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Low-N protein engineering with data-efficient deep learning

Abstract

Protein engineering has enormous academic and industrial potential. However, it is limited by the lack of experimental assays that are consistent with the design goal and sufficiently high throughput to find rare, enhanced variants. Here we introduce a machine learning-guided paradigm that can use as few as 24 functionally assayed mutant sequences to build an accurate virtual fitness landscape and screen ten million sequences via in silico directed evolution. As demonstrated in two dissimilar proteins, GFP from Aequorea victoria (avGFP) and E. coli strain TEM-1 β-lactamase, top candidates from a single round are diverse and as active as engineered mutants obtained from previous high-throughput efforts. By distilling information from natural protein sequence landscapes, our model learns a latent representation of ‘unnaturalness’, which helps to guide search away from nonfunctional sequence neighborhoods. Subsequent low-N supervision then identifies improvements to the activity of interest. In sum, our approach enables efficient use of resource-intensive high-fidelity assays without sacrificing throughput, and helps to accelerate engineered proteins into the fermenter, field and clinic.

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Fig. 1: UniRep-guided in silico directed evolution for low-N protein engineering.
Fig. 2: eUniRep enables low-N engineering of avGFP.
Fig. 3: eUniRep enables low-N engineering of the enzyme TEM-1 β-lactamase using only single mutants as training data.
Fig. 4: eUniRep designs are structurally non-trivial and require both unsupervised training and low-N supervised training to discover >WT variants.

Data availability

Data required to reproduce all analyses in this work are provided or can be found at https://github.com/churchlab/low-N-protein-engineering. All referenced PDB structures were obtained from https://www.rcsb.org/. The Sarkisyan dataset was obtained from https://figshare.com/articles/dataset/Local_fitness_landscape_of_the_green_fluorescent_protein/3102154.

Code availability

Code for UniRep model training and inference with trained weights along with links to all necessary data is available at https://github.com/churchlab/UniRep. Code required to reproduce all analyses in this work is provided at https://github.com/churchlab/low-N-protein-engineering.

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Acknowledgements

We thank M. AlQuraishi, C. Bakerlee, A. Chiappino-Pepe, A. Eremina, K. Fish, S. Gosai, X. Guo, E. Kelsic, S. Kosuri, P. Ogden, S. Sinai, M. Schubert, A. Taylor-Weiner, D. Thompson and A. Tucker for feedback on earlier drafts of this manuscript. We thank members of the Esvelt and Church laboratories for valuable discussion. S.B. was supported by an NSF GRFP Fellowship under grant number DGE1745303. G.K. was supported by a grant from the Center for Effective Altruism. E.C.A. was supported by a scholarship from the Open Philanthropy Project. This material is based upon work supported by the US Department of Energy, Office of Science under award number DE‐FG02‐02ER63445. Computational resources were, in part, generously provided by the AWS Cloud Credits for Research Program and Lambda Labs, Inc.

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S.B., G.K. and E.C.A. conceived the study. S.B. performed wet-lab experiments and managed data. S.B., G.K. and E.C.A. performed machine learning modeling and data analyses. K.M.E. and G.M.C. supervised the project. S.B., G.K. and E.C.A. wrote the manuscript with help from all authors.

Corresponding author

Correspondence to George M. Church.

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Competing interests

A full list of G.M.C.’s technology transfer, advisory roles and funding sources can be found on the laboratory’s website at http://arep.med.harvard.edu/gmc/tech.html. S.B. is employed by and holds equity in Nabla Bio, Inc. G.K. is employed by and holds equity in Telis Bioscience Inc. E.C.A. and K.M.E. declare no competing interests.

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Peer review information Nature Methods thanks Gabriel Rocklin, Guillaume Lamoureux, and the other, anonymous reviewer, for their contribution to the peer review of this work. Arunima Singh was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Biswas, S., Khimulya, G., Alley, E.C. et al. Low-N protein engineering with data-efficient deep learning. Nat Methods 18, 389–396 (2021). https://doi.org/10.1038/s41592-021-01100-y

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