A generalized platform for artificial intelligence-powered autonomous enzyme engineering
@NatureComms
1.Researchers present a general-purpose, autonomous enzyme engineering platform that integrates protein language models, machine learning (ML), and robotic biofoundry automation. The platform requires only a protein sequence and a quantifiable fitness assay, eliminating the need for human intuition or domain expertise.
2.In just four iterative design-build-test-learn cycles over four weeks, the platform engineered two enzymes: AtHMT with a 90-fold improvement in substrate preference and 16-fold enhancement in ethyltransferase activity, and YmPhytase with a 26-fold increase in activity at neutral pH.
3.Unlike previous systems limited by cloud labs or expensive gene synthesis, this method uses high-fidelity site-directed mutagenesis combined with modular automation, making it more cost-effective, faster, and broadly applicable.
4.The workflow leverages ESM-2, a protein language model, and EVmutation for generating a diverse, high-quality initial variant library. Then, supervised low-N ML models are trained iteratively on experimental data to guide the next rounds of mutation selection.
5.The robotic iBioFAB platform automates the entire experimental cycle: mutagenesis PCR, DNA assembly, transformation, colony picking, plasmid prep, protein expression, and enzyme assay—all integrated with scheduling software and robotic arms for continuous operation.
6.Results show a high mutagenesis success rate (~95%) and clear improvement across rounds. For AtHMT, the best mutant showed 16-fold higher activity; for YmPhytase, the best mutant achieved over 25-fold activity improvement at neutral pH.
7.Importantly, the ML-guided models outperformed human-intuition-based mutational strategies. For instance, predicted triple mutants surpassed rationally designed combinations, suggesting that the ML approach captures complex epistatic effects between distant residues.
8.The entire system can be accessed via a natural language interface powered by OpenAI’s assistant API. Users can input commands like “design an initial library for AtHMT,” making advanced protein engineering accessible even to non-programmers.
9.The approach stands out for its scalability, generalizability, and modularity. It supports diverse protein types and assay formats (e.g., in vitro, growth-coupled), and is adaptable to future improvements in ML models or biofoundry capabilities.
10.Limitations include dependency on homologous sequences for EVmutation, variable predictive power of the low-N model, and challenges with high GC content during PCR. Nonetheless, this study sets a new benchmark for AI-powered, hands-free protein engineering.
💻Code:
github.com/Zhao-Group/closed… github.com/Zhao-Group/Primer…
📜Paper:
nature.com/articles/s41467-0…
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