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Aguirre-Sampieri S, Casañal A, Emsley P, Garza-Ramos G. Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis. J Struct Biol 2024; 216:108093. [PMID: 38615726 PMCID: PMC7616060 DOI: 10.1016/j.jsb.2024.108093] [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: 01/17/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Many enzymes can self-assemble into higher-order structures with helical symmetry. A particularly noteworthy example is that of nitrilases, enzymes in which oligomerization of dimers into spiral homo-oligomers is a requirement for their enzymatic function. Nitrilases are widespread in nature where they catalyze the hydrolysis of nitriles into the corresponding carboxylic acid and ammonia. Here, we present the Cryo-EM structure, at 3 Å resolution, of a C-terminal truncate nitrilase from Rhodococcus sp. V51B that assembles in helical filaments. The model comprises a complete turn of the helical arrangement with a substrate-intermediate bound to the catalytic cysteine. The structure was solved having added the substrate to the protein. The length and stability of filaments was made more substantial in the presence of the aromatic substrate, benzonitrile, but not for aliphatic nitriles or dinitriles. The overall structure maintains the topology of the nitrilase family, and the filament is formed by the association of dimers in a chain-like mechanism that stabilizes the spiral. The active site is completely buried inside each monomer, while the substrate binding pocket was observed within the oligomerization interfaces. The present structure is in a closed configuration, judging by the position of the lid, suggesting that the intermediate is one of the covalent adducts. The proximity of the active site to the dimerization and oligomerization interfaces, allows the dimer to sense structural changes once the benzonitrile was bound, and translated to the rest of the filament, stabilizing the helical structure.
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Affiliation(s)
- Sergio Aguirre-Sampieri
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico
| | - Ana Casañal
- Human Technopole, Palazzo Italia, Viale Rita Levi‑Montalcini, 1, 20157 Milan, Italy
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Structural Studies Division, Francis Crick Avenue, CB2 0QH Cambridge, England
| | - Georgina Garza-Ramos
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico.
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2
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Mikhaylina A, Lekontseva N, Marchenkov V, Kolesnikova V, Khairetdinova A, Nikonov O, Balobanov V. The New Functional Hybrid Chaperone Protein ADGroEL-SacSm. Molecules 2023; 28:6196. [PMID: 37687025 PMCID: PMC10488932 DOI: 10.3390/molecules28176196] [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: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The creation of new proteins by combining natural domains is a commonly used technique in protein engineering. In this work, we have tested the possibilities and limitations of using circular homo-oligomeric Sm-like proteins as a basis for attaching other domains. Attachment to such a stable base should bring target domains together and keep them in the correct mutual orientation. We chose a circular homoheptameric Sm-like protein from Sulfolobus acidocaldarius as a stable backbone and the apical domain of the GroEL chaperone protein as the domain of study. This domain by itself, separated from the rest of the GroEL molecule, does not form an oligomeric ring. In our design, the hyperstable SacSm held the seven ADGroELs together and forced them to oligomerize. The designed hybrid protein was obtained and studied with various physical and chemical methods. Stepwise assembly and self-organization of this protein have been shown. First, the SacSm base was assembled, and then ADGroEL was folded on it. Functional testing showed that the obtained fusion protein was able to bind the same non-native proteins as the full-length GroEL chaperone. It also reduced the aggregation of a number of proteins when they were heated, which confirms its chaperone activity. Thus, the engineering path we chose made it possible to create an efficient thermostable chaperone. The result obtained shows the productivity of the way we chose for the creation and stabilization of oligomeric proteins.
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Affiliation(s)
| | | | | | | | | | | | - Vitalii Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str. 4, 142290 Pushchino, Russia
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3
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López-Laguna H, Sánchez JM, Carratalá JV, Rojas-Peña M, Sánchez-García L, Parladé E, Sánchez-Chardi A, Voltà-Durán E, Serna N, Cano-Garrido O, Flores S, Ferrer-Miralles N, Nolan V, de Marco A, Roher N, Unzueta U, Vazquez E, Villaverde A. Biofabrication of functional protein nanoparticles through simple His-tag engineering. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2021; 9:12341-12354. [PMID: 34603855 PMCID: PMC8483566 DOI: 10.1021/acssuschemeng.1c04256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Indexed: 05/03/2023]
Abstract
We have developed a simple, robust, and fully transversal approach for the a-la-carte fabrication of functional multimeric nanoparticles with potential biomedical applications, validated here by a set of diverse and unrelated polypeptides. The proposed concept is based on the controlled coordination between Zn2+ ions and His residues in His-tagged proteins. This approach results in a spontaneous and reproducible protein assembly as nanoscale oligomers that keep the original functionalities of the protein building blocks. The assembly of these materials is not linked to particular polypeptide features, and it is based on an environmentally friendly and sustainable approach. The resulting nanoparticles, with dimensions ranging between 10 and 15 nm, are regular in size, are architecturally stable, are fully functional, and serve as intermediates in a more complex assembly process, resulting in the formation of microscale protein materials. Since most of the recombinant proteins produced by biochemical and biotechnological industries and intended for biomedical research are His-tagged, the green biofabrication procedure proposed here can be straightforwardly applied to a huge spectrum of protein species for their conversion into their respective nanostructured formats.
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Affiliation(s)
- Hèctor López-Laguna
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Julieta M. Sánchez
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Universidad
Nacional de Córdoba, Facultad de
Ciencias Exactas, Físicas y Naturales, ICTA and Departamento
de Química, Cátedra de Química
Biológica, Av. Vélez Sársfield
1611, Córdoba 5016, Argentina
- CONICET-Universidad
Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas
(IIByT), Av. Velez Sarsfield
1611, Córdoba, 5016, Argentina
| | - José Vicente Carratalá
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Mauricio Rojas-Peña
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Laura Sánchez-García
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Eloi Parladé
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Alejandro Sánchez-Chardi
- Servei de
Microscòpia, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat
de Biologia, Universitat de Barcelona, Av. Diagonal 643, Barcelona 08028, Spain
| | - Eric Voltà-Durán
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Naroa Serna
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Olivia Cano-Garrido
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Sandra Flores
- Universidad
Nacional de Córdoba, Facultad de
Ciencias Exactas, Físicas y Naturales, ICTA and Departamento
de Química, Cátedra de Química
Biológica, Av. Vélez Sársfield
1611, Córdoba 5016, Argentina
- CONICET-Universidad
Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas
(IIByT), Av. Velez Sarsfield
1611, Córdoba, 5016, Argentina
| | - Neus Ferrer-Miralles
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Verónica Nolan
- Universidad
Nacional de Córdoba, Facultad de
Ciencias Exactas, Físicas y Naturales, ICTA and Departamento
de Química, Cátedra de Química
Biológica, Av. Vélez Sársfield
1611, Córdoba 5016, Argentina
- CONICET-Universidad
Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas
(IIByT), Av. Velez Sarsfield
1611, Córdoba, 5016, Argentina
| | - Ario de Marco
- Laboratory
for Environmental and Life Sciences, University
of Nova Gorica, Nova Gorica 5000, Slovenia
| | - Nerea Roher
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
- Departament
de Biologia Cel·lular, Fisiologia Animal i Immunologia, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Ugutz Unzueta
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
- Biomedical
Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Ma Claret 167, Barcelona 08025, Spain
| | - Esther Vazquez
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
| | - Antonio Villaverde
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, Madrid 28029, Spain
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4
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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: 31] [Impact Index Per Article: 10.3] [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.
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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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5
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A Supramolecular Assembly of Hemoproteins Formed in a Star-Shaped Structure via Heme-Heme Pocket Interactions. Int J Mol Sci 2021; 22:ijms22031012. [PMID: 33498330 PMCID: PMC7864044 DOI: 10.3390/ijms22031012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/17/2022] Open
Abstract
Proteins have been used as building blocks to provide various supramolecular structures in efforts to develop nano-biomaterials possessing broad biological functionalities. A series of unique structures have been obtained from the engineering of hemoproteins which contain the iron porphyrin known as heme, as a prosthetic group. This work in developing assembling systems is extended using cytochrome b562, a small electron transfer hemoprotein engineered to include an externally-attached heme moiety. The engineered units, which form a one-dimensional assembly via interprotein heme–heme pocket interactions, are conjugated to an apo-form of hexameric tyrosine-coordinated hemoprotein (apoHTHP) to provide a branching unit promoting the assembly of a star-shaped structure. The incorporation of the heme moiety attached to the protein surface of cytochrome b562 into apoHTHP can be accelerated by elevating the reaction temperature to generate a new assembly. The formation of a new larger assembly structure was confirmed by size exclusion chromatography. The ratio of the heme-containing units in the assemblies was analyzed by UV-Vis spectroscopy and the population of protein units estimated from SDS PAGE suggests the presence of plausible star-shaped structures, which are supported by hydrodynamic diameter data obtained by dynamic light scattering.
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6
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Chakraborty S, Khamrui R, Ghosh S. Redox responsive activity regulation in exceptionally stable supramolecular assembly and co-assembly of a protein. Chem Sci 2020; 12:1101-1108. [PMID: 34163877 PMCID: PMC8179030 DOI: 10.1039/d0sc05312k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/14/2020] [Indexed: 11/23/2022] Open
Abstract
Supramolecular assembly of biomolecules/macromolecules stems from the desire to mimic complex biological structures and functions of living organisms. While DNA nanotechnology is already in an advanced stage, protein assembly is still in its infancy as it is a significantly difficult task due to their large molecular weight, conformational complexity and structural instability towards variation in temperature, pH or ionic strength. This article reports highly stable redox-responsive supramolecular assembly of a protein Bovine serum albumin (BSA) which is functionalized with a supramolecular structure directing unit (SSDU). The SSDU consists of a benzamide functionalized naphthalene-diimide (NDI) chromophore which is attached with the protein by a bio-reducible disulfide linker. The SSDU attached protein (NDI-BSA) exhibits spontaneous supramolecular assembly in water by off-set π-stacking among the NDI chromophores, leading to the formation of spherical nanoparticles (diameter: 150-200 nm). The same SSDU when connected with a small hydrophilic wedge (NDI-1) instead of the large globular protein, exhibits a different π-stacking mode with relatively less longitudinal displacement which results in a fibrillar network and hydrogelation. Supramolecular co-assembly of NDI-BSA and NDI-1 (3 : 7) produces similar π-stacking and an entangled 1D morphology. Both the spherical assembly of NDI-BSA or the fibrillar co-assembly of NDI-BSA + NDI-1 (3 : 7) provide sufficient thermal stability to the protein as its thermal denaturation could be completely surpassed while the secondary structure remained intact. However, the esterase like activity of the protein reduced significantly as a result of such supramolecular assembly indicating limited access by the substrate to the active site of the enzyme located in the confined environment. In the presence of glutathione (GSH), a biologically important tri-peptide, due to the cleavage of the disulfide bond, the protein became free and was released, resulting in fully regaining its enzymatic activity. Such supramolecular assembly provided excellent protection to the protein against enzymatic hydrolysis as the relative hydrolysis was estimated to be <30% for the co-assembled protein with respect to the free protein under identical conditions. Similar to bioactivity, the enzymatic hydrolysis also became prominent after GSH-treatment, confirming that the lack of hydrolysis in the supramolecularly assembled state is indeed related to the confinement of the protein in the nanostructure assembly.
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Affiliation(s)
- Saptarshi Chakraborty
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Rajesh Khamrui
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
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7
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The application of helix fusion methods in structural biology. Curr Opin Struct Biol 2020; 60:110-116. [PMID: 31968282 DOI: 10.1016/j.sbi.2019.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 10/31/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022]
Abstract
Methods generating fusion proteins with rigid and predictable structures have been developed in recent years. Among them, helix fusion methods that link two proteins by connecting their terminal alpha helices into a single and extended alpha helix can be particularly useful because designing fusion helices is conceptually and technically simple. These methods have been shown crucial in obtaining crystals that diffract x-rays to high resolution or attaching large and symmetrical backbone proteins to small target proteins for cryo-EM analysis. The structural rigidity of the fusion helix is crucial for these applications, and the reduction of structural ambiguity and flexibility at the fusion sites will further enhance the usefulness of this method.
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8
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Liu H, Cao M, Wang Y, Lv B, Li C. Bioengineering oligomerization and monomerization of enzymes: learning from natural evolution to matching the demands for industrial applications. Crit Rev Biotechnol 2020; 40:231-246. [PMID: 31914816 DOI: 10.1080/07388551.2019.1711014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
It is generally accepted that oligomeric enzymes evolve from their monomeric ancestors, and the evolution process generates superior structural benefits for functional advantages. Furthermore, adjusting the transition between different oligomeric states is an important mechanism for natural enzymes to regulate their catalytic functions for adapting environmental fluctuations in nature, which inspires researchers to mimic such a strategy to develop artificially oligomerized enzymes through protein engineering for improved performance under specific conditions. On the other hand, transforming oligomeric enzymes into their monomers is needed in fundamental research for deciphering catalytic mechanisms as well as exploring their catalytic capacities for better industrial applications. In this article, strategies for developing artificially oligomerized and monomerized enzymes are reviewed and highlighted by their applications. Furthermore, advances in the computational prediction of oligomeric structures are introduced, which would accelerate the systematic design of oligomeric and monomeric enzymes. Finally, the current challenges and future directions in this field are discussed.
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Affiliation(s)
- Hu Liu
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Mingming Cao
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ying Wang
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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9
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Carné-Sánchez A, Carmona FJ, Kim C, Furukawa S. Porous materials as carriers of gasotransmitters towards gas biology and therapeutic applications. Chem Commun (Camb) 2020; 56:9750-9766. [DOI: 10.1039/d0cc03740k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review highlights the strategies employed to load and release gasotransmitters such as NO, CO and H2S from different kinds of porous materials, including zeolites, mesoporous silica, metal–organic frameworks and protein assemblies.
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Affiliation(s)
- Arnau Carné-Sánchez
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto
- Japan
- Catalan Institute of Nanoscience and Nanotechnology (ICN2)
| | - Francisco J. Carmona
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto
- Japan
| | - Chiwon Kim
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto
- Japan
- Department of Synthetic Chemistry and Biological Chemistry
| | - Shuhei Furukawa
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto
- Japan
- Department of Synthetic Chemistry and Biological Chemistry
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10
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Rose J, Visser F, Müller B, Senft M, Groscurth S, Sicking KF, Twyman RM, Prüfer D, Noll GA. Identification and molecular analysis of interaction sites in the MtSEO-F1 protein involved in forisome assembly. Int J Biol Macromol 2019; 144:603-614. [PMID: 31843608 DOI: 10.1016/j.ijbiomac.2019.12.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022]
Abstract
Forisomes are large mechanoprotein complexes found solely in legumes such as Medicago truncatula. They comprise several "sieve element occlusion by forisome" (SEO-F) subunits, with MtSEO-F1 as the major structure-forming component. SEO-F proteins possess three conserved domains -an N-terminal domain (SEO-NTD), a potential thioredoxin fold, and a C-terminal domain (SEO-CTD)- but structural and biochemical data are scarce and little is known about the contribution of these domains to forisome assembly. To identify key amino acids involved in MtSEO-F1 dimerization and complex formation, we investigated protein-protein interactions by bimolecular fluorescence complementation and the analysis of yeast two-hybrid and random mutagenesis libraries. We identified a SEO-NTD core region as the major dimerization site, with abundant hydrophobic residues and rare charged residues suggesting dimerization is driven by the hydrophobic effect. We also found that ~45% of the full-length MtSEO-F1 sequence must be conserved for higher-order protein assembly, indicating that large interaction surfaces facilitate stable interactions, contributing to the high resilience of forisome bodies. Interestingly, the removal of 62 amino acids from the C-terminus did not disrupt forisome assembly. This is the first study unraveling interaction sites and mechanisms within the MtSEO-F1 protein at the level of dimerization and complex formation.
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Affiliation(s)
- Judith Rose
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Franziska Visser
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Boje Müller
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Matthias Senft
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Sira Groscurth
- Stem Cell Network North Rhine-Westphalia, Merowingerplatz 1, 40225 Düsseldorf, Germany
| | - Kevin F Sicking
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | | | - Dirk Prüfer
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Gundula A Noll
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany.
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11
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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12
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Kuan SL, Bergamini FRG, Weil T. Functional protein nanostructures: a chemical toolbox. Chem Soc Rev 2018; 47:9069-9105. [PMID: 30452046 PMCID: PMC6289173 DOI: 10.1039/c8cs00590g] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 01/08/2023]
Abstract
Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.
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Affiliation(s)
- Seah Ling Kuan
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
| | - Fernando R. G. Bergamini
- Institute of Chemistry
, Federal University of Uberlândia – UFU
,
38400-902 Uberlândia
, MG
, Brazil
| | - Tanja Weil
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
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13
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Atomic insights into the genesis of cellular filaments by globular proteins. Nat Struct Mol Biol 2018; 25:705-714. [PMID: 30076408 PMCID: PMC6185745 DOI: 10.1038/s41594-018-0096-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/21/2018] [Indexed: 02/04/2023]
Abstract
Self-assembly of proteins into filaments, such as actin and tubulin filaments, underlies essential cellular processes in all three domains of life. The early emergence of filaments in evolutionary history suggests that filament genesis might be a robust process. Here we describe the fortuitous construction of GFP fusion proteins that self-assemble as fluorescent polar filaments in Escherichia coli. Filament formation is achieved by appending as few as 12 residues. Crystal structures reveal that the protomers each donate an appendage to fill a groove between two following protomers along the filament. This exchange of appendages resembles runaway domain swapping but is distinguished by higher efficiency because monomers cannot competitively bind their own appendages. Ample evidence of this “runaway domain coupling” mechanism in nature suggests it could facilitate the evolutionary pathway from globular protein to polar filament, requiring a minimal extension of protein sequence and no significant refolding.
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14
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Diaz D, Care A, Sunna A. Bioengineering Strategies for Protein-Based Nanoparticles. Genes (Basel) 2018; 9:E370. [PMID: 30041491 PMCID: PMC6071185 DOI: 10.3390/genes9070370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP's intrinsic properties and to impart them with novel functionalities.
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Affiliation(s)
- Dennis Diaz
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia.
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15
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Lutomski CA, Lyktey NA, Pierson EE, Zhao Z, Zlotnick A, Jarrold MF. Multiple Pathways in Capsid Assembly. J Am Chem Soc 2018; 140:5784-5790. [PMID: 29672035 DOI: 10.1021/jacs.8b01804] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For a three-dimensional structure to spontaneously self-assemble from many identical components, the steps on the pathway must be kinetically accessible. Many virus capsids are icosahedral and assembled from hundreds of identical proteins, but how they navigate the assembly process is poorly understood. Capsid assembly is thought to involve stepwise addition of subunits to a growing capsid fragment. Coarse-grained models suggest that the reaction occurs on a downhill energy landscape, so intermediates are expected to be fleeting. In this work, charge detection mass spectrometry (CDMS) has been used to track assembly of the hepatitis B virus (HBV) capsid in real time. The icosahedral T = 4 capsid of HBV is assembled from 120 capsid protein dimers. Our results indicate that there are multiple pathways for assembly. Under conditions that favor a modest association energy there is no accumulation of large intermediates, which indicates that available pathways include ones on a downhill energy surface. Under higher salt conditions, where subunit interactions are strengthened, around half of the products of the initial assembly reaction have masses close to the T = 4 capsid and the other half are stalled intermediates which emerge abruptly at around 90 dimers, indicating a bifurcation in the ensemble of assembly paths. When incubated at room temperature, the 90-dimer intermediates accumulate dimers and gradually shift to higher mass and merge with the capsid peak. Though free subunits are present in solution, the stalled intermediates indicate the presence of a local minima on the energy landscape. Some intermediates may result from hole closure, where the growing capsid distorts to close the hole due to the missing capsid proteins or from a species where subsequent additions are particularly labile.
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16
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Oohora K, Onuma Y, Tanaka Y, Onoda A, Hayashi T. A supramolecular assembly based on an engineered hemoprotein exhibiting a thermal stimulus-driven conversion to a new distinct supramolecular structure. Chem Commun (Camb) 2018; 53:6879-6882. [PMID: 28604909 DOI: 10.1039/c7cc02678a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Supramolecular assembly of an engineered hemoprotein with an externally-attached heme moiety via an azobenzene or stilbene linker demonstrates drastic structural transitions between two distinct forms: the thermodynamically stable fiber-type assembly and the kinetically trapped metastable micelle-type assembly induced by transient thermal stimulus.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan.
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17
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Pandit G, Roy K, Agarwal U, Chatterjee S. Self-Assembly Mechanism of a Peptide-Based Drug Delivery Vehicle. ACS OMEGA 2018; 3:3143-3155. [PMID: 30023862 PMCID: PMC6045401 DOI: 10.1021/acsomega.7b01871] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/05/2018] [Indexed: 05/03/2023]
Abstract
We report the mechanism of the concentration-dependent self-assembly of a tetrapeptide. Peptide Boc-Trp-Leu-Trp-Leu-OMe self-assembles to form discrete nanospheres at a low concentration. Tryptophan side chains point outwards of the nanospheres while leucine side chains point towards the core of the nanospheres. The nanospheres fuse together to become microspheres with the increase in the peptide concentration. At higher concentrations of the peptide, the microspheres start clustering. This is stabilized by the aromatic interactions between the side chains of the tryptophan residues that cover the outer surface of the peptide microspheres. In addition to behaving like the conventional hollow sphere-based drug delivery vehicles which entraps the drug and performs stimuli-responsive release, this prototype can interact, stabilize, and intercalate hydrophobic dye carboxyfluorescein and anti-cancer drug curcumin even on the surface through aromatic interactions. The dye/drug can be released in acidic pH and in the presence of physiologically relevant ions such as potassium.
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Affiliation(s)
- Gopal Pandit
- Department of Chemistry, Indian
Institute of Technology, Guwahati, North Guwahati, Guwahati, Assam 781039, India
| | - Karabi Roy
- Department of Chemistry, Indian
Institute of Technology, Guwahati, North Guwahati, Guwahati, Assam 781039, India
| | - Umang Agarwal
- Department of Chemistry, Indian
Institute of Technology, Guwahati, North Guwahati, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian
Institute of Technology, Guwahati, North Guwahati, Guwahati, Assam 781039, India
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18
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de Pinho Favaro MT, Sánchez-García L, Sánchez-Chardi A, Roldán M, Unzueta U, Serna N, Cano-Garrido O, Azzoni AR, Ferrer-Miralles N, Villaverde A, Vázquez E. Protein nanoparticles are nontoxic, tuneable cell stressors. Nanomedicine (Lond) 2018; 13:255-268. [DOI: 10.2217/nnm-2017-0294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Nanoparticle–cell interactions can promote cell toxicity and stimulate particular behavioral patterns, but cell responses to protein nanomaterials have been poorly studied. Results: By repositioning oligomerization domains in a simple, modular self-assembling protein platform, we have generated closely related but distinguishable homomeric nanoparticles. Composed by building blocks with modular domains arranged in different order, they share amino acid composition. These materials, once exposed to cultured cells, are differentially internalized in absence of toxicity and trigger distinctive cell adaptive responses, monitored by the emission of tubular filopodia and enhanced drug sensitivity. Conclusion: The capability to rapidly modulate such cell responses by conventional protein engineering reveals protein nanoparticles as tuneable, versatile and potent cell stressors for cell-targeted conditioning.
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Affiliation(s)
- Marianna Teixeira de Pinho Favaro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av Candido Rondon, 400, 13083–875 Campinas, SP, Brazil
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Laura Sánchez-García
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Spain
| | | | - Mónica Roldán
- Unitat de Microscòpia Confocal, IPER, Hospital Sant Joan de Déu, Passeig de Sant Joan de Déu, 2, 08950 Esplugues de Llobregat, Barcelona
| | - Ugutz Unzueta
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Spain
| | - Olivia Cano-Garrido
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Adriano Rodrigues Azzoni
- Departamento de Engenharia Química, Escola Politécnica, Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, No. 380, 05508-900, São Paulo, SP, Brazil
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08193 Cerdanyola del Vallès, Spain
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19
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Song Z, Fu H, Wang R, Pacheco LA, Wang X, Lin Y, Cheng J. Secondary structures in synthetic polypeptides from N-carboxyanhydrides: design, modulation, association, and material applications. Chem Soc Rev 2018; 47:7401-7425. [DOI: 10.1039/c8cs00095f] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article highlights the conformation-specific properties and functions of synthetic polypeptides derived from N-carboxyanhydrides.
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Affiliation(s)
- Ziyuan Song
- Department of Materials Science and Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Hailin Fu
- Department of Chemistry and Polymer Program at the Institute of Materials Science
- University of Connecticut
- Storrs
- USA
| | - Ruibo Wang
- Department of Materials Science and Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Lazaro A. Pacheco
- Department of Materials Science and Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
| | - Xu Wang
- Department of Materials Science and Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics)
| | - Yao Lin
- Department of Chemistry and Polymer Program at the Institute of Materials Science
- University of Connecticut
- Storrs
- USA
| | - Jianjun Cheng
- Department of Materials Science and Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
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20
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Sant S, Coutinho DF, Gaharwar AK, Neves NM, Reis RL, Gomes ME, Khademhosseini A. Self-assembled Hydrogel Fiber Bundles from Oppositely Charged Polyelectrolytes Mimic Micro-/nanoscale Hierarchy of Collagen. ADVANCED FUNCTIONAL MATERIALS 2017; 27:1606273. [PMID: 31885528 PMCID: PMC6934367 DOI: 10.1002/adfm.201606273] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fiber bundles are present in many tissues throughout the body. In most cases, collagen subunits spontaneously self-assemble into a fibrilar structure that provides ductility to bone and constitutes the basis of muscle contraction. Translating these natural architectural features into a biomimetic scaffold still remains a great challenge. Here, we propose a simple strategy to engineer biomimetic fiber bundles that replicate the self-assembly and hierarchy of natural collagen fibers. The electrostatic interaction of methacrylated gellan gum (MeGG) with a countercharged chitosan (CHT) polymer led to the complexation of the polyelectrolytes. When directed through a polydimethylsiloxane (PDMS) channel, the polyelectrolytes formed a hierarchical fibrous hydrogel demonstrating nano-scale periodic light/dark bands similar to D-periodic bands in native collagen and aligned parallel fibrils at micro-scale. Importantly, collagen-mimicking hydrogel fibers exhibited robust mechanical properties (MPa scale) at a single fiber bundle level and enabled encapsulation of cells inside the fibers under cell-friendly mild conditions. Presence of carboxyl- (in gellan gum) or amino- (in chitosan) functionalities further enabled controlled peptide functionalization such as RGD for biochemical mimicry (cell adhesion sites) of native collagen. This biomimetic aligned fibrous hydrogel system can potentially be used as a scaffold for tissue engineering as well as a drug/gene delivery vehicle.
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Affiliation(s)
- Shilpa Sant
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Currently at Department of Pharmaceutical Sciences, School of Pharmacy, Department of Bioengineering, Swanson School of Engineering, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Daniela F Coutinho
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- 3B's Research Group - Biomaterials, Biodegradables and Biomimetics, Dept. of Polymer Engineering, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Akhilesh K Gaharwar
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Currently at the Department of Biomedical Engineering and Department of Materials Science & Engineering, Texas A&M University, College Station, TX 77841, USA
| | - Nuno M Neves
- 3B's Research Group - Biomaterials, Biodegradables and Biomimetics, Dept. of Polymer Engineering, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Rui L Reis
- 3B's Research Group - Biomaterials, Biodegradables and Biomimetics, Dept. of Polymer Engineering, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuela E Gomes
- 3B's Research Group - Biomaterials, Biodegradables and Biomimetics, Dept. of Polymer Engineering, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ali Khademhosseini
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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21
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Xia H, Fu H, Zhang Y, Shih KC, Ren Y, Anuganti M, Nieh MP, Cheng J, Lin Y. Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ. J Am Chem Soc 2017; 139:11106-11116. [DOI: 10.1021/jacs.7b04986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Yanfeng Zhang
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | | | | | | | - Jianjun Cheng
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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22
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Heddle JG, Chakraborti S, Iwasaki K. Natural and artificial protein cages: design, structure and therapeutic applications. Curr Opin Struct Biol 2017; 43:148-155. [DOI: 10.1016/j.sbi.2017.03.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/21/2017] [Accepted: 03/09/2017] [Indexed: 01/28/2023]
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23
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Cieślik-Boczula K. Alpha-helix to beta-sheet transition in long-chain poly-l-lysine: Formation of alpha-helical fibrils by poly-l-lysine. Biochimie 2017; 137:106-114. [PMID: 28315381 DOI: 10.1016/j.biochi.2017.03.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/12/2017] [Indexed: 01/06/2023]
Abstract
The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains. Under these conditions, PLL molecules aggregate into α-helical fibrils. PLLs dominated by extended antiparallel β-sheet structures with highly ordered trans-rich hydrocarbon side chains are formed in a high-temperature range at alkaline pD and aggregate into fibrillar, protofibrillar, and spherical forms. Presented data support the idea that fibrillar aggregation is a varied phenomenon possible in repetitive structural elements with not only a β-sheet-rich conformation, but also an α-helical-rich conformation.
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24
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Sciore A, Marsh ENG. Symmetry-Directed Design of Protein Cages and Protein Lattices and Their Applications. Subcell Biochem 2017; 83:195-224. [PMID: 28271478 DOI: 10.1007/978-3-319-46503-6_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The assembly of individual protein subunits into large-scale structures is important in many biological contexts. Proteins may assemble into geometrical cages or extended lattices that are characterized by a high degree of symmetry; examples include viral capsids and bacterial S-layers. The precisely defined higher order structure exhibited by these assemblies has inspired efforts to design such structures de novo by applying the principles of symmetry evident in natural protein assemblies. Here we discuss progress towards this goal and also examples of natural protein cages and lattices that have been engineered to repurpose them towards a diverse range of applications in materials science and nano-medicine.
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Affiliation(s)
- Aaron Sciore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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Bhaskar S, Lim S. Engineering protein nanocages as carriers for biomedical applications. NPG ASIA MATERIALS 2017; 9:e371. [PMID: 32218880 PMCID: PMC7091667 DOI: 10.1038/am.2016.128] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/26/2016] [Accepted: 04/12/2016] [Indexed: 05/02/2023]
Abstract
Protein nanocages have been explored as potential carriers in biomedicine. Formed by the self-assembly of protein subunits, the caged structure has three surfaces that can be engineered: the interior, the exterior and the intersubunit. Therapeutic and diagnostic molecules have been loaded in the interior of nanocages, while their external surfaces have been engineered to enhance their biocompatibility and targeting abilities. Modifications of the intersubunit interactions have been shown to modulate the self-assembly profile with implications for tuning the molecular release. We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity.
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Affiliation(s)
- Sathyamoorthy Bhaskar
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
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Cougnon FBL. Engineering Protein Self-Assembly: A New Approach for the Design of Octahedral Cages. Chembiochem 2016; 17:2296-2298. [DOI: 10.1002/cbic.201600526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Fabien B. L. Cougnon
- Department of Organic Chemistry; University of Geneva; 30 Quai Ernest-Ansermet 1211 Geneva 4 Switzerland
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28
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Luo Q, Hou C, Bai Y, Wang R, Liu J. Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. Chem Rev 2016; 116:13571-13632. [PMID: 27587089 DOI: 10.1021/acs.chemrev.6b00228] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.
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Affiliation(s)
- Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR 999078, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
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Yeates TO, Liu Y, Laniado J. The design of symmetric protein nanomaterials comes of age in theory and practice. Curr Opin Struct Biol 2016; 39:134-143. [DOI: 10.1016/j.sbi.2016.07.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/02/2016] [Accepted: 07/03/2016] [Indexed: 12/25/2022]
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Abstract
The assembly of individual protein subunits into large-scale symmetrical structures is widespread in nature and confers new biological properties. Engineered protein assemblies have potential applications in nanotechnology and medicine; however, a major challenge in engineering assemblies de novo has been to design interactions between the protein subunits so that they specifically assemble into the desired structure. Here we demonstrate a simple, generalizable approach to assemble proteins into cage-like structures that uses short de novo designed coiled-coil domains to mediate assembly. We assembled eight copies of a C3-symmetric trimeric esterase into a well-defined octahedral protein cage by appending a C4-symmetric coiled-coil domain to the protein through a short, flexible linker sequence, with the approximate length of the linker sequence determined by computational modeling. The structure of the cage was verified using a combination of analytical ultracentrifugation, native electrospray mass spectrometry, and negative stain and cryoelectron microscopy. For the protein cage to assemble correctly, it was necessary to optimize the length of the linker sequence. This observation suggests that flexibility between the two protein domains is important to allow the protein subunits sufficient freedom to assemble into the geometry specified by the combination of C4 and C3 symmetry elements. Because this approach is inherently modular and places minimal requirements on the structural features of the protein building blocks, it could be extended to assemble a wide variety of proteins into structures with different symmetries.
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31
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Pfeifer W, Saccà B. From Nano to Macro through Hierarchical Self-Assembly: The DNA Paradigm. Chembiochem 2016; 17:1063-80. [DOI: 10.1002/cbic.201600034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
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32
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Sandhya S, Mudgal R, Kumar G, Sowdhamini R, Srinivasan N. Protein sequence design and its applications. Curr Opin Struct Biol 2016; 37:71-80. [PMID: 26773478 DOI: 10.1016/j.sbi.2015.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/14/2023]
Abstract
Design of proteins has far-reaching potentials in diverse areas that span repurposing of the protein scaffold for reactions and substrates that they were not naturally meant for, to catching a glimpse of the ephemeral proteins that nature might have sampled during evolution. These non-natural proteins, either in synthesized or virtual form have opened the scope for the design of entities that not only rival their natural counterparts but also offer a chance to visualize the protein space continuum that might help to relate proteins and understand their associations. Here, we review the recent advances in protein engineering and design, in multiple areas, with a view to drawing attention to their future potential.
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Affiliation(s)
- Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Richa Mudgal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, India
| | - Gayatri Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences-TIFR, UAS-GKVK Campus, Bangalore 560065, India
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33
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Krieg E, Bastings MMC, Besenius P, Rybtchinski B. Supramolecular Polymers in Aqueous Media. Chem Rev 2016; 116:2414-77. [DOI: 10.1021/acs.chemrev.5b00369] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Pol Besenius
- Institute
of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Mainz 55128, Germany
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Kia K, Arief I, Sumantri C, Budiman C. Plantaricin IIA-1A5 from Lactobacillus plantarum IIA-1A5 Retards Pathogenic Bacteria in Beef Meatball Stored at Room Temperature. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ajft.2016.37.43] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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35
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López-Sagaseta J, Malito E, Rappuoli R, Bottomley MJ. Self-assembling protein nanoparticles in the design of vaccines. Comput Struct Biotechnol J 2015; 14:58-68. [PMID: 26862374 PMCID: PMC4706605 DOI: 10.1016/j.csbj.2015.11.001] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/10/2015] [Indexed: 01/09/2023] Open
Abstract
For over 100 years, vaccines have been one of the most effective medical interventions for reducing infectious disease, and are estimated to save millions of lives globally each year. Nevertheless, many diseases are not yet preventable by vaccination. This large unmet medical need demands further research and the development of novel vaccines with high efficacy and safety. Compared to the 19th and early 20th century vaccines that were made of killed, inactivated, or live-attenuated pathogens, modern vaccines containing isolated, highly purified antigenic protein subunits are safer but tend to induce lower levels of protective immunity. One strategy to overcome the latter is to design antigen nanoparticles: assemblies of polypeptides that present multiple copies of subunit antigens in well-ordered arrays with defined orientations that can potentially mimic the repetitiveness, geometry, size, and shape of the natural host-pathogen surface interactions. Such nanoparticles offer a collective strength of multiple binding sites (avidity) and can provide improved antigen stability and immunogenicity. Several exciting advances have emerged lately, including preclinical evidence that this strategy may be applicable for the development of innovative new vaccines, for example, protecting against influenza, human immunodeficiency virus, and respiratory syncytial virus. Here, we provide a concise review of a critical selection of data that demonstrate the potential of this field. In addition, we highlight how the use of self-assembling protein nanoparticles can be effectively combined with the emerging discipline of structural vaccinology for maximum impact in the rational design of vaccine antigens.
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Affiliation(s)
| | - Enrico Malito
- GlaxoSmithKline Vaccines S.r.l., Via Fiorentina 1, 53100 Siena, Italy
| | - Rino Rappuoli
- GlaxoSmithKline Vaccines S.r.l., Via Fiorentina 1, 53100 Siena, Italy
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36
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Tu Y, Peng F, Adawy A, Men Y, Abdelmohsen LKEA, Wilson DA. Mimicking the Cell: Bio-Inspired Functions of Supramolecular Assemblies. Chem Rev 2015; 116:2023-78. [DOI: 10.1021/acs.chemrev.5b00344] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yingfeng Tu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Fei Peng
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alaa Adawy
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yongjun Men
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Loai K. E. A. Abdelmohsen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daniela A. Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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37
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Bellapadrona G, Sinkar S, Sabanay H, Liljeström V, Kostiainen M, Elbaum M. Supramolecular Assembly and Coalescence of Ferritin Cages Driven by Designed Protein–Protein Interactions. Biomacromolecules 2015; 16:2006-11. [DOI: 10.1021/acs.biomac.5b00435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Giuliano Bellapadrona
- Department
of Materials and Interfaces, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shwetali Sinkar
- Indian Institute of Technology, Bombay, Mumbai Area 400076, India
| | - Helena Sabanay
- Department
of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ville Liljeström
- Biohybrid
Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, 00076 Aalto, Finland
| | - Mauri Kostiainen
- Biohybrid
Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, 00076 Aalto, Finland
| | - Michael Elbaum
- Department
of Materials and Interfaces, Weizmann Institute of Science, 76100 Rehovot, Israel
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38
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Yoshinari N, Kakuya A, Lee R, Konno T. Parity-Controlled Self-Assembly of Supramolecular Helices in a Gold(I)–Copper(II) Coordination System with Penicillamine and Bis(diphenylphosphino)alkane. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140253] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nobuto Yoshinari
- Department of Chemistry, Graduate School of Science, Osaka University
| | - Atsushi Kakuya
- Department of Chemistry, Graduate School of Science, Osaka University
| | - Raeeun Lee
- Department of Chemistry, Graduate School of Science, Osaka University
| | - Takumi Konno
- Department of Chemistry, Graduate School of Science, Osaka University
- CREST, Japan Science and Technology Agency
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39
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Ahlers P, Frisch H, Besenius P. Tuneable pH-regulated supramolecular copolymerisation by mixing mismatched dendritic peptide comonomers. Polym Chem 2015. [DOI: 10.1039/c5py01241d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The co-assembly of oppositely charged phenylalanine-rich dendritic comonomers yields supramolecular alternating copolymers, whose stability and pH-triggered disassembly is tuned by mismatching a strong with a weak β-sheet encoded comonomer.
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Affiliation(s)
- P. Ahlers
- Institut für Organische Chemie
- Johannes Gutenberg-Universität Mainz
- 55128 Mainz
- Germany
- Organisch-Chemisches Institut
| | - H. Frisch
- Institut für Organische Chemie
- Johannes Gutenberg-Universität Mainz
- 55128 Mainz
- Germany
- Organisch-Chemisches Institut
| | - P. Besenius
- Institut für Organische Chemie
- Johannes Gutenberg-Universität Mainz
- 55128 Mainz
- Germany
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40
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Sanii B, Haxton TK, Olivier GK, Cho A, Barton B, Proulx C, Whitelam S, Zuckermann RN. Structure-determining step in the hierarchical assembly of peptoid nanosheets. ACS NANO 2014; 8:11674-11684. [PMID: 25327498 DOI: 10.1021/nn505007u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Organic two-dimensional nanomaterials are of growing importance, yet few general synthetic methods exist to produce them in high yields and to precisely functionalize them. We previously developed an efficient hierarchical supramolecular assembly route to peptoid bilayer nanosheets, where the organization of biomimetic polymer sequences is catalyzed by an air-water interface. Here we determine at which stages of assembly the nanoscale and atomic-scale order appear. We used X-ray scattering, grazing incidence X-ray scattering at the air-water interface, electron diffraction, and a recently developed computational coarse-grained peptoid model to probe the molecular ordering at various stages of assembly. We found that lateral packing and organization of the chains occurs during the formation of a peptoid monolayer, prior to its collapse into a bilayer. Identifying the structure-determining step enables strategies to influence nanosheet order, to predict and optimize production yields, and to further engineer this class of material. More generally, our results provide a guide for using fluid interfaces to catalytically assemble 2D nanomaterials.
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Affiliation(s)
- Babak Sanii
- The Molecular Foundry, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
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41
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Oohora K, Hayashi T. Hemoprotein-based supramolecular assembling systems. Curr Opin Chem Biol 2014; 19:154-61. [PMID: 24658057 DOI: 10.1016/j.cbpa.2014.02.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
Abstract
Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures such as fibrils, vesicles/micelles, or networks. Interestingly, several of these assembled structures maintain the intrinsic functions of monomer units. The chemical and/or biological strategies described in this review will lead to the creation of unique hemoprotein-based functional biomaterials.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University Suita, 565-0871, Japan.
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42
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Bellapadrona G, Elbaum M. Supramolecular Protein Assemblies in the Nucleus of Human Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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43
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Bellapadrona G, Elbaum M. Supramolecular protein assemblies in the nucleus of human cells. Angew Chem Int Ed Engl 2014; 53:1534-7. [PMID: 24453074 DOI: 10.1002/anie.201309163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 01/29/2023]
Abstract
Genetically encoded supramolecular protein assemblies (SMPAs) are induced to form in living cells by combination of distinct self-assembly properties. A single fusion construct contains genes encoding the heavy chain (H) of human ferritin and the citrine fluorescent protein, the latter exposing a weak dimerization interface, as well as a nuclear localization signal. Upon expression in HeLa cells, in vivo confocal fluorescence and differential interference contrast imaging revealed extended SMPA structures exclusively in the nuclei. Assemblies were typically round and took alveolar, shell-like, or hybrid structure. Transmission electron microscopy revealed a crystalline packing. Site-specific mutagenesis of the citrine dimerization interface clarified the mechanism of SMPA formation. The constituent proteins retained their activity in iron binding and fluorescence emission, thus suggesting a general strategy for formation of synthetic cellular bodies with specific biochemical function.
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Affiliation(s)
- Giuliano Bellapadrona
- Dept of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100 (Israel)
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44
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Skubatz H, Howald WN. Two global conformation states of a novel NAD(P) reductase like protein of the thermogenic appendix of the Sauromatum guttatum inflorescence. Protein J 2014; 32:399-410. [PMID: 23794126 DOI: 10.1007/s10930-013-9497-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A novel NAD(P) reductase like protein (RL) belonging to a class of reductases involved in phenylpropanoid synthesis was previously purified to homogeneity from the Sauromatum guttatum appendix. The Sauromatum appendix raises its temperature above ambient temperature to ~30 °C on the day of inflorescence opening (D-day). Changes in the charge state distribution of the protein in electrospray ionization-mass spectrometry spectra were observed during the development of the appendix. RL adopted two conformations, state A (an extended state) that appeared before heat-production (D - 4 to D - 2), and state B (a compact state) that began appearing on D - 1 and reached a maximum on D-day. RL in healthy leaves of Arabidopsis is present in state A, whereas in thermogenic sporophylls of male cones of Encephalartos ferox is present in state B. These conformational changes strongly suggest an involvement of RL in heat-production. The biophysical properties of this protein are remarkable. It is self-assembled in aqueous solutions into micrometer sizes of organized morphologies. The assembly produces a broad range of cyclic and linear morphologies that resemble micelles, rods, lamellar micelles, as well as vesicles. The assemblies could also form network structures. RL molecules entangle with each other and formed branched, interconnected networks. These unusual assemblies suggest that RL is an oligomer, and its oligomerization can provide additional information needed for thermoregulation. We hypothesize that state A controls the plant basal temperature and state B allows a shift in the temperature set point to above ambient temperature.
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45
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Fairhead M, Krndija D, Lowe ED, Howarth M. Plug-and-play pairing via defined divalent streptavidins. J Mol Biol 2014; 426:199-214. [PMID: 24056174 PMCID: PMC4047826 DOI: 10.1016/j.jmb.2013.09.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/07/2013] [Accepted: 09/12/2013] [Indexed: 11/29/2022]
Abstract
Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.
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Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Denis Krndija
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ed D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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46
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Sontz PA, Song WJ, Tezcan FA. Interfacial metal coordination in engineered protein and peptide assemblies. Curr Opin Chem Biol 2014; 19:42-9. [PMID: 24780278 DOI: 10.1016/j.cbpa.2013.12.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 12/29/2022]
Abstract
Metal ions are frequently found in natural protein-protein interfaces, where they stabilize quaternary or supramolecular protein structures, mediate transient protein-protein interactions, and serve as catalytic centers. Paralleling these natural roles, coordination chemistry of metal ions is being increasingly utilized in creative ways toward engineering and controlling the assembly of functional supramolecular peptide and protein architectures. Here we provide a brief overview of this emerging branch of metalloprotein/peptide engineering and highlight a few select examples from the recent literature that best capture the diversity and future potential of approaches that are being developed.
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Affiliation(s)
- Pamela A Sontz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
| | - Woon Ju Song
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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47
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Mazzier D, Mba M, Zerbetto M, Moretto A. Bulky toroidal and vesicular self-assembled nanostructures from fullerene end-capped rod-like polymers. Chem Commun (Camb) 2014; 50:4571-4. [DOI: 10.1039/c4cc01477d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this work, we present novel fullerene (C60) end-capped rod-like polypeptide-polymers, obtained by one-pot thiol–ene chemistry.
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Affiliation(s)
- D. Mazzier
- Department of Chemical Sciences
- University of Padova
- 35131 Padova, Italy
| | - M. Mba
- Department of Chemical Sciences
- University of Padova
- 35131 Padova, Italy
| | - M. Zerbetto
- Department of Chemical Sciences
- University of Padova
- 35131 Padova, Italy
| | - A. Moretto
- Department of Chemical Sciences
- University of Padova
- 35131 Padova, Italy
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48
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Patterson DP, Su M, Franzmann TM, Sciore A, Skiniotis G, Marsh ENG. Characterization of a highly flexible self-assembling protein system designed to form nanocages. Protein Sci 2013; 23:190-9. [PMID: 24318954 DOI: 10.1002/pro.2405] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 11/06/2022]
Abstract
The design of proteins that self-assemble into well-defined, higher order structures is an important goal that has potential applications in synthetic biology, materials science, and medicine. We previously designed a two-component protein system, designated A-(+) and A-(-), in which self-assembly is mediated by complementary electrostatic interactions between two coiled-coil sequences appended to the C-terminus of a homotrimeric enzyme with C3 symmetry. The coiled-coil sequences are attached through a short, flexible spacer sequence providing the system with a high degree of conformational flexibility. Thus, the primary constraint guiding which structures the system may assemble into is the symmetry of the protein building block. We have now characterized the properties of the self-assembling system as a whole using native gel electrophoresis and analytical ultracentrifugation (AUC) and the properties of individual assemblies using cryo-electron microscopy (EM). We show that upon mixing, A-(+) and A-(-) form only six different complexes in significant concentrations. The three predominant complexes have hydrodynamic properties consistent with the formation of heterodimeric, tetrahedral, and octahedral protein cages. Cryo-EM of size-fractionated material shows that A-(+) and A-(-) form spherical particles with diameters appropriate for tetrahedral or octahedral protein cages. The particles varied in diameter in an almost continuous manner suggesting that their structures are extremely flexible.
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Affiliation(s)
- Dustin P Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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49
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Hoersch D, Roh SH, Chiu W, Kortemme T. Reprogramming an ATP-driven protein machine into a light-gated nanocage. NATURE NANOTECHNOLOGY 2013; 8:928-32. [PMID: 24270642 PMCID: PMC3859876 DOI: 10.1038/nnano.2013.242] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 10/16/2013] [Indexed: 05/06/2023]
Abstract
Natural protein assemblies have many sophisticated architectures and functions, creating nanoscale storage containers, motors and pumps. Inspired by these systems, protein monomers have been engineered to self-assemble into supramolecular architectures including symmetrical, metal-templated and cage-like structures. The complexity of protein machines, however, has made it difficult to create assemblies with both defined structures and controllable functions. Here we report protein assemblies that have been engineered to function as light-controlled nanocontainers. We show that an adenosine-5'-triphosphate-driven group II chaperonin, which resembles a barrel with a built-in lid, can be reprogrammed to open and close on illumination with different wavelengths of light. By engineering photoswitchable azobenzene-based molecules into the structure, light-triggered changes in interatomic distances in the azobenzene moiety are able to drive large-scale conformational changes of the protein assembly. The different states of the assembly can be visualized with single-particle cryo-electron microscopy, and the nanocages can be used to capture and release non-native cargos. Similar strategies that switch atomic distances with light could be used to build other controllable nanoscale machines.
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Affiliation(s)
- Daniel Hoersch
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158
| | - Soung-Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158
- Correspondence to: Tanja Kortemme, University of California, San Francisco, 1700 4 Street, Byers Hall 308E, San Francisco, CA 94158, Phone: (415)514-1368, Fax: (415)514-4797,
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50
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Petkau-Milroy K, Sonntag MH, Colditz A, Brunsveld L. Multivalent protein assembly using monovalent self-assembling building blocks. Int J Mol Sci 2013; 14:21189-201. [PMID: 24152447 PMCID: PMC3821665 DOI: 10.3390/ijms141021189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/13/2013] [Accepted: 10/08/2013] [Indexed: 11/17/2022] Open
Abstract
Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard to streptavidin. Next to tetravalent streptavidin, monovalent streptavidin was used to study the protein assembly along the supramolecular polymer in detail without the interference of cross-linking. Upon self-assembly of the monovalent biotinylated discotics, multivalent proteins can be assembled along the supramolecular polymer. The concentration of discotics, which influences the length of the final polymers at the same time dictates the amount of assembled proteins.
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Affiliation(s)
- Katja Petkau-Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| | - Michael H. Sonntag
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| | - Alexander Colditz
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, Eindhoven 5612AZ, The Netherlands; E-Mails: (K.P.-M.); (M.H.S.); (A.C.)
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