Bottom-up de novo design of functional proteins with complex structural features

Che Yang, Fabian Sesterhenn, Jaume Bonet, Eva A. van Aalen, Leo Scheller, Luciano A. Abriata, Johannes T. Cramer, Xiaolin Wen, Stéphane Rosset, Sandrine Georgeon, Theodore Jardetzky, Thomas Krey, Martin Fussenegger, Maarten Merkx, Bruno E. Correia (Corresponding author)

Research output: Contribution to journalArticleAcademicpeer-review

52 Citations (Scopus)

Abstract

De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structures. Here, we used a bottom-up approach to build de novo proteins tailored to accommodate structurally complex functional motifs. We applied the bottom-up strategy to successfully design five folds for four distinct binding motifs, including a bifunctionalized protein with two motifs. Crystal structures confirmed the atomic-level accuracy of the computational designs. These de novo proteins were functional as components of biosensors to monitor antibody responses and as orthogonal ligands to modulate synthetic signaling receptors in engineered mammalian cells. Our work demonstrates the potential of bottom-up approaches to accommodate complex structural motifs, which will be essential to endow de novo proteins with elaborate biochemical functions, such as molecular recognition or catalysis. [Figure not available: see fulltext.]

Original languageEnglish
Pages (from-to)492-500
Number of pages9
JournalNature Chemical Biology
Volume17
Issue number4
DOIs
Publication statusPublished - Apr 2021

Funding

We thank K. Lau, A. Reynaud, L. Durrer, S. Quinche, D. Hacker and F. Pojer in the PTPSP facility at EPFL for protein expression and X-ray crystallography support, D. Demurtas from CIME and S. Nazarov from PTBIOEM for electron microscopy support, L. Menin from the EPFL proteomics core facility for mass spectrometry support, the flow cytometry core facility for technical support and the gene expression core facility for help with next-generation sequencing. We thank V. Olieric at the Paul Scherrer Institute for operation of the X06DA beamline. The computational simulations were facilitated by the CSCS Swiss National Supercomputing Centre as well by SCITAS at EPFL. This work was supported by the Swiss initiative for systems biology (SystemsX.ch), the European Research Council (starting grant no. 716058), the Swiss National Science Foundation (grant no. 310030_163139), the NCCR Molecular Systems Engineering and the NCCR Chemical Biology. F.S. was supported by an SNF/Innosuisse BRIDGE Proof-of-Concept grant, and J.B. was funded by the EPFL Fellows postdoctoral fellowship. T.K. received funding from the Cluster of Excellence RESIST (grant no. EXC 2155) of the German Research foundation and from the German Center of Infection Research, J.T.C. was supported by the ERA-Net PrionImmunity project no. 01GM1503 of the German Federal Ministry of Education and Research. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

FundersFunder number
Cluster of Excellence RESISTEXC 2155
German Center of Infection Research01GM1503
Innosuisse BRIDGE
NCCR Molecular Systems Engineering
Horizon 2020 Framework Programme716058
H2020 European Research Council
European Research Council
Deutsche Forschungsgemeinschaft
École Polytechnique Fédérale de Lausanne
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung310030_163139
Bundesministerium für Bildung und Forschung

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