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Zhao Z, Yuwen W, Duan Z, Zhu C, Fan D. Novel Collagen Analogs with Multicopy Mucin-Type Sequences for Multifunctional Enhancement Properties Using SUMO Fusion Tags. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39318025 DOI: 10.1021/acs.jafc.4c07179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Multifunctional enhanced collagen materials in green biomanufacturing are highly desired yet challenging due to the poor comprehensive performance caused by the adoption of targeting monofunctional peptides. Herein, novel collagen analog design strategy using multicopy tandem of mucin-type sequence (GAPGAPGSQGAPGLQ) derived from human COL1α1 to construct basic building blocks is reported, in which SUMO tag is added to the N-terminal of the protein as a stabilizing core. In particular, novel collagen analogs (named S1506, S1511, S1523, and S1552) with multicopy mucin-type sequences (repeated 6, 11, 23, and 52 times), which were constructed in Escherichia coli, have distinct orientation preferences of functional enhancement (including cell proliferation, differentiation, migration, antioxidant activity, and anti-inflammatory property) compared to COL1α1 in HaCaT and THP-1 cell experiments due to variant three-dimensional structures (the different-length mucin-type polypeptide chains wind around central SUMO tag). Our findings suggest that the innovative protein design and synthesis approaches employed in the construction of these novel S15 proteins have the potential to advance the development of new types of recombinant collagen analogs.
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Affiliation(s)
- Zilong Zhao
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Shaanxi Key Laboratory of Biomaterials and Synthetic Biology, Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710127, China
| | - Weigang Yuwen
- Shaanxi Key Laboratory of Biomaterials and Synthetic Biology, Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710127, China
| | - Zhiguang Duan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Shaanxi Key Laboratory of Biomaterials and Synthetic Biology, Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710127, China
| | - Chenhui Zhu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Shaanxi Key Laboratory of Biomaterials and Synthetic Biology, Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710127, China
| | - Daidi Fan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Shaanxi Key Laboratory of Biomaterials and Synthetic Biology, Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710127, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710127, China
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2
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Dowling QM, Park YJ, Gerstenmaier N, Yang EC, Wargacki A, Hsia Y, Fries CN, Ravichandran R, Walkey C, Burrell A, Veesler D, Baker D, King NP. Hierarchical design of pseudosymmetric protein nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545393. [PMID: 37398374 PMCID: PMC10312784 DOI: 10.1101/2023.06.16.545393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions 1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry 4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.
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Affiliation(s)
- Quinton M Dowling
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Neil Gerstenmaier
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adam Wargacki
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Yang Hsia
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Chelsea N Fries
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Carl Walkey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anika Burrell
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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3
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Chen H, Ma L, Dai H, Fu Y, Wang H, Zhang Y. Advances in Rational Protein Engineering toward Functional Architectures and Their Applications in Food Science. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4522-4533. [PMID: 35353517 DOI: 10.1021/acs.jafc.2c00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein biomolecules including enzymes, cagelike proteins, and specific peptides have been continuously exploited as functional biomaterials applied in catalysis, nutrient delivery, and food preservation in food-related areas. However, natural proteins usually function well in physiological conditions, not industrial conditions, or may possess undesirable physical and chemical properties. Currently, rational protein design as a valuable technology has attracted extensive attention for the rational engineering or fabrication of ideal protein biomaterials with novel properties and functionality. This article starts with the underlying knowledge of protein folding and assembly and is followed by the introduction of the principles and strategies for rational protein design. Basic strategies for rational protein engineering involving experienced protein tailoring, computational prediction, computation redesign, and de novo protein design are summarized. Then, we focus on the recent progress of rational protein engineering or design in the application of food science, and a comprehensive summary ranging from enzyme manufacturing to cagelike protein nanocarriers engineering and antimicrobial peptides preparation is given. Overall, this review highlights the importance of rational protein engineering in food biomaterial preparation which could be beneficial for food science.
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Affiliation(s)
- Hai Chen
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Liang Ma
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Hongjie Dai
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Hongxia Wang
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
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4
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Hu XX, Zhang M, Xu F. Benzylic bromide induced peptide cross-linking for nanofiber assembly. NEW J CHEM 2022. [DOI: 10.1039/d2nj04355f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Herein, we report a cross-linking method for the assembly of coiled-coil peptides into long fibers under mild conditions.
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Affiliation(s)
- Xiao-Xiang Hu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Meng Zhang
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
| | - Fei Xu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, 214122, Wuxi, China
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5
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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: 107] [Impact Index Per Article: 35.7] [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.
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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
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6
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Chen Z, Duan H, Gai Y, Xie W, Deng W, Jiang F. Separation of the host-guest system for ferrocene derivatives in octahedral nanocages by electrochemical ionization. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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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: 32] [Impact Index Per Article: 10.7] [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.
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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
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8
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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.
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Affiliation(s)
- Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
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9
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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: 13] [Impact Index Per Article: 3.3] [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.
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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
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10
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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.
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Affiliation(s)
| | - E. Neil G. Marsh
- Department of ChemistryUniversity of MichiganAnn ArborMichigan
- Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
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11
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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.
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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
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12
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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: 52] [Impact Index Per Article: 10.4] [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.
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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.
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13
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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.
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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.
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