Topology Prediction Improvement of α-helical Transmembrane Proteins Through Helix-tail Modeling and Multiscale Deep Learning Fusion

Abstract

Transmembrane proteins (TMPs) play important roles in many biological processes, such as cell recognition and communication. Their structures are crucial for revealing complex functions but are hard to obtain. A variety of computational algorithms have been proposed to fill the gap by predicting structures from primary sequences. In this study, we mainly focus on α-helical TMP and develop a multiscale deep learning pipeline, MemBrain 3.0, to improve topology prediction. This new protocol includes two submodules. The first module is transmembrane helix (TMH) prediction, which features the capability of accurately predicting TMH with the tail part through the incorporation of tail modeling. The prediction engine contains a multiscale deep learning model and a dynamic threshold strategy. The deep learning model is comprised of a small-scale residue-based residual neural network and a large-scale entire-sequence-based residual neural network. Dynamic threshold strategy is designed to binarize the raw prediction scores and solve the under-split problem. The second module is orientation prediction, which consists of a support vector machine (SVM) classifier and a new Max-Min assignment (MMA) strategy. One typical merit of MemBrain 3.0 is the decision mode composed of the dynamic threshold strategy and the MMA strategy, which makes it more effective for hard TMHs, such as half-TMH, back-to-back TMH, and long-TMH. Systematic experiments have demonstrated the efficacy of the new model, which is available at: www.csbio.sjtu.edu.cn/bioinf/MemBrain/.

Keywords: bioinformatics; deep learning; membrane protein; structure prediction; topology.