Building Better Enzymes through combinatorial assembly from modular building blocks

Good news!

"... 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.

New proteins might lead to the reversal of antibiotic resistance in certain bacteria

Very recommendable! Potentially, a breakthrough in defeating antibiotic resistance! Very nice interdisciplinary research!

"Bacteria may be most dangerous when they connect -- banding together to build fortress-like structures known as biofilms that afford them resistance to antibiotics. ...
Further analysis suggested the enzyme first helps the antibiotic kill the bacteria in the oxygenated outer regions of the biofilm in a way that had not before been seen, leading, in short time, to a significant reduction in the total number of viable biofilm cells. ..."

"Pseudomonas aeruginosa is a major cause of hospital-acquired infections due to its formation of biofilms that are highly tolerant to antibiotics. ...
One way in which P. aeruginosa builds robust biofilms is through the production of redox-active phenazines such as pyocyanin. We identified an enzyme that degrades pyocyanin but were stymied in studying its potential to combat biofilms due to its poor expression yield. Here we show how protein design can stabilize the enzyme to improve purification yields, enabling physiological studies to reveal a novel enzyme’s therapeutic potential. ..."

Evolved to Stop Bacteria, Designed for Stability New proteins, created through long-distance collaboration, might lead to the reversal of antibiotic resistance in certain bacteria

Unfortunately, the link to the underlying research article was not provided. Here is what I believe the link is:

Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrant Pseudomonas aeruginosa biofilms