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揭示人类互动组中蛋白质三胞胎中的合作和竞争相互作用

Aimilia-Christina Vagiona¹, Pablo Mier², Miguel A Andrade-Navarro³

¹Insitute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.

Scientific reports

|September 15, 2025

概括

本研究介绍了一种计算方法,将蛋白质三胞胎分类为人类蛋白质相互作用网络中的合作或竞争. 过度几何学和机器学习准确地预测了这些复杂的关系,揭示了蛋白质复杂组织的洞察力.

科学领域:

计算生物学是一种计算生物学.
系统生物学系统生物学
生物信息学是一种生物信息学.

背景情况:

了解蛋白质与蛋白质相互作用 (PPI) 对细胞功能至关重要.
大多数PPI网络分析专注于二进制相互作用,忽视了诸如蛋白质三胞胎之类的更高阶动机.
在蛋白质三胞胎中,区分合作与竞争关系是具有挑战性的.

研究的目的:

开发一种计算框架,将人类蛋白相互作用网络 (hPIN) 中的蛋白质三胞胎分类为合作性或竞争性.
为了利用超标几何学来建模复杂的生物网络.
研究合作性和竞争性蛋白质相互作用的结构基础.

主要方法:

使用LaBNE+HM算法将hPIN嵌入到超标空间中.
在Interactome3D的结构验证三胞胎上训练一个随机森林分类器.
利用角和过度的距离作为关键的预测特征.

主要成果:

在分类蛋白质三胞胎中获得了高精度 (AUC=0.88).
在预测的合作三胞胎中确定了丰富的类似合作伙伴,表明不重叠的结合面.
AlphaFold 3 建模支持预测,显示合作伙伴的独特绑定站点和竞争对手的重叠站点.

结论:

超标几何学对于捕捉蛋白质复合体中的功能组织非常有价值.
开发的框架准确地区分了合作性和竞争性蛋白质三胞胎.
这些发现提供了对蛋白质复合体和相似相互作用的结构组织的见解.

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