1
|
Plaper T, Merljak E, Fink T, Satler T, Ljubetič A, Lainšček D, Jazbec V, Benčina M, Stevanoska S, Džeroski S, Jerala R. Designed allosteric protein logic. Cell Discov 2024; 10:8. [PMID: 38228615 DOI: 10.1038/s41421-023-00635-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024] Open
Abstract
The regulation of protein function by external or internal signals is one of the key features of living organisms. The ability to directly control the function of a selected protein would represent a valuable tool for regulating biological processes. Here, we present a generally applicable regulation of proteins called INSRTR, based on inserting a peptide into a loop of a target protein that retains its function. We demonstrate the versatility and robustness of coiled-coil-mediated regulation, which enables designs for either inactivation or activation of selected protein functions, and implementation of two-input logic functions with rapid response in mammalian cells. The selection of insertion positions in tested proteins was facilitated by using a predictive machine learning model. We showcase the robustness of the INSRTR strategy on proteins with diverse folds and biological functions, including enzymes, signaling mediators, DNA binders, transcriptional regulators, reporters, and antibody domains implemented as chimeric antigen receptors in T cells. Our findings highlight the potential of INSRTR as a powerful tool for precise control of protein function, advancing our understanding of biological processes and developing biotechnological and therapeutic interventions.
Collapse
Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tina Fink
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Tadej Satler
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Vid Jazbec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | - Sintija Stevanoska
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Sašo Džeroski
- Department of knowledge technologies, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
- Centre for Technologies of Gene and Cell Therapy, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.
| |
Collapse
|
2
|
Satler T, Hadži S, Jerala R. Crystal Structure of de Novo Designed Coiled-Coil Protein Origami Triangle. J Am Chem Soc 2023; 145:16995-17000. [PMID: 37486611 PMCID: PMC10416210 DOI: 10.1021/jacs.3c05531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 07/25/2023]
Abstract
Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks and topological principles to design polyhedral structures distinct from those of natural globular proteins. While the CCPO strategy has proven successful in designing diverse protein topologies, no high-resolution structural information has been available about these novel protein folds. Here we report the crystal structure of a single-chain CCPO in the shape of a triangle. While neither cyclization nor the addition of nanobodies enabled crystallization, it was ultimately facilitated by the inclusion of a GCN2 homodimer. Triangle edges are formed by the orthogonal parallel coiled-coil dimers P1:P2, P3:P4, and GCN2 connected by short linkers. A triangle has a large central cavity and is additionally stabilized by side-chain interactions between neighboring segments at each vertex. The crystal lattice is densely packed and stabilized by a large number of contacts between triangles. Interestingly, the polypeptide chain folds into a trefoil-type protein knot topology, and AlphaFold2 fails to predict the correct fold. The structure validates the modular CC-based protein design strategy, providing molecular insight underlying CCPO stabilization and new opportunities for the design.
Collapse
Affiliation(s)
- Tadej Satler
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- Interdisciplinary
Doctoral Programme in Biomedicine, University
of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- Department
of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department
of Synthetic Biology and Immunology, National
Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, 1000 Ljubljana, Slovenia
| |
Collapse
|
3
|
Strmšek Ž, Snoj J, Satler T, Jerala R. Coiled-Coil Protein Origami: Design, Isolation, and Characterization. Methods Mol Biol 2023; 2671:3-48. [PMID: 37308636 DOI: 10.1007/978-1-0716-3222-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Coiled-coil protein origami (CCPO) is a rationally designed de novo protein fold, constructed by concatenating coiled-coil forming segments into a polypeptide chain, that folds into polyhedral nano-cages. To date, nanocages in the shape of a tetrahedron, square pyramid, trigonal prism, and trigonal bipyramid have been successfully designed and extensively characterized following the design principles of CCPO. These designed protein scaffolds and their favorable biophysical properties are suitable for functionalization and other various biotechnological applications. To further facilitate the development, we are presenting a detailed guide to the world of CCPO, starting from design (CoCoPOD, an integrated platform for designing CCPO strictures) and cloning (modified Golden-gate assembly) to fermentation and isolation (NiNTA, Strep-trap, IEX, and SEC) concluding with standard characterization techniques (CD, SEC-MALS, and SAXS).
Collapse
Affiliation(s)
- Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tadej Satler
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
| |
Collapse
|