Predicting pH Optimum for Activity of Beta-Glucosidases

Shaomin Yan,Guang Wu

doi:10.4236/jbise.2019.127027

Abstract

The working conditions for enzymatic reaction are elegant, but not many optimal conditions are documented in literatures. For newly mutated and newly found enzymes, the optimal working conditions can only be extrapolated from our previous experience. Therefore a question raised here is whether we can use the knowledge on enzyme structure to predict the optimal working conditions. Although working conditions for enzymes can be easily measured in experiments, the predictions of working conditions for enzymes are still important because they can minimize the experimental cost and time. In this study, we develop a 20-1 feedforward backpropagation neural network with information on amino acid sequence to predict the pH optimum for the activity of beta-glucosidase, because this enzyme has drawn much attention for its role in bio-fuel industries. Among 25 features of amino acids being screened, the results show that 11 features can be used as predictors in this model and the amino-acid distribution probability is the best in predicting the pH optimum for the activity of beta-glucosidases. Our study paves the way for predicting the optimal working conditions of enzymes based on the amino-acid features.

Highlights

Enzymatic reactions require many elegant conditions, which are usually determined through experiments
Those elegant experimental conditions are valuable for any new experiments with new enzymes because they can save much time and money for experimenters
Many elegant experimental conditions are not always available in literature, so the valuable experience could not be fully useful for fellow researchers

Summary

INTRODUCTION

Enzymatic reactions require many elegant conditions, which are usually determined through experiments. With fast development on computational chemistry and bioinformatics, it could be possible to use models to predict the optimal working conditions for enzymatic reactions with newly designed enzymes This is plausible because currently a lot of information on primary, secondary, tertiary, and quaternary structures is readily available, and many studies have been done on account of structure-function relationship of proteins [1, 2]. The β-glucosidase (EC 3.2.1.21) plays an important role in biological processes because it cuts the β-bond linkage in glucose molecules [3], of which celluloses got much recent attention because of interests in its role in biofuels [4] With such great interest, more efforts are made to search for new β-glucosidases and to mutate current β-glucosidases, so we have more and more β-glucosidases with clear annotations of their primary structures but without their working conditions for enzymatic reactions, for example, pH optimum. We attempted to use the knowledge about amino-acid features from β-glucosidase sequences to predict the pH optimum for the activity of β-glucosidases

MATERIALS AND METHODS

Predictors

Predictive Model

Validation of Predictions

Statistics

RESULTS AND DISCUSSION