Mapping the overlapping fitness landscapes of a superfamily of promiscuous enzymes: strategies for directed evolution?

Proteins are Nature’s all-purpose functional molecules that work with unsurpassed precision under mild conditions. Their exceptional selectivity enables them to identify a single molecule out of thousands within a cell, while their efficacy, characterized by tight binding and efficient catalytic turnover, allows them to engage with target molecules and either neutralize, cleave, or process them. Being able to emulate Nature’s ability to create tailor-made molecules in the laboratory could bring transformational change to various aspects of our lives, such as ‘green’ industrial production, resource-efficient bioprocessing, and more selective therapeutic interventions.

Understanding enzyme catalysis remains a formidable challenge, despite extensive research efforts in both basic and applied fields. Current knowledge falls short when it comes to creating catalysts with the efficiency of natural enzymes. Directed evolution offers a promising approach to this issue by creating large collections of molecular variants and testing each to identify rare, effective catalysts. The success of this method depends on conducting numerous tests, a principle that mirrors Nature’s own process of gradual molecular evolution.

To enhance this process, the project has developed a high-throughput testing system using microfluidic devices capable of evaluating over 10 million mutants per day. This technological advancement allows for the acceleration of directed evolution and improves catalyst discovery.