Protein dynamics at slow timescales in engineered ß-lactamases does not limit evolvability

Understanding the underlying mechanisms in the evolution of new protein functions is key to better directing enzyme engineering efforts. Intragenic epistasis (the non-additive interaction of mutations affecting function) is a key feature of protein evolution. For example, in TEM-1 ß-lactamase, the mutations E104K and G238S show positive epistasis in that their combination show a greater than expected increase in antibiotic resistance1. Here, we aim to understand the impact of protein dynamics at slow timescales on epistasis. Large conformational rearrangements associated with ligand-binding, turnover of substrate or allostery occur at this timescale2. The readily evolvable antibiotic-resistant TEM-1 ß-lactamase and two of its variants that are more dynamic at slow timescales serve as models for this study. Our models show similar catalytic activity and substrate recognition, thermal stability, as well as conserved motions in fast (ps-ns) and intermediate (ns-ms) timescales but different motions at slow timescales (ms-ms)123. Please click Additional Files below to see the full abstract

Indigo Formation and Rapid NADPH Consumption Provide Robust Prediction of Raspberry Ketone Synthesis by Engineered Cytochrome P450 BM3

Natural raspberry ketone has a high value in the flavor, fragrance and pharmaceutical industries. Its extraction is costly, justifying the search for biosynthetic routes. We hypothesized that cytochrome P450 BM3 (P450 BM3) could be engineered to catalyze the hydroxylation of 4‐phenyl‐2‐butanone, a naturally sourceable precursor, to raspberry ketone. The synthesis of indigo by variants of P450 BM3 has previously served as a predictor of promiscuous oxidation reactions. To this end, we screened 53 active‐site variants of P450 BM3 using orthogonal high‐throughput workflows to identify the most streamlined route to all indigo‐forming variants. Among the three known and 13 new indigo‐forming variants, eight hydroxylated 4‐phenyl‐2‐butanone to raspberry ketone. Previously unreported variant A82Q displayed the highest initial rates and coupling efficiencies in synthesis of indigo and of raspberry ketone. It produced the highest total concentration of raspberry ketone despite producing less total indigo than previously reported variants. Its productivity, although modest, clearly demonstrates the potential for development of a biocatalytic route to raspberry ketone. In addition to validating indigo as a robust predictor of this promiscuous activity, we demonstrate that monitoring rapid NADPH consumption serves as an alternative predictor of a promiscuous reactivity in P450 BM3