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Mezgec K, Snoj J, Ulčakar L, Ljubetič A, Tušek Žnidarič M, Škarabot M, Jerala R. Coupling of Spectrin Repeat Modules for the Assembly of Nanorods and Presentation of Protein Domains. ACS NANO 2024. [PMID: 39392430 DOI: 10.1021/acsnano.4c07701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Modular protein engineering is a powerful approach for fabricating high-molecular-weight assemblies and biomaterials with nanoscale precision. Herein, we address the challenge of designing an extended nanoscale filamentous architecture inspired by the central rod domain of human dystrophin, which protects sarcolemma during muscle contraction and consists of spectrin repeats composed of three-helical bundles. A module of three tandem spectrin repeats was used as a rigid building block self-assembling via coiled-coil (CC) dimer-forming peptides. CC peptides were precisely integrated to maintain the spectrin α-helix continuity in an appropriate frame to form extended nanorods. An orthogonal set of customizable CC heterodimers was harnessed for modular rigid domain association, which could be additionally regulated by metal ions and chelators. We achieved a robust assembly of rigid rods several micrometers in length, determined by atomic force microscopy and negative stain transmission electron microscopy. Furthermore, these rigid rods can serve as a scaffold for the decoration of diverse proteins or biologically active peptides along their length with adjustable spacing up to tens of nanometers, as confirmed by the DNA-PAINT super-resolution microscopy. This demonstrates the potential of modular bottom-up protein engineering and tunable CCs for the fabrication of functionalized protein biomaterials.
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Affiliation(s)
- Klemen Mezgec
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Liza Ulčakar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI-1000 Ljubljana, Slovenia
| | - Miha Škarabot
- Condensed Matter Department, Jozef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- CTGCT, Centre of Technology of Gene and Cell Therapy, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Solomonov A, Kozell A, Shimanovich U. Designing Multifunctional Biomaterials via Protein Self-Assembly. Angew Chem Int Ed Engl 2024; 63:e202318365. [PMID: 38206201 DOI: 10.1002/anie.202318365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Protein self-assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self-assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self-assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self-assembly: how the protein structure and self-assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self-assembly monitoring. Finally, based on the cutting-edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self-assembly and link it to biomaterials' performance.
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Affiliation(s)
- Aleksei Solomonov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Anna Kozell
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
| | - Ulyana Shimanovich
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 234 Herzl st., Rehovot, 76100, Israel
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3
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Bethel NP, Borst AJ, Parmeggiani F, Bick MJ, Brunette TJ, Nguyen H, Kang A, Bera AK, Carter L, Miranda MC, Kibler RD, Lamb M, Li X, Sankaran B, Baker D. Precisely patterned nanofibres made from extendable protein multiplexes. Nat Chem 2023; 15:1664-1671. [PMID: 37667012 PMCID: PMC10695826 DOI: 10.1038/s41557-023-01314-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 09/06/2023]
Abstract
Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
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Affiliation(s)
- Neville P Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Fabio Parmeggiani
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Bristol Biodesign Institute, University of Bristol, Bristol, UK
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Miller J, Urvoas A, Gigant B, Ouldali M, Arteni A, Mesneau A, Valerio-Lepiniec M, Artzner F, Dujardin E, Minard P. Engineering of brick and staple components for ordered assembly of synthetic repeat proteins. J Struct Biol 2023; 215:108012. [PMID: 37567372 DOI: 10.1016/j.jsb.2023.108012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Synthetic ɑRep repeat proteins are engineered as Brick and Staple protein pairs that together self-assemble into helical filaments. In most cases, the filaments spontaneously form supercrystals. Here, we describe an expanded series of ɑRep Bricks designed to stabilize the interaction between consecutive Bricks, to control the length of the assembled multimers, or to alter the spatial distribution of the Staple on the filaments. The effects of these Brick modifications on the assembly, on the final filament structure and on the crystal symmetry are analyzed by biochemical methods, electron microscopy and small angle X-ray scattering. We further extend the concept of Brick/Staple protein origami by designing a new type of "Janus"-like Brick protein that is equally assembled by orthogonal staples binding its inner or outer surfaces and thus ending inside or outside the filaments. The relative roles of longitudinal and lateral associations in the assembly process are discussed. This set of results demonstrates important proofs-of-principle for engineering these remarkably versatile proteins toward nanometer-to-micron scale constructions.
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Affiliation(s)
- Jessalyn Miller
- Emory University Department of Chemistry, 1515 Dickey Drive, Atlanta, GA 30322, USA(1); Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Benoit Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Ana Arteni
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agnes Mesneau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Franck Artzner
- Institut de Physique de Rennes (IPR), CNRS, UMR 6251, Université de Rennes 1, F-35042 Rennes, France
| | - Erik Dujardin
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS UMR 6303, Université de Bourgogne Franche-Comté, 21000 Dijon, France.
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France.
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