拉索Pred:一个工具来预测拉索的3D结构
Xingyu Ouyang1,2, Xinchun Ran2, Han Xu3
1State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
Nature communications
|July 2, 2025
概括
研究人员开发了LassoPred,这是一种用于预测拉索 (LaP) 结构的新工具. 这推动了对这些复杂分子的研究,使得新抗生素和生物医学应用的发现成为可能.
科学领域:
- 生物化学 生物化学
- 结构生物学 结构生物学
- 生物信息学是一种生物信息学.
背景情况:
- 拉索 (LaPs) 是一大类核糖体合成和转化后修饰 (RiPPs),具有多种生物功能,包括作为抗生素和酶抑制剂的作用.
- 尽管有众多预测的序列,但由于其复杂,纠的滑结状结构和异类键的存在,只有大约50种不同的LaPs在结构上得到了特征.
- 现有的蛋白质结构预测工具,如AlphaFold2,AlphaFold3和ESMfold,对于准确建模LaP结构是不够的.
研究的目的:
- 开发一种能够准确预测拉索的3D结构的计算工具.
- 创建迄今为止最大的in silico预测的拉索结构数据库.
- 为了促进未来的结构-功能关系研究和发现新的功能性LAP.
主要方法:
- 开发LassoPred,这是一种新的计算工具,包含用于注释LaP序列组件 (环,循环,尾) 的分类器和用于构建3D结构的构造器.
- 应用LassoPred来预测4749个独特的LaP核心序列的3D结构.
- 通过Web界面和命令行工具向公众发布LassoPred.
主要成果:
- 使用LassoPred.成功预测了4749个独特的拉索核序列的3D结构.
- 创建了最大的in silico预测的拉索结构数据库.
- 证明LassoPred能够克服现有预测工具对LPs的局限性.
结论:
- 拉索普雷德有效地预测了拉索的结构,解决了当前计算生物学工具中的重大差距.
- 生成的数据库显著扩大了对LPs的结构知识,支持进一步的研究.
- 拉索普雷德是探索LaP结构功能关系和加速化学和生物医学应用LaP发现的宝贵资源.
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