IL-6-Inducing Peptide Prediction Based on 3D Structure and Graph Neural Network.

Abstract

Interleukin-6 (IL-6) is a potent glycoprotein that plays a crucial role in regulating innate and adaptive immunity, as well as metabolism. The expression and release of IL-6 are closely correlated with the severity of various diseases. IL-6-inducing peptides are critical for the development of immunotherapy and diagnostic biomarkers for some diseases. Most existing methods for predicting IL-6-induced peptides use traditional machine learning methods, whose feature selection is based on prior knowledge. In addition, none of these methods take into account the three-dimensional (3D) structure of peptides, which is essential for their functional properties. In this study, we propose a novel IL-6-inducing peptide prediction method called DGIL-6, which integrates 3D structural information with graph neural networks. DGIL-6 represents a peptide sequence as a graph, where each amino acid is treated as a node, and the adjacency matrix, representing the relationships between nodes, is derived from the predicted residue contact graph of the peptide sequence. In addition to commonly used amino acid representations, such as one-hot encoding and position encoding, the pre-trained model ESM-1b is employed to extract amino acid features as node features. In order to simultaneously consider node weights and information updates, a dual-channel method combining Graph Attention Network (GAT) and Graph Convolutional Network (GCN) is adopted. Finally, the extracted features from both channels are merged for the classification of IL-6-inducing peptides. A series of experiments including cross-validation, independent testing, ablation studies, and visualizations demonstrate the effectiveness of the DGIL-6 method.