Context-dependent design of induced-fit enzymes using deep learning generates well-expressed, thermally stable and active enzymes

Abstract

The potential of engineered enzymes in industrial applications is often limited by their expression levels, thermal stability, and catalytic diversity. De novo enzyme design faces challenges due to the complexity of enzymatic catalysis. An alternative approach involves expanding natural enzyme capabilities for new substrates and parameters. Here, we introduce CoSaNN (Conformation Sampling using Neural Network), an enzyme design strategy using deep learning for structure prediction and sequence optimization. CoSaNN controls enzyme conformations to expand chemical space beyond simple mutagenesis. It employs a context-dependent approach for generating enzyme designs, considering non-linear relationships in sequence and structure space. We also developed SolvIT, a graph NN predicting protein solubility in Escherichia coli , optimizing enzyme expression selection from larger design sets. Using this method, we engineered enzymes with superior expression levels, with 54% expressed in E. coli , and increased thermal stability, with over 30% having higher Tm than the template, with no high-throughput screening. Our research underscores AI’s transformative role in protein design, capturing high-order interactions and preserving allosteric mechanisms in extensively modified enzymes, and notably enhancing expression success rates. This method’s ease of use and efficiency streamlines enzyme design, opening broad avenues for biotechnological applications and broadening field accessibility.