1
|
Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
Collapse
Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| |
Collapse
|
2
|
Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579038. [PMID: 38370832 PMCID: PMC10871247 DOI: 10.1101/2024.02.05.579038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein capsids are a widespread form of compartmentalisation in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximises the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of novel symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryo-EM, we determine the structures of a precedented 60-mer icosahedral assembly and an unprecedented 36-mer tetrahedron that features significant geometric rearrangements around a novel interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple point mutation to various amino acids, and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent the first example of tetrahedral geometry across all characterised encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in protein sequence.
Collapse
Affiliation(s)
- Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| |
Collapse
|
3
|
Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023; 24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [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: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical reactions. Precise computational design of de novo protein polyhedra is possible through two main types of approaches: methods from first principles, using physical and geometrical rules, and more recent data-driven methods based on artificial intelligence (AI), including deep learning (DL). Here, we retrospect first principle- and AI-based approaches for designing finite polyhedral protein assemblies, as well as advances in the structure prediction of such assemblies. We further highlight the possible applications of these materials and explore how the presented approaches can be combined to overcome current challenges and to advance the design of functional protein-based biomaterials.
Collapse
Affiliation(s)
- Bhoomika Basu Mallik
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Jenna Stanislaw
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Tharindu Madhusankha Alawathurage
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Alena Khmelinskaia
- Transdisciplinary Research Area, "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, 53121, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
- Current address: Department of Chemistry, Ludwig Maximillian University, 80539, Munich, Germany
| |
Collapse
|
4
|
Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
Collapse
Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
| |
Collapse
|
5
|
Li L, Chen G. Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. J Am Chem Soc 2022; 144:16232-16251. [PMID: 36044681 DOI: 10.1021/jacs.2c04418] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.
Collapse
Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China.,Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, People's Republic of China
| |
Collapse
|
6
|
Miller JE, Srinivasan Y, Dharmaraj NP, Liu A, Nguyen PL, Taylor SD, Yeates TO. Designing Protease-Triggered Protein Cages. J Am Chem Soc 2022; 144:12681-12689. [PMID: 35802879 DOI: 10.1021/jacs.2c02165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins that self-assemble into enclosed polyhedral cages, both naturally and by design, are garnering attention for their prospective utility in the fields of medicine and biotechnology. Notably, their potential for encapsulation and surface display are attractive for experiments that require protection and targeted delivery of cargo. The ability to control their opening or disassembly would greatly advance the development of protein nanocages into widespread molecular tools. Toward the development of protein cages that disassemble in a systematic manner and in response to biologically relevant stimuli, here we demonstrate a modular protein cage system that is opened by highly sequence-specific proteases, based on sequence insertions at strategically chosen loop positions in the protein cage subunits. We probed the generality of the approach in the context of protein cages built using the two prevailing methods of construction: genetic fusion between oligomeric components and (non-covalent) computational interface design between oligomeric components. Our results suggest that the former type of cage may be more amenable than the latter for endowing proteolytically controlled disassembly. We show that a successfully designed cage system, based on oligomeric fusion, is modular with regard to its triggering protease. One version of the cage is targeted by an asparagine protease implicated in cancer and Alzheimer's disease, whereas the second version is responsive to the blood-clotting protease, thrombin. The approach demonstrated here should guide future efforts to develop therapeutic vectors to treat disease states where protease induction or mis-regulation occurs.
Collapse
Affiliation(s)
- Justin E Miller
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Yashes Srinivasan
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Nithin P Dharmaraj
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Andrew Liu
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Phillip L Nguyen
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Scott D Taylor
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Todd O Yeates
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| |
Collapse
|
7
|
The development of natural and designed protein nanocages for encapsulation and delivery of active compounds. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
8
|
Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
Collapse
Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| |
Collapse
|
9
|
Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
Collapse
Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| |
Collapse
|
10
|
Generation of ordered protein assemblies using rigid three-body fusion. Proc Natl Acad Sci U S A 2021; 118:2015037118. [PMID: 34074752 DOI: 10.1073/pnas.2015037118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein nanomaterial design is an emerging discipline with applications in medicine and beyond. A long-standing design approach uses genetic fusion to join protein homo-oligomer subunits via α-helical linkers to form more complex symmetric assemblies, but this method is hampered by linker flexibility and a dearth of geometric solutions. Here, we describe a general computational method for rigidly fusing homo-oligomer and spacer building blocks to generate user-defined architectures that generates far more geometric solutions than previous approaches. The fusion junctions are then optimized using Rosetta to minimize flexibility. We apply this method to design and test 92 dihedral symmetric protein assemblies using a set of designed homodimers and repeat protein building blocks. Experimental validation by native mass spectrometry, small-angle X-ray scattering, and negative-stain single-particle electron microscopy confirms the assembly states for 11 designs. Most of these assemblies are constructed from designed ankyrin repeat proteins (DARPins), held in place on one end by α-helical fusion and on the other by a designed homodimer interface, and we explored their use for cryogenic electron microscopy (cryo-EM) structure determination by incorporating DARPin variants selected to bind targets of interest. Although the target resolution was limited by preferred orientation effects and small scaffold size, we found that the dual anchoring strategy reduced the flexibility of the target-DARPIN complex with respect to the overall assembly, suggesting that multipoint anchoring of binding domains could contribute to cryo-EM structure determination of small proteins.
Collapse
|
11
|
Khmelinskaia A, Wargacki A, King NP. Structure-based design of novel polyhedral protein nanomaterials. Curr Opin Microbiol 2021; 61:51-57. [PMID: 33784513 DOI: 10.1016/j.mib.2021.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
Organizing matter at the atomic scale is a central goal of nanotechnology. Bottom-up approaches, in which molecular building blocks are programmed to assemble via supramolecular interactions, are a proven and versatile route to new and useful nanomaterials. Although a wide variety of molecules have been used as building blocks, proteins have several intrinsic features that present unique opportunities for designing nanomaterials with sophisticated functions. There has been tremendous recent progress in designing proteins to fold and assemble to highly ordered structures. Here we review the leading approaches to the design of closed polyhedral protein assemblies, highlight the importance of considering the assembly process itself, and discuss various applications and future directions for the field. We emphasize throughout the exciting opportunities presented by recent advances as well as challenges that remain.
Collapse
Affiliation(s)
- Alena Khmelinskaia
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Adam Wargacki
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Neil P King
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA.
| |
Collapse
|
12
|
Laniado J, Cannon KA, Miller JE, Sawaya MR, McNamara DE, Yeates TO. Geometric Lessons and Design Strategies for Nanoscale Protein Cages. ACS NANO 2021; 15:4277-4286. [PMID: 33683103 DOI: 10.1021/acsnano.0c07167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein molecules bring a rich functionality to the field of designed nanoscale architectures. High-symmetry protein cages are rapidly finding diverse applications in biomedicine, nanotechnology, and imaging, but methods for their reliable and predictable construction remain challenging. In this study we introduce an approach for designing protein assemblies that combines ideas and favorable elements adapted from recent work. Cubically symmetric cages can be created by combining two simpler symmetries, following recently established principles. Here, two different oligomeric protein components are brought together in a geometrically specific arrangement by their separate genetic fusion to individual components of a heterodimeric coiled-coil polypeptide motif of known structure. Fusions between components are made by continuous α-helices to limit flexibility. After a computational design, we tested 10 different protein cage constructions experimentally, two of which formed larger assemblies. One produced the intended octahedral cage, ∼26 nm in diameter, while the other appeared to produce the intended tetrahedral cage as a minor component, crystallizing instead in an alternate form representing a collapsed structure of lower stoichiometry and symmetry. Geometric distinctions between the two characterized designs help explain the different degrees of success, leading to clearer principles and improved prospects for the routine creation of nanoscale protein architectures using diverse methods.
Collapse
Affiliation(s)
- Joshua Laniado
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Kevin A Cannon
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Michael R Sawaya
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095, United States
| | - Dan E McNamara
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- Institute for Genomics and Proteomics, UCLA-DOE, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| |
Collapse
|
13
|
Lv C, Zhang X, Liu Y, Zhang T, Chen H, Zang J, Zheng B, Zhao G. Redesign of protein nanocages: the way from 0D, 1D, 2D to 3D assembly. Chem Soc Rev 2021; 50:3957-3989. [PMID: 33587075 DOI: 10.1039/d0cs01349h] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compartmentalization is a hallmark of living systems. Through compartmentalization, ubiquitous protein nanocages such as viral capsids, ferritin, small heat shock proteins, and DNA-binding proteins from starved cells fulfill a variety of functions, while their shell-like structures hold great promise for various applications in the field of nanomedicine and nanotechnology. However, the number and structure of natural protein nanocages are limited, and these natural protein nanocages may not be suited for a given application, which might impede their further application as nanovehicles, biotemplates or building blocks. To overcome these shortcomings, different strategies have been developed by scientists to construct artificial protein nanocages, and 1D, 2D and 3D protein arrays with protein nanocages as building blocks through genetic and chemical modification to rival the size and functionality of natural protein nanocages. This review outlines the recent advances in the field of the design and construction of artificial protein nanocages and their assemblies with higher order, summarizes the strategies for creating the assembly of protein nanocages from zero-dimension to three dimensions, and introduces their corresponding applications in the preparation of nanomaterials, electrochemistry, and drug delivery. The review will highlight the roles of both the inter-subunit/intermolecular interactions at the key interface and the protein symmetry in constructing and controlling protein nanocage assemblies with different dimensions.
Collapse
Affiliation(s)
- Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Božič Abram S, Gradišar H, Aupič J, Round AR, Jerala R. Triangular in Vivo Self-Assembling Coiled-Coil Protein Origami. ACS Chem Biol 2021; 16:310-315. [PMID: 33476117 PMCID: PMC7901019 DOI: 10.1021/acschembio.0c00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Coiled-coil protein
origami (CCPO) polyhedra are designed self-assembling
nanostructures constructed from coiled coil (CC)-forming modules connected
into a single chain. For testing new CCPO building modules, simpler
polyhedra could be used that should maintain most features relevant
to larger scaffolds. We show the design and characterization of nanoscale
single-chain triangles, composed of six concatenated parallel CC dimer-forming
segments connected by flexible linker peptides. The polypeptides self-assembled
in bacteria in agreement with the design, and the shape of the polypeptides
was confirmed with small-angle X-ray scattering. Fusion with split-fluorescent
protein domains was used as a functional assay in bacteria, based
on the discrimination between the correctly folded and misfolded nanoscale
triangles comprising correct, mismatched, or truncated modules. This
strategy was used to evaluate the optimal size of linkers between
CC segments which comprised eight amino acid residues.
Collapse
Affiliation(s)
- Sabina Božič Abram
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Helena Gradišar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Adam R. Round
- EMBL Grenoble outstation, 38042 Grenoble, France
- School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, 1000 Ljubljana, Slovenia
| |
Collapse
|
15
|
Groaz A, Moghimianavval H, Tavella F, Giessen TW, Vecchiarelli AG, Yang Q, Liu AP. Engineering spatiotemporal organization and dynamics in synthetic cells. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1685. [PMID: 33219745 DOI: 10.1002/wnan.1685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/13/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022]
Abstract
Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
Collapse
Affiliation(s)
| | | | | | | | | | - Qiong Yang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
16
|
Majsterkiewicz K, Azuma Y, Heddle JG. Connectability of protein cages. NANOSCALE ADVANCES 2020; 2:2255-2264. [PMID: 36133365 PMCID: PMC9416917 DOI: 10.1039/d0na00227e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 06/14/2023]
Abstract
Regular, hollow proteinaceous nanoparticles are widespread in nature. The well-defined structures as well as diverse functions of naturally existing protein cages have inspired the development of new nanoarchitectures with desired capabilities. In such approaches, a key functionality is "connectability". Engineering of interfaces between cage building blocks to modulate intra-cage connectability leads to protein cages with new morphologies and assembly-disassembly properties. Modification of protein cage surfaces to control inter-cage connectability enables their arrangement into lattice-like nanomaterials. Here, we review the current progress in control of intra- and inter-cage connectability for protein cage-based nanotechnology development.
Collapse
Affiliation(s)
- Karolina Majsterkiewicz
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
- Postgraduate School of Molecular Medicine Trojdena 2a 02-091 Warsaw Poland
| | - Yusuke Azuma
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
| | - Jonathan G Heddle
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
| |
Collapse
|
17
|
Park WM. Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures. Int J Mol Sci 2020; 21:E3584. [PMID: 32438665 PMCID: PMC7278914 DOI: 10.3390/ijms21103584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.
Collapse
Affiliation(s)
- Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
18
|
Zhou W, Šmidlehner T, Jerala R. Synthetic biology principles for the design of protein with novel structures and functions. FEBS Lett 2020; 594:2199-2212. [PMID: 32324903 DOI: 10.1002/1873-3468.13796] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/29/2020] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Nature provides a large number of functional proteins that evolved during billions of years of evolution. The diversity of natural proteins encompasses versatile functions and more than a thousand different folds, which, however, represents only a tiny fraction of all possible folds and polypeptide sequences. Recent advances in the rational design of proteins demonstrate that it is possible to design de novo protein folds unseen in nature. Novel protein topologies have been designed based on similar principles as natural proteins using advanced computational modelling or modular construction principles, such as oligomerization domains. Designed proteins exhibit several interesting features such as extreme stability, designability of 3D topologies and folding pathways. Moreover, designed protein assemblies can implement symmetry similar to the viral capsids, while, on the other hand, single-chain pseudosymmetric designs can address each position independently. Recently, the design is expanding towards the introduction of new functions into designed proteins, and we may soon be able to design molecular machines.
Collapse
Affiliation(s)
- Weijun Zhou
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tamara Šmidlehner
- 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
|
19
|
Cannon KA, Nguyen VN, Morgan C, Yeates TO. Design and Characterization of an Icosahedral Protein Cage Formed by a Double-Fusion Protein Containing Three Distinct Symmetry Elements. ACS Synth Biol 2020; 9:517-524. [PMID: 32050070 DOI: 10.1021/acssynbio.9b00392] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Exploiting simple types of symmetry common to many natural protein oligomers as a starting point, several recent studies have succeeded in engineering complex self-assembling protein architectures reminiscent but distinct from those evolved in the natural world. Designing symmetric protein cages with a wide range of properties has been of particular interest for potential applications in the fields of medicine, energy, imaging, and more. In this study we genetically fused three naturally symmetric protein components together-a pentamer, trimer, and dimer-in a fashion designed to create a self-assembling icosahedral protein cage built from 60 copies of the protein subunit. The connection between the pentamer and dimer was based on a continuous shared α helix in order to control the relative orientation of those components. Following selection of suitable components by computational methods, a construct with favorable design properties was tested experimentally. Negative stain electron microscopy and solution-state methods indicated successful formation of a 60-subunit icosahedral cage, 2.5 MDa in mass and 30 nm in diameter. Diverse experimental studies also suggested substantial degrees of flexibility and asymmetric deformation of the assembled particle in solution. The results add further examples of successes and challenges in designing atomically precise protein materials.
Collapse
Affiliation(s)
- Kevin A. Cannon
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, United States
| | - Vy N. Nguyen
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, United States
| | - Christian Morgan
- UCLA Department of Ecology and Evolutionary Biology, Los Angeles, California 90095, United States
| | - Todd O. Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, United States
- UCLA Molecular Biology Institute, 611 Charles E Young Drive East, Los Angeles, California 90095, United States
- California Nanosystems Institute, Los Angeles, California 90095, United States
| |
Collapse
|
20
|
McConnell SA, Cannon KA, Morgan C, McAllister R, Amer BR, Clubb RT, Yeates TO. Designed Protein Cages as Scaffolds for Building Multienzyme Materials. ACS Synth Biol 2020; 9:381-391. [PMID: 31922719 DOI: 10.1021/acssynbio.9b00407] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functions of enzymes can be strongly affected by their higher-order spatial arrangements. In this study we combine multiple new technologies-designer protein cages and sortase-based enzymatic attachments between proteins-as a novel platform for organizing multiple enzymes (of one or more types) in specified configurations. As a scaffold we employ a previously characterized 24-subunit designed protein cage whose termini are outwardly exposed for attachment. As a first-use case, we test the attachment of two cellulase enzymes known to act synergistically in cellulose degradation. We show that, after endowing the termini of the cage subunits with a short "sort-tag" sequence (LPXTG) and the opposing termini of the cellulase enzymes with a short polyglycine sequence tag, addition of sortase covalently attaches the enzymes to the cage with good reactivity and high copy number. The doubly modified cages show enhanced activity in a cellulose degradation assay compared to enzymes in solution, and compared to a combination of singly modified cages. These new engineering strategies could be broadly useful in the development of enzymatic material and synthetic biology applications.
Collapse
Affiliation(s)
- Scott A. McConnell
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Kevin A. Cannon
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Christian Morgan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, United States
| | - Rachel McAllister
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Brendan R. Amer
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Robert T. Clubb
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Todd O. Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| |
Collapse
|
21
|
Edgell CL, Smith AJ, Beesley JL, Savery NJ, Woolfson DN. De Novo Designed Protein-Interaction Modules for In-Cell Applications. ACS Synth Biol 2020; 9:427-436. [PMID: 31977192 DOI: 10.1021/acssynbio.9b00453] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein-protein interactions control a wide variety of natural biological processes. α-Helical coiled coils frequently mediate such protein-protein interactions. Due to the relative simplicity of their sequences and structures and the ease with which properties such as strength and specificity of interaction can be controlled, coiled coils can be designed de novo to deliver a variety of non-natural protein-protein interaction domains. Herein, several de novo designed coiled coils are tested for their ability to mediate protein-protein interactions in Escherichia coli cells. The set includes a parallel homodimer, a parallel homotetramer, an antiparallel homotetramer, and a newly designed heterotetramer, all of which have been characterized in vitro by biophysical and structural methods. Using a transcription repression assay based on reconstituting the Lac repressor, we find that the modules behave as designed in the cellular environment. Each design imparts a different property to the resulting Lac repressor-coiled coil complexes, resulting in the benefit of being able to reconfigure the system in multiple ways. Modification of the system also allows the interactions to be controlled: assembly can be tuned by controlling the expression of the constituent components, and complexes can be disrupted through helix sequestration. The small and straightforward de novo designed components that we deliver are highly versatile and have considerable potential as protein-protein interaction domains in synthetic biology where proteins must be assembled in highly specific ways. The relative simplicity of the designs makes them amenable to future modifications to introduce finer control over their assembly and to adapt them for different contexts.
Collapse
Affiliation(s)
- Caitlin L. Edgell
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Abigail J. Smith
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Joseph L. Beesley
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| |
Collapse
|
22
|
Cannon KA, Park RU, Boyken SE, Nattermann U, Yi S, Baker D, King NP, Yeates TO. Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering. Protein Sci 2019; 29:919-929. [PMID: 31840320 DOI: 10.1002/pro.3802] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 01/06/2023]
Abstract
In recent years, new protein engineering methods have produced more than a dozen symmetric, self-assembling protein cages whose structures have been validated to match their design models with near-atomic accuracy. However, many protein cage designs that are tested in the lab do not form the desired assembly, and improving the success rate of design has been a point of recent emphasis. Here we present two protein structures solved by X-ray crystallography of designed protein oligomers that form two-component cages with tetrahedral symmetry. To improve on the past tendency toward poorly soluble protein, we used a computational protocol that favors the formation of hydrogen-bonding networks over exclusively hydrophobic interactions to stabilize the designed protein-protein interfaces. Preliminary characterization showed highly soluble expression, and solution studies indicated successful cage formation by both designed proteins. For one of the designs, a crystal structure confirmed at high resolution that the intended tetrahedral cage was formed, though several flipped amino acid side chain rotamers resulted in an interface that deviates from the precise hydrogen-bonding pattern that was intended. A structure of the other designed cage showed that, under the conditions where crystals were obtained, a noncage structure was formed wherein a porous 3D protein network in space group I21 3 is generated by an off-target twofold homomeric interface. These results illustrate some of the ongoing challenges of developing computational methods for polar interface design, and add two potentially valuable new entries to the growing list of engineered protein materials for downstream applications.
Collapse
Affiliation(s)
- Kevin A Cannon
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California.,UCLA Department of Chemistry and Biochemistry, Los Angeles, California
| | - Rachel U Park
- University of Washington Institute for Protein Design, Seattle, Washington
| | - Scott E Boyken
- University of Washington Institute for Protein Design, Seattle, Washington.,University of Washington Department of Biochemistry, Seattle, Washington
| | - Una Nattermann
- University of Washington Institute for Protein Design, Seattle, Washington.,University of Washington Department of Biochemistry, Seattle, Washington.,University of Washington Graduate Program in Biological Physics, Structure & Design, Seattle, Washington
| | - Sue Yi
- University of Washington Institute for Protein Design, Seattle, Washington.,University of Washington Department of Biochemistry, Seattle, Washington
| | - David Baker
- University of Washington Institute for Protein Design, Seattle, Washington.,University of Washington Department of Biochemistry, Seattle, Washington.,Howard Hughes Medical Institute, Seattle, Washington
| | - Neil P King
- University of Washington Institute for Protein Design, Seattle, Washington.,University of Washington Department of Biochemistry, Seattle, Washington
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California.,UCLA Department of Chemistry and Biochemistry, Los Angeles, California.,UCLA Molecular Biology Institute, Los Angeles, California
| |
Collapse
|
23
|
Sztatelman O, Kopeć K, Pędziwiatr M, Trojnar M, Worch R, Wielgus-Kutrowska B, Jemioła-Rzemińska M, Bzowska A, Grzyb J. Heterodimerizing helices as tools for nanoscale control of the organization of protein-protein and protein-quantum dots. Biochimie 2019; 167:93-105. [PMID: 31560933 DOI: 10.1016/j.biochi.2019.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/19/2019] [Indexed: 01/11/2023]
Abstract
In this study, we tested the possibility of creating complexes of two proteins by fusing them with heterodimerizing helices. We used the fluorescent proteins GFP and mCHERRY expressed with a His-tag as our model system. We added heterodimer-forming sequences at the C- or N- termini of the proteins, opposite to the His-tag position. Heterodimerization was tested for both helices at the C-terminus or at the N- terminus and C-terminus. We observed complex formation with a nanomolar dissociation constant in both cases that was higher by one order of magnitude than the Kds measured for helices alone. The binding of two C-terminal helices was accompanied by an increased enthalpy change. The binding between helices could be stabilized by introducing an additional turn of the helix with cysteine, which was capable of forming disulphide bridges. Covalently linked proteins were obtained using this strategy and observed using fluorescence cross-correlation spectroscopy. Finally, we demonstrated the formation of complexes of protein dimers and quantum dots.
Collapse
Affiliation(s)
- Olga Sztatelman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, PL02106, Warsaw, Poland
| | - Katarzyna Kopeć
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, PL02668, Warsaw, Poland
| | - Marta Pędziwiatr
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, PL02668, Warsaw, Poland
| | - Martyna Trojnar
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie Str. 14a, PL50383, Wrocław, Poland
| | - Remigiusz Worch
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, PL02668, Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, PL02093, Warsaw, Poland
| | - Małgorzata Jemioła-Rzemińska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, PL30387, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, PL30387, Krakow, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, PL02093, Warsaw, Poland
| | - Joanna Grzyb
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie Str. 14a, PL50383, Wrocław, Poland.
| |
Collapse
|
24
|
Cristie‐David AS, Marsh ENG. Metal-dependent assembly of a protein nano-cage. Protein Sci 2019; 28:1620-1629. [PMID: 31278804 PMCID: PMC6699099 DOI: 10.1002/pro.3676] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022]
Abstract
Short, alpha-helical coiled coils provide a simple, modular method to direct the assembly of proteins into higher order structures. We previously demonstrated that by genetically fusing de novo-designed coiled coils of the appropriate oligomerization state to a natural trimeric protein, we could direct the assembly of this protein into various geometrical cages. Here, we have extended this approach by appending a coiled coil designed to trimerize in response to binding divalent transition metal ions and thereby achieve metal ion-dependent assembly of a tetrahedral protein cage. Ni2+ , Co2+ , Cu2+ , and Zn2+ ions were evaluated, with Ni2+ proving the most effective at mediating protein assembly. Characterization of the assembled protein indicated that the metal ion-protein complex formed discrete globular structures of the diameter expected for a complex containing 12 copies of the protein monomer. Protein assembly could be reversed by removing metal ions with ethylenediaminetetraacetic acid or under mildly acidic conditions.
Collapse
Affiliation(s)
| | - E. Neil G. Marsh
- Department of ChemistryUniversity of MichiganAnn ArborMichigan
- Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
| |
Collapse
|
25
|
Cristie-David AS, Chen J, Nowak DB, Bondy AL, Sun K, Park SI, Banaszak Holl MM, Su M, Marsh ENG. Coiled-Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability. J Am Chem Soc 2019; 141:9207-9216. [PMID: 31117640 DOI: 10.1021/jacs.8b13604] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Furthermore, the stabilization of enzyme activity has many practical applications in biotechnology and medicine. Here we describe the symmetry-directed design of an extremely stable, enzymatically active, hollow protein cage of Mr ≈ 2.1 MDa with dimensions similar to those of a small icosahedral virus. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain, and cryo-EM and by atomic force and IR-photoinduced force microscopy established that Ico8 assembles into a flexible hollow cage comprising 20 copies of the esterase trimer, 60 protein subunits in total, with overall icosahedral geometry. Notably, the cages formed by Ico8 proved to be extremely stable toward thermal and chemical denaturation: whereas TriEst was unfolded by heating ( Tm ≈ 75 °C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 °C or in 8 M guanidine hydrochloride. The increased stability of the cages is a new property that emerges from the higher-order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.
Collapse
Affiliation(s)
- Ajitha S Cristie-David
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Junjie Chen
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Derek B Nowak
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Amy L Bondy
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Kai Sun
- Michigan Center for Materials Characterization , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Sung I Park
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Mark M Banaszak Holl
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - E Neil G Marsh
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| |
Collapse
|
26
|
Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S. Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins. ACS Synth Biol 2019; 8:1112-1120. [PMID: 30966743 DOI: 10.1021/acssynbio.9b00019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Self-assembled protein nanostructures have gained interest, owing to their potential applications in biomaterials; however, successful design and construction of protein nanostructures are limited. Herein, we constructed fusion protein 1 by linking the C-terminus of a dimerization domain and the N-terminus of another dimerization domain with a three-helix bundle protein, where it self-assembled mainly into tetramers. By replacing the C-terminal dimerization domain of 1 with a trimerization domain (fusion protein 2), hexamers were mainly obtained. According to ab initio structural models reconstructed from the small-angle X-ray scattering data, the tetramer of 1 and hexamer of 2 adopted quadrangle and cage-like structures, respectively, although they were combinations of different conformations. High-speed atomic force microscopy observations indicated that the tetramer and hexamer exhibit conformational dynamics. These results show that the present method utilizing three-helix bundle-linked fusion proteins is useful in the construction of protein nanostructures.
Collapse
Affiliation(s)
- Takaaki Miyamoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yugo Hayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keito Yoshida
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| |
Collapse
|
27
|
Beesley JL, Woolfson DN. The de novo design of α-helical peptides for supramolecular self-assembly. Curr Opin Biotechnol 2019; 58:175-182. [PMID: 31039508 DOI: 10.1016/j.copbio.2019.03.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
One approach to designing de novo proteinaceous assemblies and materials is to develop simple, standardised building blocks and then to combine these symmetrically to construct more-complex higher-order structures. This has been done extensively using β-structured peptides to produce peptide fibres and hydrogels. Here, we focus on building with de novo α-helical peptides. Because of their self-contained, well-defined structures and clear sequence-to-structure relationships, α helices are highly programmable making them robust building blocks for biomolecular construction. The progress made with this approach over the past two decades is astonishing and has led to a variety of de novo assemblies, including discrete nanoscale objects, and fibrous, nanotube, sheet and colloidal materials. This body of work provides an exceptionally strong foundation for advancing the field beyond in vitro design and into in vivo applications including what we call protein design in cells.
Collapse
Affiliation(s)
- Joseph L Beesley
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK; BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| |
Collapse
|
28
|
Cannon KA, Ochoa JM, Yeates TO. High-symmetry protein assemblies: patterns and emerging applications. Curr Opin Struct Biol 2019; 55:77-84. [PMID: 31005680 DOI: 10.1016/j.sbi.2019.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/06/2019] [Indexed: 12/28/2022]
Abstract
The accelerated elucidation of three-dimensional structures of protein complexes, both natural and designed, is providing new examples of large supramolecular assemblies with intriguing shapes. Those with high symmetry - based on the geometries of the Platonic solids - are particularly notable as their innately closed forms create interior spaces with varying degrees of enclosure. We survey known protein assemblies of this type and discuss their geometric features. The results bear on issues of protein function and evolution, while also guiding novel bioengineering applications. Recent successes using high-symmetry protein assemblies for applications in interior encapsulation and exterior display are highlighted.
Collapse
Affiliation(s)
- Kevin A Cannon
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States
| | - Jessica M Ochoa
- UCLA Department of Chemistry and Biochemistry, United States; UCLA Molecular Biology Institute, United States
| | - Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States; UCLA Molecular Biology Institute, United States.
| |
Collapse
|
29
|
Ross JF, Wildsmith GC, Johnson M, Hurdiss DL, Hollingsworth K, Thompson RF, Mosayebi M, Trinh CH, Paci E, Pearson AR, Webb ME, Turnbull WB. Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages. J Am Chem Soc 2019; 141:5211-5219. [PMID: 30856321 PMCID: PMC6449800 DOI: 10.1021/jacs.8b11480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The self-assembly
of proteins into higher order structures is ubiquitous
in living systems. It is also an essential process for the bottom-up
creation of novel molecular architectures and devices for synthetic
biology. However, the complexity of protein–protein interaction
surfaces makes it challenging to mimic natural assembly processes
in artificial systems. Indeed, many successful computationally designed
protein assemblies are prescreened for “designability”,
limiting the choice of components. Here, we report a simple and pragmatic
strategy to assemble chosen multisubunit proteins into more complex
structures. A coiled-coil domain appended to one face of the pentameric
cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular
supra-molecular complexes. Analysis of a tubular structure determined
by X-ray crystallography has revealed a hierarchical assembly process
that displays features reminiscent of the polymorphic assembly of
polyomavirus proteins. The approach provides a simple and straightforward
method to direct the assembly of protein building blocks which present
either termini on a single face of an oligomer. This scaffolding approach
can be used to generate bespoke supramolecular assemblies of functional
proteins. Additionally, structural resolution of the scaffolded assemblies
highlight “native-state” forced protein–protein
interfaces, which may prove useful as starting conformations for future
computational design.
Collapse
Affiliation(s)
- James F Ross
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Gemma C Wildsmith
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Michael Johnson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Daniel L Hurdiss
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Kristian Hollingsworth
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Majid Mosayebi
- School of Mathematics , University of Bristol , Bristol BS8 1TW , United Kingdom.,BrisSynBio, Life Sciences Building , University of Bristol , Bristol BS8 1TQ , United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics , Universität Hamburg , Hamburg D-22761 , Germany
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - W Bruce Turnbull
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| |
Collapse
|
30
|
Simon AJ, Zhou Y, Ramasubramani V, Glaser J, Pothukuchy A, Gollihar J, Gerberich JC, Leggere JC, Morrow BR, Jung C, Glotzer SC, Taylor DW, Ellington AD. Supercharging enables organized assembly of synthetic biomolecules. Nat Chem 2019; 11:204-212. [DOI: 10.1038/s41557-018-0196-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 11/09/2022]
|
31
|
Chen H, Zhou K, Wang Y, Zang J, Zhao G. Self-assembly of engineered protein nanocages into reversible ordered 3D superlattices mediated by zinc ions. Chem Commun (Camb) 2019; 55:11299-11302. [DOI: 10.1039/c9cc06262a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Zinc ion triggered self-assembly of re-engineered Dps nanocages into highly ordered architectures with a bcc structure.
Collapse
Affiliation(s)
- H. Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing Key Laboratory of Functional Food from Plant Resources
- Beijing
| | - K. Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing Key Laboratory of Functional Food from Plant Resources
- Beijing
| | - Y. Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing Key Laboratory of Functional Food from Plant Resources
- Beijing
| | - J. Zang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing Key Laboratory of Functional Food from Plant Resources
- Beijing
| | - G. Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- China Agricultural University
- Beijing Key Laboratory of Functional Food from Plant Resources
- Beijing
| |
Collapse
|
32
|
Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
| |
Collapse
|
33
|
Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
| |
Collapse
|
34
|
Cristie‐David AS, Koldewey P, Meinen BA, Bardwell JCA, Marsh ENG. Elaborating a coiled-coil-assembled octahedral protein cage with additional protein domains. Protein Sci 2018; 27:1893-1900. [PMID: 30113093 PMCID: PMC6201728 DOI: 10.1002/pro.3497] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 01/28/2023]
Abstract
De novo design of protein nano-cages has potential applications in medicine, synthetic biology, and materials science. We recently developed a modular, symmetry-based strategy for protein assembly in which short, coiled-coil sequences mediate the assembly of a protein building block into a cage. The geometry of the cage is specified by the combination of rotational symmetries associated with the coiled-coil and protein building block. We have used this approach to design well-defined octahedral and tetrahedral cages. Here, we show that the cages can be further elaborated and functionalized by the addition of another protein domain to the free end of the coiled-coil: in this case by fusing maltose-binding protein to an octahedral protein cage to produce a structure with a designed molecular weight of ~1.8 MDa. Importantly, the addition of the maltose binding protein domain dramatically improved the efficiency of assembly, resulting in ~ 60-fold greater yield of purified protein compared to the original cage design. This study shows the potential of using small, coiled-coil motifs as off-the-shelf components to design MDa-sized protein cages to which additional structural or functional elements can be added in a modular manner.
Collapse
Affiliation(s)
| | - Philipp Koldewey
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109
| | - Ben A. Meinen
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109
| | - James C. A. Bardwell
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109
- Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan48109
- Howard Hughes Medical InstituteChevy ChaseMaryland
| | - E. Neil G. Marsh
- Department of ChemistryUniversity of MichiganAnn ArborMichigan48109
| |
Collapse
|
35
|
Anderson G, Shriver-Lake LC, Liu JL, Goldman ER. Orthogonal Synthetic Zippers as Protein Scaffolds. ACS OMEGA 2018; 3:4810-4815. [PMID: 30023904 PMCID: PMC6045340 DOI: 10.1021/acsomega.8b00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Protein scaffolds have proven useful for co-localization of enzymes, providing control over stoichiometry and leading to higher local enzyme concentrations, which have led to improved product formation. To broaden their usefulness, it is necessary to have a wide choice of building blocks to mix and match for scaffold generation. Ideally, the scaffold building blocks should function at any location within the scaffold and have high affinity interactions with their binding partners. We examined the utility of orthogonal synthetic coiled coils (zippers) as scaffold components. The orthogonal zippers are coiled coil domains that form heterodimers only with their specific partner and not with other zipper domains. Focusing on two orthogonal zipper pairs, we demonstrated that they are able to function on either end or in the middle of a multiblock assembly. Surface plasmon resonance was employed to assess the binding kinetics of zipper pairs placed at the start, middle, or end of a construct. Size-exclusion chromatography was used to demonstrate the ability of a scaffold with two zipper domains to bind their partners simultaneously. We then expanded the study to examine the binding kinetics and cross-reactivities of three additional zipper pairs. By validating the affinities and specificities of synthetic zipper pairs, we demonstrated the potential for zipper domains to provide an expanded library of scaffolding parts for tethering enzymes in complex pathways for synthetic biology applications.
Collapse
Affiliation(s)
- George
P. Anderson
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Lisa C. Shriver-Lake
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Jinny L. Liu
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Ellen R. Goldman
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| |
Collapse
|
36
|
Oda A, Nagao S, Yamanaka M, Ueda I, Watanabe H, Uchihashi T, Shibata N, Higuchi Y, Hirota S. Construction of a Triangle-Shaped Trimer and a Tetrahedron Using an α-Helix-Inserted Circular Permutant of Cytochrome c
555. Chem Asian J 2018; 13:964-967. [DOI: 10.1002/asia.201800252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Akiya Oda
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Satoshi Nagao
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Masaru Yamanaka
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Ikki Ueda
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| | - Hiroki Watanabe
- Department of Physics; Nagoya University; Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Takayuki Uchihashi
- Department of Physics; Nagoya University; Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naoki Shibata
- Department of Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho Sayo-gun, Hyogo 679-5148 Japan
| | - Yoshiki Higuchi
- Department of Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho Sayo-gun, Hyogo 679-5148 Japan
| | - Shun Hirota
- Graduate School of Materials Science; Nara Institute of Science and Technology; 8916-5 Takayama Ikoma Nara 630-0192 Japan
| |
Collapse
|