Machine learning-assisted directed protein evolution with combinatorial libraries

To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow. Combinatorial sequence space can be quite expensive to sample experimentally, but machine learning models trained on tested variants provide a fast method for testing sequence space computationally. We validate this approach on a large published empirical fitness landscape for human GB1 binding protein, demonstrating that machine learning-guided directed evolution finds variants with higher fitness than those found by other directed evolution approaches. We then provide an example application in evolving an enzyme to produce each of the two possible product enantiomers (stereodivergence) of a new-to-nature carbene Si-H insertion reaction. The approach predicted libraries enriched in functional enzymes and fixed seven mutations in two rounds of evolution to identify variants for selective catalysis with 93% and 79% ee. By greatly increasing throughput with in silico modeling, machine learning enhances the quality and diversity of sequence solutions for a protein engineering problem.
Comment: Corrected best S-selective variant sequence in Figure 4. Corrected less R-selective variant sequences from Round II Input library in Table 2 and Supp Table 4. Corrections may also be found on PNAS version https://www.pnas.org/content/early/2019/12/26/1921770117