用拓扑方法分析突变对蛋白稳定性与溶解度的影响,提升预测准确性与可解释性。
Persistent Sheaf Laplacian Analysis of Protein Stability and Solubility Changes upon Mutation
- 基于持久层拉普拉斯理论,融合电荷等物理化学信息进行拓扑建模。
- 在S2648、S350和PON-Sol2数据集上均达到当前最佳性能。
- 适合蛋白质工程与疾病相关突变研究者使用。
基因突变常破坏蛋白质的结构、稳定性和溶解度,是多种疾病的主要诱因。尽管这些分子变化至关重要,现有计算模型往往缺乏可解释性,且未能整合关键的理化相互作用。为此,我们提出SheafLapNet,一个基于拓扑深度学习(TDL)和持久层拉普拉斯(PSL)数学理论的统一预测框架。与传统拓扑数据分析工具如持久同调不同,PSL将部分电荷等具体物理化学信息直接编码到拓扑分析中。SheafLapNet结合层论不变量、先进的蛋白质变换器特征及辅助物理描述符,以多尺度、机制化的方式捕捉内在分子相互作用。通过在回归与分类任务上的严格基准测试验证:稳定性预测采用S2648和S350数据集;溶解度预测采用包含增加、降低或中性变化标注的PON-Sol2数据集。综合多视角特征后,SheafLapNet在多个基准上均达到当前最优表现,证明层论建模显著提升了预测突变引起的结构与功能变化时的可解释性与泛化能力。
原文摘要 · Abstract (English)
Genetic mutations frequently disrupt protein structure, stability, and solubility, acting as primary drivers for a wide spectrum of diseases. Despite the critical importance of these molecular alterations, existing computational models often lack interpretability, and fail to integrate essential physicochemical interaction. To overcome these limitations, we propose SheafLapNet, a unified predictive framework grounded in the mathematical theory of Topological Deep Learning (TDL) and Persistent Sheaf Laplacian (PSL). Unlike standard Topological Data Analysis (TDA) tools such as persistent homology, which are often insensitive to heterogeneous information, PSL explicitly encodes specific physical and chemical information such as partial charges directly into the topological analysis. SheafLapNet synergizes these sheaf-theoretic invariants with advanced protein transformer features and auxiliary physical descriptors to capture intrinsic molecular interactions in a multiscale and mechanistic manner. To validate our framework, we employ rigorous benchmarks for both regression and classification tasks. For stability prediction, we utilize the comprehensive S2648 and S350 datasets. For solubility prediction, we employ the PON-Sol2 dataset, which provides annotations for increased, decreased, or neutral solubility changes. By integrating these multi-perspective features, SheafLapNet achieves state-of-the-art performance across these diverse benchmarks, demonstrating that sheaf-theoretic modeling significantly enhances both interpretability and generalizability in predicting mutation-induced structural and functional changes.
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