Enriching productive mutational paths accelerates enzyme evolution.

Darwinian evolution has given rise to all the enzymes that enable life on Earth. Mimicking natural selection, scientists have learned to tailor these biocatalysts through recursive cycles of mutation, selection and amplification, often relying on screening large protein libraries to productively modulate the complex interplay between protein structure, dynamics and function. Here we show that by removing destabilizing mutations at the library design stage and taking advantage of recent advances in gene synthesis, we can accelerate the evolution of a computationally designed enzyme. In only five rounds of evolution, we generated a Kemp eliminase-an enzymatic model system for proton transfer from carbon-that accelerates the proton abstraction step >108-fold over the uncatalyzed reaction. Recombining the resulting variant with a previously evolved Kemp eliminase HG3.17, which exhibits similar activity but differs by 29 substitutions, allowed us to chart the topography of the designer enzyme's fitness landscape, highlighting that a given protein scaffold can accommodate several, equally viable solutions to a specific catalytic problem.

Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning.

Tailored enzymes are crucial for the transition to a sustainable bioeconomy. However, enzyme engineering is laborious and failure-prone due to its reliance on serendipity. The efficiency and success rates of engineering campaigns may be improved by applying machine learning to map the sequence-activity landscape based on small experimental data sets. Yet, it often proves challenging to reliably model large sequence spaces while keeping the experimental effort tractable. To address this challenge, we present an integrated pipeline combining large-scale screening with active machine learning, which we applied to engineer an artificial metalloenzyme (ArM) catalyzing a new-to-nature hydroamination reaction. Combining lab automation and next-generation sequencing, we acquired sequence-activity data for several thousand ArM variants. We then used Gaussian process regression to model the activity landscape and guide further screening rounds. Critical characteristics of our pipeline include the cost-effective generation of information-rich data sets, the integration of an explorative round to improve the model's performance, and the inclusion of experimental noise. Our approach led to an order-of-magnitude boost in the hit rate while making efficient use of experimental resources. Search strategies like this should find broad utility in enzyme engineering and accelerate the development of novel biocatalysts.

MakeSense: Automated Sensor Design for Proprioceptive Soft Robots.

Soft robots have applications in safe human-robot interactions, manipulation of fragile objects, and locomotion in challenging and unstructured environments. In this article, we present a computational method for augmenting soft robots with proprioceptive sensing capabilities. Our method automatically computes a minimal stretch-receptive sensor network to user-provided soft robotic designs, which is optimized to perform well under a set of user-specified deformation-force pairs. The sensorized robots are able to reconstruct their full deformation state, under interaction forces. We cast our sensor design as a subselection problem, selecting a minimal set of sensors from a large set of fabricable ones, which minimizes the error when sensing specified deformation-force pairs. Unique to our approach is the use of an analytical gradient of our reconstruction performance measure with respect to selection variables. We demonstrate our technique on a bending bar and gripper example, illustrating more complex designs with a simulated tentacle.