Language Model-Enhanced Geometric Learning for Metalloprotein Pathogenic Mutations

The interaction between proteins and metal ions plays a pivotal role in the pathogenesis of various diseases. Base pair substitution subsequently triggers single-amino acid substitutions, leading to missense mutations that may impair protein function and consequently cause severe human diseases. Predicting the pathogenicity or benign nature of mutation sites in metalloproteins is crucial for early disease diagnosis and the acceleration of innovative drug development. In this study, we propose MetalDiagnosis, a deep learning framework that integrates an improved equivariant graph neural network with a pre-trained protein language model to predict disease-associated mutation sites in metal-binding proteins. Specifically, MetalDiagnosis employs a sliding-window strategy to extract deep contextual semantic information from the pre-trained protein language model ESM Cambrian, thereby overcoming the limitations of manual feature extraction. In parallel, three-dimensional geometric features are extracted by the equivariant graph neural network, which learns global patterns through positional encoding and virtual nodes. MetalDiagnosis integrates sequence and structural representations at both the residue and geometric levels to ensure comprehensive feature incorporation. Experimental results demonstrate that MetalDiagnosis outperforms state-of-the-art methods on the independent test set. When applied to 611 variants of uncertain significance (VUS), it produces fewer ambiguous predictions and reclassifies more VUS into likely pathogenic or likely benign categories with higher confidence. Furthermore, case studies demonstrate that MetalDiagnosis can accurately identify pathogenic mutations located in functionally critical regions. These results suggest that MetalDiagnosis offers an effective computational framework for identifying disease-associated mutations in metalloproteins.