使用大规模并行设计,合成和测试对蛋白质折叠的全球分析
Gabriel J Rocklin1, Tamuka M Chidyausiku1,2, Inna Goreshnik1
1Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
概括
研究人员设计并测试了15000多种新型蛋白质,以了解它们的序列如何决定蛋白质的折叠和稳定性. 这种数据驱动的方法显著提高了蛋白质设计的成功率.
科学领域:
- 生物化学
- 结构生物学
- 计算生物学
背景情况:
- 蛋白质结构是由弱相互作用决定的,但由于自然蛋白质以功能而不是稳定性而演变,解码这些力量是复杂的.
- 了解序列稳定性关系对于蛋白质工程至关重要.
研究的目的:
- 系统地检查氨基酸序列如何决定新型蛋白质结构中的蛋白质折叠和稳定性.
- 通过将计算方法与高通量实验验证相结合,开发一种数据驱动的蛋白质设计方法.
主要方法:
- 使用计算式蛋白质设计,下一代基因合成和高通量蛋白酶敏感性测试.
- 对超过15,000个新设计的小蛋白,1,000个自然蛋白,10,000个点突变和30,000个负对照序列进行了折叠和稳定性的评估.
主要成果:
- 在四个基本折叠中识别了超过2500个稳定设计的蛋白质,为分析序列稳定性关系提供了数据集.
- 通过代设计和实验反, 设计成功率从6%提高到47%.
- 产生具有新拓性的稳定蛋白质,并在优化过程中揭示了微妙的稳定性贡献.
结论:
- 在计算设计和实验验证之间建立了紧密的反循环,将蛋白质设计转化为数据驱动的科学.
- 在未知序列空间中设计具有可预测折叠性能的稳定蛋白质的潜力.
- 开发的方法为推进蛋白质工程和理解基本蛋白质生物物理提供了一个强大的平台.
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