Building Better Enzymes through combinatorial assembly from modular building blocks

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"... a computational method for designing thousands of different active enzymes with unprecedented efficiency by assembling them from engineered modular building blocks. ...
The inspiration for this new approach came from within: our immune system, which is capable of making billions of different antibodies – proteins that in principle can counter any harmful microorganism – just from the bits dictated by a relatively small number of genes. “Antibodies are the only family of proteins in nature known to be generated in a modular way,” ... “Their huge diversity is achieved by recombining preexisting genetic fragments ..."

"Fishing for the right puzzle piece

Recombination can be a good strategy to generate natural protein diversity while retaining function, but it also causes problems if the starting sequences are too dissimilar and cannot fit together properly to form a functional protein. [researchers]  developed a machine learning strategy to piece together fragments sourced from highly divergent natural enzymes to generate a million structurally diverse protein backbones. This step is then followed by mutagenesis and structural optimization to create stable, functional active sites. Isolation by high-throughput yeast display and activity-based profiling recovered thousands of functional enzyme variants. A second-generation model trained on preorganization of the active site was nearly 10-fold more efficient and provides valuable insights for enzyme design strategies across the board."

From the abstract:

"The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles."

Building Better Enzymes – by Breaking Them Down - Chemistry | Weizmann Wonder Wander - News, Features and Discoveries In a major step toward greener industry, Weizmann Institute scientists create a computational method for generating enzymes with unprecedented efficiency

Combinatorial assembly and design of enzymes (no public access)

Here is the link to the preprint: https://www.biorxiv.org/node/2896090.full

Fig. 1. Key steps in the CADENZ workflow.