用AlphaFold2和统计学习识别能变构的蛋白质,提升功能理解。
Classifying Metamorphic versus Single-Fold Proteins with Statistical Learning and AlphaFold2
- 通过多序列比对采样生成蛋白构象集合,提取多样性特征。
- 在基准数据集上平均AUC达0.869,准确区分变构与单一构象蛋白。
- 发现多个潜在变构蛋白,包括参与抗菌防御的S30蛋白。
AlphaFold2在从氨基酸序列精确预测蛋白质原子级结构方面取得显著成功,但其核心范式——一序列对应一结构——仅适用于具有单一稳定构象的单构象蛋白。变构蛋白可采取多种不同构象,其构象多样性无法被AlphaFold2充分建模。因此,判断给定蛋白是否为变构蛋白,仍是实验与计算方法中的关键挑战。为此,我们提出一种新分类框架:通过多序列比对采样重用AlphaFold2生成构象集合,并从中提取表征构象集合模态性与结构离散度的综合特征。基于精心构建的已知变构与单构象蛋白基准数据集,训练的随机森林分类器在交叉验证中平均AUC达0.869,证明了该整合方法的有效性。进一步将该分类器应用于从蛋白质数据库中随机选取的600个蛋白,识别出多个潜在变构蛋白候选,包括40S核糖体蛋白S30,其构象变化对其在抗菌防御中的次级功能至关重要。本研究结合人工智能驱动的蛋白质结构预测与统计学习,为发现变构蛋白提供了强大新方法,并深化了对它们分子功能作用的理解。
原文摘要 · Abstract (English)
The remarkable success of AlphaFold2 in providing accurate atomic-level prediction of protein structures from their amino acid sequence has transformed approaches to the protein folding problem. However, its core paradigm of mapping one sequence to one structure may only be appropriate for single-fold proteins with one stable conformation. Metamorphic proteins, which can adopt multiple distinct conformations, have conformational diversity that cannot be adequately modeled by AlphaFold2. Hence, classifying whether a given protein is metamorphic or single-fold remains a critical challenge for both laboratory experiments and computational methods. To address this challenge, we developed a novel classification framework by re-purposing AlphaFold2 to generate conformational ensembles via a multiple sequence alignment sampling method. From these ensembles, we extract a comprehensive set of features characterizing the conformational ensemble's modality and structural dispersion. A random forest classifier trained on a carefully curated benchmark dataset of known metamorphic and single-fold proteins achieves a mean AUC of 0.869 with cross-validation, demonstrating the effectiveness of our integrated approach. Furthermore, by applying our classifier to 600 randomly sampled proteins from the Protein Data Bank, we identified several potential metamorphic protein candidates -- including the 40S ribosomal protein S30, whose conformational change is crucial for its secondary function in antimicrobial defense. By combining AI-driven protein structure prediction with statistical learning, our work provides a powerful new approach for discovering metamorphic proteins and deepens our understanding of their role in their molecular function.
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