Deep-Learning-Assisted Affinity Classification for Humoral Immunoprotein Complexes

Abstract

Immunoglobulins are important building blocks in biology and biotechnology. With the emergence of comprehensive deep-learning approaches, there are enormous opportunities for fast and accurate methods of classification of protein–protein interactions to arise. Herein, widely accessible image classification algorithms for species-specific typification of a range of different immunoglobulin G (IgG) complexes are repurposed. Droplets of various immunoglobulins mixed with a B-cell superantigen (SAg) (recombinant staphylococcal Protein A) are deposited onto hydrophobic polymer substrates and the resulting protein stains are imaged using polarized light microscopy. A comprehensive study based on 23 745 images finds that the pretrained convolutional neural network (CNN) InceptionV3 not only successfully categorizes IgGs from four different species but also predicts their binding affinity to Protein A: averaged over 36 binding pairs, the following are observed: 1) an overall accuracy of 81.4%, 2) the highest prediction accuracy for human IgG, the antibody with the highest binding affinity for Protein A, and 3) that the classification accuracy regarding the various IgG/Protein A ratios generally correlates with the binding strength of the protein–protein–complex as determined via circular dichroism spectroscopy. In addition, the CNN pretrained with IgG/Protein A stain images has been challenged with a new set of images using a different superantigen (SAg, Protein G). Despite the use of the unknown SAg, the CNN correctly classifies the images of human IgG and Protein G as indicated by a 94% accuracy over the various molar binding ratios. These findings are noteworthy because they demonstrate that appropriately pretrained CNNs can be used for the prediction of protein–protein interactions beyond the scope of the original training set. Aided by deep-learning methods, simple stains of mixed protein solutions may serve as accurate predictors of the strength of protein–protein interactions with relevance to protein engineering, self-aggregation, or protein stability in complex media.