Develop machine learning based predictive models for engineering protein solubility

TL;DR

This paper develops machine learning models to predict protein solubility as a continuous variable from amino acid sequences, aiding protein engineering and potentially serving as an indirect predictor of protein activity.

Contribution

It introduces a novel approach predicting protein solubility in continuous values, improving upon binary models and achieving 76.28% accuracy with SVM.

Findings

Achieved 76.28% prediction accuracy using SVM.

Predicted solubility as continuous values enhances protein engineering.

Models can indirectly predict protein activity from sequence.

Abstract

Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is highly desired, as it aids experimental improvement of proteins. However, only limited data for protein activity are currently available, which prevents the development of such models. Since protein activity and solubility are correlated for some proteins, the publicly available solubility dataset may be adopted to develop models that can predict protein solubility from sequence. The models could serve as a tool to indirectly predict protein activity from sequence. In literature, predicting protein solubility from sequence has been intensively explored, but the predicted solubility represented in binary values from all the developed models was not suitable for guiding experimental designs to improve protein solubility. Here we propose new machine learning models for improving protein solubility in vivo. We first implemented a novel approach that predicted protein solubility in continuous numerical values instead of binary ones. After combing it with various machine learning algorithms, we achieved a prediction accuracy of 76.28 percent when Support Vector Machine algorithm was used. Continuous values of solubility are more meaningful in protein engineering, as they enable researchers to choose proteins with higher predicted solubility for experimental validation, while binary values fail to distinguish proteins with the same value. There are only two possible values so many proteins have the same one.