GAP突变,预计可以恢复G12DRas的催化活性.
结论:
- 该研究提供了Ras GTP水解的验证机制和设计蛋白质催化剂的计算框架.
- 开发的选方案可以快速准确地设计具有增强催化活性的蛋白质序列.
- 针对Ras-GAP活动提供了一个潜在的治疗策略,以抵消Ras驱动的异常信号传递.
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