101
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Misra R, Saseendran A, Dey S, Gopi HN. Metal‐Helix Frameworks from Short Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2019; 58:2251-2255. [DOI: 10.1002/anie.201810849] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Rajkumar Misra
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
| | - Abhijith Saseendran
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
| | - Sanjit Dey
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
| | - Hosahudya N. Gopi
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
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102
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Wang L, Gong C, Yuan X, Wei G. Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E285. [PMID: 30781679 PMCID: PMC6410314 DOI: 10.3390/nano9020285] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 02/02/2023]
Abstract
Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π⁻π stacking, DNA base pairing, and ligand⁻receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.
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Affiliation(s)
- Li Wang
- Key Laboratory of Preparation and Application of Environmental Friendly Materials (Jilin Normal University), Ministry of Education, Changchun 130103, China.
| | - Coucong Gong
- Faculty of Production Engineering, University of Bremen, D-28359 Bremen, Germany.
| | - Xinzhu Yuan
- Key Laboratory of Preparation and Application of Environmental Friendly Materials (Jilin Normal University), Ministry of Education, Changchun 130103, China.
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen, D-28359 Bremen, Germany.
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103
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Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages. Nat Commun 2019; 10:778. [PMID: 30770832 PMCID: PMC6377661 DOI: 10.1038/s41467-019-08788-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/23/2019] [Indexed: 01/16/2023] Open
Abstract
Constructing different protein nanostructures with high-order discrete architectures by using one single building block remains a challenge. Here, we present a simple, effective disulfide-mediated approach to prepare a set of protein nanocages with different geometries from single building block. By genetically deleting an inherent intra-subunit disulfide bond, we can render the conversion of an 8-mer bowl-like protein architecture (NF-8) into a 24-mer ferritin-like nanocage in solution, while selective insertion of an inter-subunit disulfide bond into NF-8 triggers its conversion into a 16-mer lenticular nanocage. Deletion of the same intra-subunit disulfide bond and insertion of the inter-subunit disulfide bond results in the conversion of NF-8 into a 48-mer protein nanocage in solution. Thus, in the laboratory, simple mutation of one protein building block can generate three different protein nanocages in a manner that is highly reminiscent of natural pentamer building block originating from viral capsids that self-assemble into protein assemblies with different symmetries.
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104
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Zhao N, Coyne J, Xu M, Zhang X, Suzuki A, Shi P, Lai J, Fong GH, Xiong N, Wang Y. Assembly of Bifunctional Aptamer-Fibrinogen Macromer for VEGF Delivery and Skin Wound Healing. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2019; 31:1006-1015. [PMID: 31558852 PMCID: PMC6761992 DOI: 10.1021/acs.chemmater.8b04486] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Macromolecular assembly has been studied for various applications. However, while macromolecules can recognize one another for assembly, their assembled structures usually lack the function of specific molecular recognition. We hypothesized that bifunctional aptamer-protein macromers would possess dual functions of molecular assembly and recognition. The data show that hybrid aptamer-fibrinogen macromers can assemble to form hydrogels. Moreover, the assembled hydrogels can recognize vascular endothelial growth factor (VEGF) for sustained release. When the VEGF-loaded hydrogels are implanted in vivo, they can promote angiogenesis and skin wound healing. Thus, this work has successfully demonstrated a promising macromolecular system for broad applications such as drug delivery and regenerative medicine.
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Affiliation(s)
- Nan Zhao
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - James Coyne
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ming Xu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Xiaolong Zhang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Akiho Suzuki
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jinping Lai
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Guo-Hua Fong
- Center for Vascular Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Na Xiong
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence can be addressed to Dr. Yong Wang (; Phone: 814-865-6867)
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105
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Misra R, Saseendran A, Dey S, Gopi HN. Metal-Helix Frameworks from Short Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rajkumar Misra
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
| | - Abhijith Saseendran
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
| | - Sanjit Dey
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
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106
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Lach M, Künzle M, Beck T. Proteins as Sustainable Building Blocks for the Next Generation of Bioinorganic Nanomaterials. Biochemistry 2019; 58:140-141. [PMID: 30281280 DOI: 10.1021/acs.biochem.8b00966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel Lach
- Institute of Inorganic Chemistry , RWTH Aachen University , 52074 Aachen , Germany
| | - Matthias Künzle
- Institute of Inorganic Chemistry , RWTH Aachen University , 52074 Aachen , Germany
| | - Tobias Beck
- Institute of Inorganic Chemistry , RWTH Aachen University , 52074 Aachen , Germany.,I3TM , RWTH Aachen University , 52074 Aachen , Germany.,JARA SOFT and JARA FIT , RWTH Aachen University , 52074 Aachen , Germany
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107
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Zhang X, Gong C, Akakuru OU, Su Z, Wu A, Wei G. The design and biomedical applications of self-assembled two-dimensional organic biomaterials. Chem Soc Rev 2019; 48:5564-5595. [DOI: 10.1039/c8cs01003j] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling 2D organic biomaterials exhibit versatile abilities for structural and functional tailoring, as well as high potential for biomedical applications.
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Affiliation(s)
- Xiaoyuan Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- China
- Faculty of Physics and Astronomy
- University of Jena
| | - Coucong Gong
- Faculty of Production Engineering
- University of Bremen
- Bremen
- Germany
| | - Ozioma Udochukwu Akakuru
- Cixi Institute of Biomedical Engineering
- CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- China
| | - Aiguo Wu
- Cixi Institute of Biomedical Engineering
- CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo
| | - Gang Wei
- Faculty of Production Engineering
- University of Bremen
- Bremen
- Germany
- Cixi Institute of Biomedical Engineering
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108
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Zhou K, Chen H, Zhang S, Wang Y, Zhao G. Disulfide-mediated reversible two-dimensional self-assembly of protein nanocages. Chem Commun (Camb) 2019; 55:7510-7513. [DOI: 10.1039/c9cc03085a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Disulfide-mediated 2D protein self-assembly was achieved by single point mutation of hot spots at the C4 interface of ferritin.
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Affiliation(s)
- K. Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- Beijing Key Laboratory of Functional Food from Plant Resources
- China Agricultural University
- Beijing 100083
| | - H. Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- Beijing Key Laboratory of Functional Food from Plant Resources
- China Agricultural University
- Beijing 100083
| | - S. Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- Beijing Key Laboratory of Functional Food from Plant Resources
- China Agricultural University
- Beijing 100083
| | - Y. Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- Beijing Key Laboratory of Functional Food from Plant Resources
- China Agricultural University
- Beijing 100083
| | - G. Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Food Science & Nutritional Engineering
- Beijing Key Laboratory of Functional Food from Plant Resources
- China Agricultural University
- Beijing 100083
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109
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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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110
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Subramanian R, Smith SJ, Alberstein RG, Bailey JB, Zhang L, Cardone G, Suominen L, Chami M, Stahlberg H, Baker TS, Tezcan FA. Self-Assembly of a Designed Nucleoprotein Architecture through Multimodal Interactions. ACS CENTRAL SCIENCE 2018; 4:1578-1586. [PMID: 30555911 PMCID: PMC6276041 DOI: 10.1021/acscentsci.8b00745] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 06/09/2023]
Abstract
The co-self-assembly of proteins and nucleic acids (NAs) produces complex biomolecular machines (e.g., ribosomes and telomerases) that represent some of the most daunting targets for biomolecular design. Despite significant advances in protein and DNA or RNA nanotechnology, the construction of artificial nucleoprotein complexes has largely been limited to cases that rely on the NA-mediated spatial organization of protein units, rather than a cooperative interplay between protein- and NA-mediated interactions that typify natural nucleoprotein assemblies. We report here a structurally well-defined synthetic nucleoprotein assembly that forms through the synergy of three types of intermolecular interactions: Watson-Crick base pairing, NA-protein interactions, and protein-metal coordination. The fine thermodynamic balance between these interactions enables the formation of a crystalline architecture under highly specific conditions.
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Affiliation(s)
- Rohit
H. Subramanian
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Sarah J. Smith
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Robert G. Alberstein
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Jake B. Bailey
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Ling Zhang
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Giovanni Cardone
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Lauri Suominen
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Mohamed Chami
- C−CINA,
Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Henning Stahlberg
- C−CINA,
Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Timothy S. Baker
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Division
of Biological Sciences, University of California,
San Diego, La Jolla, California 92093, United States
| | - F. Akif Tezcan
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Materials
Science and Engineering, University of California,
San Diego, La Jolla, California 92093, United States
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111
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Zhou K, Zang J, Chen H, Wang W, Wang H, Zhao G. On-Axis Alignment of Protein Nanocage Assemblies from 2D to 3D through the Aromatic Stacking Interactions of Amino Acid Residues. ACS NANO 2018; 12:11323-11332. [PMID: 30265511 DOI: 10.1021/acsnano.8b06091] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aromatic-aromatic interactions between natural aromatic amino acids Phe, Tyr, and Trp play crucial roles in protein-protein recognition and protein folding. However, the function of such interactions in the preparation of different dimensional, ordered protein superstructures has not been recognized. Herein, by a combination of the directionality of the symmetry axes of protein building blocks and the strength of the aromatic-aromatic interactions coming from a group of aromatic amino acid residues, we built an engineering strategy to construct protein superlattices. Based on this strategy, substitution of single amino acid residue Glu162 around the C4 rotation axes near the outer surface of 24-mer ferritin nanocage with Phe, Tyr, and Trp, respectively, resulted in 2D and 3D protein superlattices where protein cages are aligned along the C4 axes, imposing a fixed disposition of neighboring ferritins. The self-assembly of these superlattices is reversible, which can be tuned by external stimuli (salt concentration or pH). Moreover, these superlattices can serve as biotemplates for the fabrication of 2D and 3D inorganic nanoparticle arrays.
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Affiliation(s)
- Kai Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
| | - Jiachen Zang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
| | - Hai Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
| | - Wenming Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry , Institute of Molecular Science, Shanxi University , Taiyuan 030006 , China
| | - Hongfei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry , Institute of Molecular Science, Shanxi University , Taiyuan 030006 , China
| | - Guanghua Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
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112
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Peschke T, Bitterwolf P, Gallus S, Hu Y, Oelschlaeger C, Willenbacher N, Rabe KS, Niemeyer CM. Self‐Assembling All‐Enzyme Hydrogels for Flow Biocatalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810331] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Theo Peschke
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Patrick Bitterwolf
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Sabrina Gallus
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Yong Hu
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Claude Oelschlaeger
- Karlsruhe Institute of Technology (KIT) Institute for Mechanical Process Engineering and Mechanics Gotthard-Franz-Strasse 3 76131 Karlsruhe Germany
| | - Norbert Willenbacher
- Karlsruhe Institute of Technology (KIT) Institute for Mechanical Process Engineering and Mechanics Gotthard-Franz-Strasse 3 76131 Karlsruhe Germany
| | - Kersten S. Rabe
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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113
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Peschke T, Bitterwolf P, Gallus S, Hu Y, Oelschlaeger C, Willenbacher N, Rabe KS, Niemeyer CM. Self-Assembling All-Enzyme Hydrogels for Flow Biocatalysis. Angew Chem Int Ed Engl 2018; 57:17028-17032. [PMID: 30380178 DOI: 10.1002/anie.201810331] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 12/31/2022]
Abstract
Continuous flow biocatalysis is an emerging field of industrial biotechnology that uses enzymes immobilized in flow channels for the production of value-added chemicals. We describe the construction of self-assembling all-enzyme hydrogels that are comprised of two tetrameric enzymes. The stereoselective dehydrogenase LbADH and the cofactor-regenerating glucose 1-dehydrogenase GDH were genetically fused with a SpyTag or SpyCatcher domain, respectively, to generate two complementary homo-tetrameric building blocks that polymerize under physiological conditions into porous hydrogels. Mounted in microfluidic reactors, the gels show excellent stereoselectivity with near quantitative conversion in the reduction of prochiral ketones along with high robustness under process and storage conditions. The gels function as compartment that retains intermediates thus enabling high total turnover numbers of the expensive cofactor NADP(H).
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Affiliation(s)
- Theo Peschke
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Patrick Bitterwolf
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sabrina Gallus
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Claude Oelschlaeger
- Karlsruhe Institute of Technology (KIT), Institute for Mechanical Process Engineering and Mechanics, Gotthard-Franz-Strasse 3, 76131, Karlsruhe, Germany
| | - Norbert Willenbacher
- Karlsruhe Institute of Technology (KIT), Institute for Mechanical Process Engineering and Mechanics, Gotthard-Franz-Strasse 3, 76131, Karlsruhe, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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114
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McMillan JR, Hayes OG, Remis JP, Mirkin CA. Programming Protein Polymerization with DNA. J Am Chem Soc 2018; 140:15950-15956. [PMID: 30407003 DOI: 10.1021/jacs.8b10011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chain-growth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)-DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryo-electron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP-DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.
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115
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Baarda RA, Marianchuk TL, Toney MD, Cox DL. In silico stress-strain measurements on self-assembled protein lattices. SOFT MATTER 2018; 14:8095-8104. [PMID: 30159554 DOI: 10.1039/c8sm00412a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Due to their large mechanical strength and potential for functionalization, beta-solenoid proteins show promise as building blocks in biomaterials applications such as two- and three-dimensional scaffolds. We have designed simulation models of two-dimensional square and honeycomb protein lattices by covalently linking a beta-solenoid protein, the spruce budworm antifreeze protein (SBAFP), to symmetric protein multimers. Periodic boundary conditions applied to the simulation cell allow for the simulation of an infinite lattice. We use molecular dynamics to strain the lattice by deforming the simulation cell and measuring the resulting stress tensor. We evaluate the linear portion of stress-strain curves to extract the corresponding bulk and shear elastic moduli. When strained at a rate of 0.3 nm ps-1, the lattices yield a bulk modulus of approximately 3 GPa. This large elastic modulus demonstrates that 2-dimensional structures designed from beta-solenoid proteins can be expected to retain the exceptional material strength of their building blocks.
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Affiliation(s)
- Rachel A Baarda
- Department of Physics, University of California, Davis, California, USA.
| | | | - Michael D Toney
- Department of Chemistry, University of California, Davis, California, USA
| | - Daniel L Cox
- Department of Physics, University of California, Davis, California, USA.
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116
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Zhang S, Zhang J, Fang W, Zhang Y, Wang Q, Jin J. Ultralarge Single-Layer Porous Protein Nanosheet for Precise Nanosize Separation. NANO LETTERS 2018; 18:6563-6569. [PMID: 30182720 DOI: 10.1021/acs.nanolett.8b03155] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Highly permeable and precisely size-selective membranes are the subject of continuous pursuit for energy-efficient separation of fine chemicals. However, challenges remain in the fabrication of an ultrathin selective layer with homogeneous pores, in particular, with the pore sizes in the 1-10 nm range. We report the design of a free-standing porous nanosheet assembled with a single layer of proteins. Tobacco mosaic virus mutant (TMVm), a cylinder-shaped protein containing an inner pore of 4 nm in diameter, was cross-linked via a Cu2+-catalyzed disulfide-bond-forming reaction along the 2D orientation. By such a design, ultralarge single-layer TMVm nanosheets extending over tens of micrometers in width and with well-defined nanopores were successfully developed. A ∼40 nm thick ultrafiltration membrane laminated by the single-layer TMVm nanosheets through simple vacuum filtration accomplished the precise separation of ∼4 nm sized substances. Meanwhile, the membrane exhibited water permeance up to ∼7000 L m-2 h-1 bar-1, which is an order of magnitude improvement compared with traditional ultrafiltration membranes with a similar rejection profile.
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Affiliation(s)
- Shenxiang Zhang
- i-Lab, CAS Center for Excellence in Nanoscience, and CAS Key Laboratory of Nano-Bio Interface , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , China
- School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , China
| | - Jianting Zhang
- i-Lab, CAS Center for Excellence in Nanoscience, and CAS Key Laboratory of Nano-Bio Interface , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , China
| | - Wangxi Fang
- i-Lab, CAS Center for Excellence in Nanoscience, and CAS Key Laboratory of Nano-Bio Interface , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , China
| | - Yejun Zhang
- i-Lab, CAS Center for Excellence in Nanoscience, and CAS Key Laboratory of Nano-Bio Interface , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , China
| | - Qiangbin Wang
- i-Lab, CAS Center for Excellence in Nanoscience, and CAS Key Laboratory of Nano-Bio Interface , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , China
| | - Jian Jin
- i-Lab, CAS Center for Excellence in Nanoscience, and CAS Key Laboratory of Nano-Bio Interface , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , China
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Tomar K, Kaur G, Verma S, Ramanathan G. A self-assembled tetrapeptide that acts as a “turn-on” fluorescent sensor for Hg2+ ion. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.08.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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118
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Thomas A, Matthaei JF, Baneyx F. A Self-Assembling Two-Dimensional Protein Array is a Versatile Platform for the Assembly of Multicomponent Nanostructures. Biotechnol J 2018; 13:e1800141. [PMID: 30168658 DOI: 10.1002/biot.201800141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/12/2018] [Indexed: 01/15/2023]
Abstract
Rationally designed two-dimensional (2D) arrays that support the assembly of nanoscale components are of interest for catalysis, sensing, and biomedical applications. The computational redesign of a protein called TTM that undergoes calcium-induced self-assembly into nanostructured lattices capable of growing to dozens of micrometers are previously reported. The work demonstrates here that the N- and C-termini of the constituent monomers are solvent-accessible and that they can be modified with a hexahistidine extension, a gold-binding peptide, or a biotinylation tag to decorate nickel-nitriloacetic acid beads with self-assembled protein islands, conjugate gold nanoparticles to planar arrays, or control the immobilization density of avidin molecules onto 2D lattices through co-polymerization of biotinylated and wild type TTM monomers. These results showcase the potential of TTM as a versatile 2D scaffold for the fabrication of hierarchical structures comprising a broad range of nanoscale elements.
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Affiliation(s)
- Alexander Thomas
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195, USA
| | - James F Matthaei
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195, USA
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Box 351750, Seattle, WA 98195, USA
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119
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Manuguri S, Webster K, Yewdall NA, An Y, Venugopal H, Bhugra V, Turner A, Domigan LJ, Gerrard JA, Williams DE, Malmström J. Assembly of Protein Stacks With in Situ Synthesized Nanoparticle Cargo. NANO LETTERS 2018; 18:5138-5145. [PMID: 30047268 DOI: 10.1021/acs.nanolett.8b02055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ability of proteins to form hierarchical structures through self-assembly provides an opportunity to synthesize and organize nanoparticles. Ordered nanoparticle assemblies are a subject of widespread interest due to the potential to harness their emergent functions. In this work, the toroidal-shaped form of the protein peroxiredoxin, which has a pore size of 7 nm, was used to organize iron oxyhydroxide nanoparticles. Iron in the form of Fe2+ was sequestered into the central cavity of the toroid ring using metal-binding sites engineered there and then hydrolyzed to form iron oxyhydroxide particles bound into the protein pore. By precise manipulation of the pH, the mineralized toroids were organized into stacks confining one-dimensional nanoparticle assemblies. We report the formation and the procedures leading to the formation of such nanostructures and their characterization by chromatography and microscopy. Electrostatic force microscopy clearly revealed the formation of iron-containing nanorods as a result of the self-assembly of the iron-loaded protein. This research bodes well for the use of peroxiredoxin as a template with which to form nanowires and structures for electronic and magnetic applications.
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Affiliation(s)
- Sesha Manuguri
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | | | - N Amy Yewdall
- Biomolecular Interaction Centre and School of Biological Sciences , University of Canterbury , Christchurch 8140 , New Zealand
| | | | | | - Vaibhav Bhugra
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | | | - Laura J Domigan
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | - Juliet A Gerrard
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | - David E Williams
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | - Jenny Malmström
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
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120
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Churchfield LA, Alberstein RG, Williamson LM, Tezcan FA. Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. J Am Chem Soc 2018; 140:10043-10053. [PMID: 29996654 PMCID: PMC6085756 DOI: 10.1021/jacs.8b05812] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite significant progress in protein design, the construction of protein assemblies that display complex functions (e.g., catalysis or allostery) remains a significant challenge. We recently reported the de novo construction of an allosteric supramolecular protein assembly (Zn-C38/C81/C96R14) in which the dissociation and binding of ZnII ions were coupled over a distance of 15 Å to the selective hydrolytic breakage and formation of a single disulfide bond. Zn-C38/C81/C96R14 was constructed by ZnII-templated assembly of a monomeric protein (R1, a derivative of cytochrome cb562) into a tetramer, followed by progressive incorporation of noncovalent and disulfide bonding interactions into the protein-protein interfaces to create a strained quaternary architecture. The interfacial strain thus built allowed mechanical coupling between the binding/dissociation of ZnII and formation/hydrolysis of a single disulfide bond (C38-C38) out of a possible six. While the earlier study provided structural evidence for the two end-states of allosteric coupling, the energetic basis for allosteric coupling and the minimal structural requirements for building this allosteric system were not understood. Toward this end, we have characterized the structures and Zn-binding properties of two related protein constructs (C38/C96R1 and C38R1) which also possess C38-C38 disulfide bonds. In addition, we have carried out extensive molecular dynamics simulations of C38/C81/C96R14 to understand the energetic basis for the selective cleavage of the C38-C38 disulfide bond upon ZnII dissociation. Our analyses reveal that the local interfacial environment around the C38-C38 bond is key to its selective cleavage, but this cleavage is only possible within the context of a stable quaternary architecture which enables structural coupling between ZnII coordination and the protein-protein interfaces.
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Affiliation(s)
- Lewis A. Churchfield
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
| | - Robert G. Alberstein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
| | - Laura M. Williamson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0356 United States
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121
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Gao S, Liu X, Wang Z, Jiang S, Wu M, Tian Y, Niu Z. Fluorous interaction induced self-assembly of tobacco mosaic virus coat protein for cisplatin delivery. NANOSCALE 2018; 10:11732-11736. [PMID: 29911244 DOI: 10.1039/c8nr03748e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tobacco mosaic virus coat protein was modified with a small molecular fluorous ponytail at specific sites, and self-assembled into spherical nanoparticles through fluorous interaction induced self-assembly. By loading the anti-cancer drug cisplatin through metal-ligand coordination, this spherical assembly with high stability has potential as a drug carrier.
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Affiliation(s)
- Sijia Gao
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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122
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123
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Haider MJ, Zhang HV, Sinha N, Fagan JA, Kiick KL, Saven JG, Pochan DJ. Self-assembly and soluble aggregate behavior of computationally designed coiled-coil peptide bundles. SOFT MATTER 2018; 14:5488-5496. [PMID: 29923575 PMCID: PMC6355460 DOI: 10.1039/c8sm00435h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coiled-coil peptides have proven useful in a range of materials applications ranging from the formation of well-defined fibrils to responsive hydrogels. The ability to design from first principles their oligomerization and subsequent higher order assembly offers their expanded use in producing new materials. Toward these ends, homo-tetrameric, antiparallel, coiled-coil, peptide bundles have been designed computationally, synthesized via solid-phase methods, and their solution behavior characterized. Two different bundle-forming peptides were designed and examined. Within the targeted coiled coil structure, both bundles contained the same hydrophobic core residues. However, different exterior residues on the two different designs yielded sequences with different distributions of charged residues and two different expected isoelectric points of pI 4.4 and pI 10.5. Both coiled-coil bundles were extremely stable with respect to temperature (Tm > 80 C) and remained soluble in solution even at high (millimolar) peptide concentrations. The coiled-coil tetramer was confirmed to be the dominant species in solution by analytical sedimentation studies and by small-angle neutron scattering, where the scattering form factor is well represented by a cylinder model with the dimensions of the targeted coiled coil. At high concentrations (5-15 mM), evidence of interbundle structure was observed via neutron scattering. At these concentrations, the synthetic bundles form soluble aggregates, and interbundle distances can be determined via a structure factor fit to scattering data. The data support the successful design of robust coiled-coil bundles. Despite their different sequences, each sequence forms loosely associated but soluble aggregates of the bundles, suggesting similar dissociated states for each. The behavior of the dispersed bundles is similar to that observed for natural proteins.
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Affiliation(s)
- Michael J. Haider
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Nairiti Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffrey A. Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
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124
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125
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Ghosh T, Fridman N, Kosa M, Maayan G. Self-Assembled Cyclic Structures from Copper(II) Peptoids. Angew Chem Int Ed Engl 2018; 57:7703-7708. [DOI: 10.1002/anie.201800583] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/01/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Totan Ghosh
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
| | - Natalia Fridman
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
| | - Monica Kosa
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
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126
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Ghosh T, Fridman N, Kosa M, Maayan G. Self-Assembled Cyclic Structures from Copper(II) Peptoids. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Totan Ghosh
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
| | - Natalia Fridman
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
| | - Monica Kosa
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Technion City Haifa 3200008 Israel
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127
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Abstract
Bivalent DNA conjugates of β-galactosidase (βGal), having pairs of oligonucleotides positioned closely on opposing faces of the protein, have been synthesized and characterized. These structures, due to their directional bonding characteristics, allow for the programmable access of one-dimensional protein materials. When conjugates functionalized with complementary oligonucleotides are combined under conditions that support DNA hybridization, periodic wire-type superstructures consisting of aligned proteins form. These structures have been characterized by gel electrophoresis, cryo-transmission electron microscopy, and negative-stain transmission electron microscopy. Significantly, melting experiments of complementary building blocks display narrowed and elevated melting transitions compared to the free duplex DNA, further supporting the formation of the designed binding mode, and unambiguously characterizing their association as DNA-mediated. These novel structures illustrate, for the first time, that directional DNA bonding can be realized with only a pair of DNA modifications, which will allow one to engineer directional interactions and realize new classes of superstructures not possible simply through shape control or isotropically functionalized materials.
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Affiliation(s)
- Janet R McMillan
- Department of Chemistry and International Institute for Nanotechnology , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
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128
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Kobayashi N, Inano K, Sasahara K, Sato T, Miyazawa K, Fukuma T, Hecht MH, Song C, Murata K, Arai R. Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks. ACS Synth Biol 2018; 7:1381-1394. [PMID: 29690759 DOI: 10.1021/acssynbio.8b00007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design of novel proteins that self-assemble into supramolecular complexes is important for development in nanobiotechnology and synthetic biology. Recently, we designed and created a protein nanobuilding block (PN-Block), WA20-foldon, by fusing an intermolecularly folded dimeric de novo WA20 protein and a trimeric foldon domain of T4 phage fibritin (Kobayashi et al., J. Am. Chem. Soc. 2015, 137, 11285). WA20-foldon formed several types of self-assembling nanoarchitectures in multiples of 6-mers, including a barrel-like hexamer and a tetrahedron-like dodecamer. In this study, to construct chain-like polymeric nanostructures, we designed de novo extender protein nanobuilding blocks (ePN-Blocks) by tandemly fusing two de novo binary-patterned WA20 proteins with various linkers. The ePN-Blocks with long helical linkers or flexible linkers were expressed in soluble fractions of Escherichia coli, and the purified ePN-Blocks were analyzed by native PAGE, size exclusion chromatography-multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS), and transmission electron microscopy. These results suggest formation of various structural homo-oligomers. Subsequently, we reconstructed hetero-oligomeric complexes from extender and stopper PN-Blocks by denaturation and refolding. The present SEC-MALS and SAXS analyses show that extender and stopper PN-Block (esPN-Block) heterocomplexes formed different types of extended chain-like conformations depending on their linker types. Moreover, atomic force microscopy imaging in liquid suggests that the esPN-Block heterocomplexes with metal ions further self-assembled into supramolecular nanostructures on mica surfaces. Taken together, the present data demonstrate that the design and construction of self-assembling PN-Blocks using de novo proteins is a useful strategy for building polymeric nanoarchitectures of supramolecular protein complexes.
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Affiliation(s)
- Naoya Kobayashi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | | | | | - Takaaki Sato
- Center for Energy and Environmental Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, Nagano 380-8553, Japan
| | - Keisuke Miyazawa
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Fukuma
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Ryoichi Arai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama 230-0045, Japan
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan
- Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
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129
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Teng P, Niu Z, She F, Zhou M, Sang P, Gray GM, Verma G, Wojtas L, van der Vaart A, Ma S, Cai J. Hydrogen-Bonding-Driven 3D Supramolecular Assembly of Peptidomimetic Zipper. J Am Chem Soc 2018; 140:5661-5665. [PMID: 29590526 PMCID: PMC10866394 DOI: 10.1021/jacs.7b11997] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hydrogen-bonding-driven three-dimensional (3D) assembly of a peptidomimetic zipper has been established for the first time by using an α/AApeptide zipper that assembles into a de novo lattice arrangement through two layers of hydrogen-bonded linker-directed interactions. Via a covalently bridged 1D 413-helix, drastic enhancement in stability has been achieved in the formed 3D crystalline supramolecular architecture as evidenced by gas-sorption studies. As the first example of an unnatural peptidic zipper, the dimensional augmentation of the zipper differs from metal-coordinated strategies, and may have general implications for the preparation of peptidic functional materials for a variety of future applications.
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Affiliation(s)
| | | | - Fengyu She
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Mi Zhou
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Geoffrey M. Gray
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Gaurav Verma
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Lukasz Wojtas
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Shengqian Ma
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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130
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Claim to FAME. Nat Chem 2018; 10:485-487. [DOI: 10.1038/s41557-018-0049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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131
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Zhang W, Yu X, Li Y, Su Z, Jandt KD, Wei G. Protein-mimetic peptide nanofibers: Motif design, self-assembly synthesis, and sequence-specific biomedical applications. Prog Polym Sci 2018. [DOI: 10.1016/j.progpolymsci.2017.12.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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132
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Alberstein R, Suzuki Y, Paesani F, Tezcan FA. Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly. Nat Chem 2018; 10:732-739. [PMID: 29713036 DOI: 10.1038/s41557-018-0053-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/29/2018] [Indexed: 12/27/2022]
Abstract
De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.
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Affiliation(s)
- Robert Alberstein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Yuta Suzuki
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Materials Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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133
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Hu R, Yang G, Ding HM, Ma J, Ma YQ, Gan J, Chen G. Competition between Supramolecular Interaction and Protein–Protein Interaction in Protein Crystallization: Effects of Crystallization Method and Small Molecular Bridge. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b00657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | - Hong-ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | | | - Yu-qiang Ma
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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134
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Negishi H, Abe S, Yamashita K, Hirata K, Niwase K, Boudes M, Coulibaly F, Mori H, Ueno T. Supramolecular protein cages constructed from a crystalline protein matrix. Chem Commun (Camb) 2018; 54:1988-1991. [PMID: 29405208 DOI: 10.1039/c7cc08689j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein crystals are formed via ordered arrangements of proteins, which assemble to form supramolecular structures. Here, we show a method for the assembly of supramolecular protein cages within a crystalline environment. The cages are stabilized by covalent cross-linking allowing their release via dissolution of the crystal. The high stability of the desiccated protein crystals allows cages to be constructed.
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Affiliation(s)
- Hashiru Negishi
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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135
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Han L, Wang M, Jia X, Chen W, Qian H, He F. Uniform two-dimensional square assemblies from conjugated block copolymers driven by π-π interactions with controllable sizes. Nat Commun 2018; 9:865. [PMID: 29491384 PMCID: PMC5830438 DOI: 10.1038/s41467-018-03195-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/26/2018] [Indexed: 01/22/2023] Open
Abstract
Two-dimensional (2-D) micro- and nano-architectures are attractive because of their unique properties. However, the formation of 2-D supramolecular highly symmetrical structures with considerable control is still a major challenge. Here we present a simple approach for the preparation of regular and homogeneous 2-D fluorescent square non-crystallization micelles with conjugated diblock copolymers PPV12-b-P2VPn through a process of dissolving–cooling–aging. The scale of the formed micelles can be controlled by the ratio of PPV/P2VP blocks and the concentration of the solution. The results reveal that the micelles of PPV12-b-P2VPn initially form 1-D structures and then grow into 2-D structures in solution, and the growth is driven by intermolecular π–π interactions with the PPV12 blocks. The formation of 2-D square micelles is induced by herringbone arrangement of the molecules, which is closely related to the presence of the branched alkyl chains attached to conjugated PPV12 cores. Crystallization-driven processes play a vital role in preparing 2D nanostructures which makes structures with high symmetry hard to access. Here the authors present a non-crystallization approach which is based on π–π interactions of a copolymer for the fabrication of 2D symmetric structures with good dimensional control.
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Affiliation(s)
- Liang Han
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Meijing Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiangmeng Jia
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, China
| | - Wei Chen
- Materials Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA.,Institute of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - Hujun Qian
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, China
| | - Feng He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
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136
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Zhang J, Wang X, Zhou K, Chen G, Wang Q. Self-Assembly of Protein Crystals with Different Crystal Structures Using Tobacco Mosaic Virus Coat Protein as a Building Block. ACS NANO 2018; 12:1673-1679. [PMID: 29350903 DOI: 10.1021/acsnano.7b08316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, a typical cylinder-shaped tobacco mosaic virus coat protein (TMVCP) is employed as an anisotropic building block to assemble into triclinic and hexagonal close-packed (HCP) protein crystals by introducing cysteine residues at the 1 and 3 sites and four histidine residues at the C-terminal, respectively. The engineered functional groups of cysteine and histidine in the TMVCP and the self-assembly conditions determine the thermodynamics and kinetics in the self-assembly process for forming different crystal structures. The results show that the TMVCPs are thermodynamically driven to form triclinic crystals due to the formation of disulfide bonds between neighboring TMVCPs. On the other hand, the self-assembly of HCP crystals is kinetically directed by the strong metal-histidine chelation. This work not only greatly expands TMVCP for fabricating promising nanomaterials but also represents an approach to adjusting the protein crystal structures by tuning the thermodynamics and kinetics during crystallization.
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Affiliation(s)
- Jianting Zhang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, China
| | - Xiao Wang
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Kun Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, China
| | - Gang Chen
- School of Physical Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, China
- School of Nano Technology and Nano Bionics, University of Science and Technology of China , Hefei 230026, China
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137
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Sanchez-deAlcazar D, Mejias SH, Erazo K, Sot B, Cortajarena AL. Self-assembly of repeat proteins: Concepts and design of new interfaces. J Struct Biol 2018; 201:118-129. [DOI: 10.1016/j.jsb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
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138
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Yang G, Wu L, Chen G, Jiang M. Precise protein assembly of array structures. Chem Commun (Camb) 2018; 52:10595-605. [PMID: 27384233 DOI: 10.1039/c6cc04190f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assembly of proteins into various nano-objects with regular and periodic microstructures, i.e. protein arrays, is a fast-growing field in materials science. Due to the structural complexity of proteins, reports in this field are still quite limited. In this review, we summarize the recent developments in protein array construction by different driving forces, including electrostatic interactions, metal-ligand interactions, molecular recognition and protein-protein interactions. In line with our particular interest, assemblies driven by molecular recognition are particularly explored. Finally, functionalities of the obtained protein arrays are briefly discussed.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Libin Wu
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Guosong Chen
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Ming Jiang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
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139
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Lawrie J, Song X, Niu W, Guo J. A high throughput approach for the generation of orthogonally interacting protein pairs. Sci Rep 2018; 8:867. [PMID: 29343761 PMCID: PMC5772552 DOI: 10.1038/s41598-018-19281-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022] Open
Abstract
In contrast to the nearly error-free self-assembly of protein architectures in nature, artificial assembly of protein complexes with pre-defined structure and function in vitro is still challenging. To mimic nature's strategy to construct pre-defined three-dimensional protein architectures, highly specific protein-protein interacting pairs are needed. Here we report an effort to create an orthogonally interacting protein pair from its parental pair using a bacteria-based in vivo directed evolution strategy. This high throughput approach features a combination of a negative and a positive selection. The newly developed negative selection from this work was used to remove any protein mutants that retain effective interaction with their parents. The positive selection was used to identify mutant pairs that can engage in effective mutual interaction. By using the cohesin-dockerin protein pair that is responsible for the self-assembly of cellulosome as a model system, we demonstrated that a protein pair that is orthogonal to its parent pair could be readily generated using our strategy. This approach could open new avenues to a wide range of protein-based assembly, such as biocatalysis or nanomaterials, with pre-determined architecture and potentially novel functions and properties.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Xi Song
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
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140
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Kocyła A, Krężel A. Zinc clasp-based reversible toolset for selective metal-mediated protein heterodimerization. Chem Commun (Camb) 2018; 54:13539-13542. [DOI: 10.1039/c8cc06301j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc clasp motif derived from natural Zn(ii)-mediated interaction of CD4 co-receptor and Lck protein tyrosine kinase was used for specific and efficient protein heterodimerization. Optimized set of peptide tags forms highly stable complex in the selective heterodimer framework. Utility of obtained toolset demonstrates high specificity, Zn(ii)-dependent reversibility and remarkable kinetic properties.
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Affiliation(s)
- Anna Kocyła
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- Wrocław
- Poland
| | - Artur Krężel
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- Wrocław
- Poland
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141
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Okesola BO, Mata A. Multicomponent self-assembly as a tool to harness new properties from peptides and proteins in material design. Chem Soc Rev 2018; 47:3721-3736. [DOI: 10.1039/c8cs00121a] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nature is enriched with a wide variety of complex, synergistic and highly functional protein-based multicomponent assemblies.
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Affiliation(s)
- Babatunde O. Okesola
- School of Engineering and Materials Science
- Institute of Bioengineering
- Queen Mary University of London
- UK
| | - Alvaro Mata
- School of Engineering and Materials Science
- Institute of Bioengineering
- Queen Mary University of London
- UK
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142
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Zhao L, Li Y, Wang T, Qiao S, Li X, Wang R, Luo Q, Hou C, Xu J, Liu J. Photocontrolled protein assembly for constructing programmed two-dimensional nanomaterials. J Mater Chem B 2018; 6:75-83. [DOI: 10.1039/c7tb02826a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rapid and efficient strategy was developed to construct photocontrolled 2D protein nanosheets with an orderly arrangement.
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143
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Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
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Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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144
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Functionalization of protein crystals with metal ions, complexes and nanoparticles. Curr Opin Chem Biol 2017; 43:68-76. [PMID: 29245143 DOI: 10.1016/j.cbpa.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/09/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects.
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145
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Eibling MJ, MacDermaid CM, Qian Z, Lanci CJ, Park SJ, Saven JG. Controlling Association and Separation of Gold Nanoparticles with Computationally Designed Zinc-Coordinating Proteins. J Am Chem Soc 2017; 139:17811-17823. [DOI: 10.1021/jacs.7b04786] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Matthew J. Eibling
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher M. MacDermaid
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhaoxia Qian
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher J. Lanci
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - So-Jung Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, South Korea
| | - Jeffery G. Saven
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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146
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Song WJ, Yu J, Tezcan FA. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-β-lactamases. J Am Chem Soc 2017; 139:16772-16779. [PMID: 28992705 DOI: 10.1021/jacs.7b08981] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We describe the design and evolution of catalytic hydrolase activity on a supramolecular protein scaffold, Zn4:C96RIDC14, which was constructed from cytochrome cb562 building blocks via a metal-templating strategy. Previously, we reported that Zn4:C96RIDC14 could be tailored with tripodal (His/His/Glu), unsaturated Zn coordination motifs in its interfaces to generate a variant termed Zn8:A104AB34, which in turn displayed catalytic activity for the hydrolysis of activated esters and β-lactam antibiotics. Zn8:A104AB34 was subsequently subjected to directed evolution via an in vivo selection strategy, leading to a variant Zn8:A104/G57AB34 which displayed enzyme-like Michaelis-Menten behavior for ampicillin hydrolysis. A criterion for the evolutionary utility or designability of a new protein structure is its ability to accommodate different active sites. With this in mind, we examined whether Zn4:C96RIDC14 could be tailored with alternative Zn coordination sites that could similarly display evolvable catalytic activities. We report here a detailed structural and functional characterization of new variant Zn8:AB54, which houses similar, unsaturated Zn coordination sites to those in Zn8:A104/G57AB34, but in completely different microenvironments. Zn8:AB54 displays Michaelis-Menten behavior for ampicillin hydrolysis without any optimization. Yet, the subsequent directed evolution of Zn8:AB54 revealed limited catalytic improvement, which we ascribed to the local protein rigidity surrounding the Zn centers and the lack of evolvable loop structures nearby. The relaxation of local rigidity via the elimination of adjacent disulfide linkages led to a considerable structural transformation with a concomitant improvement in β-lactamase activity. Our findings reaffirm previous observations that the delicate balance between protein flexibility and stability is crucial for enzyme design and evolution.
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Affiliation(s)
- Woon Ju Song
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States.,Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - Jaeseung Yu
- Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States
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147
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Sutherland TD, Huson MG, Rapson TD. Rational design of new materials using recombinant structural proteins: Current state and future challenges. J Struct Biol 2017; 201:76-83. [PMID: 29097186 DOI: 10.1016/j.jsb.2017.10.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 11/27/2022]
Abstract
Sequence-definable polymers are seen as a prerequisite for design of future materials, with many polymer scientists regarding such polymers as the holy grail of polymer science. Recombinant proteins are sequence-defined polymers. Proteins are dictated by DNA templates and therefore the sequence of amino acids in a protein is defined, and molecular biology provides tools that allow redesign of the DNA as required. Despite this advantage, proteins are underrepresented in materials science. In this publication we investigate the advantages and limitations of using proteins as templates for rational design of new materials.
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Affiliation(s)
| | - Mickey G Huson
- CSIRO, Black Mountain, GPO Box 1700, Acton, ACT 2601, Australia
| | - Trevor D Rapson
- CSIRO, Black Mountain, GPO Box 1700, Acton, ACT 2601, Australia
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148
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Drobnak I, Ljubetič A, Gradišar H, Pisanski T, Jerala R. Designed Protein Origami. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 940:7-27. [PMID: 27677507 DOI: 10.1007/978-3-319-39196-0_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding. As a new alternative approach to design new protein folds unseen in nature, folds can be designed as a mathematical graph, by the self-assembly of interacting polypeptide modules within the single chain. Orthogonal coiled-coil dimers seem like an ideal building module due to their shape, adjustable length, and above all their designability. Similar to the approach of DNA nanotechnology, where complex tertiary structures are designed from complementary nucleotide segments, a polypeptide chain composed of a precisely specified sequence of coiled-coil forming segments can be designed to self-assemble into polyhedral scaffolds. This modular approach encompasses long-range interactions that define complex tertiary structures. We envision that by expansion of the toolkit of building blocks and design strategies of the folding pathways protein origami technology will be able to construct diverse molecular machines.
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Affiliation(s)
- Igor Drobnak
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Helena Gradišar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tomaž Pisanski
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.,University of Primorska, Koper, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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149
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Jiang T, Magnotti EL, Conticello VP. Geometrical frustration as a potential design principle for peptide-based assemblies. Interface Focus 2017; 7:20160141. [PMID: 29147554 DOI: 10.1098/rsfs.2016.0141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Two-dimensional peptide and protein assemblies have been the focus of increased scientific research as they display significant potential for the creation of functional nanomaterials. Soluble subunits derived from a variety of protein motifs have been demonstrated to self-assemble into structurally defined nanosheets under environmentally benign conditions in which the components often retain their native structure and function. These types of two-dimensional assemblies may have an advantage for nanofabrication in that their extended planar shapes can be more straightforwardly incorporated into the current formats of nanoscale devices. However, significant challenges remain in the fabrication of these materials, particularly in devising methods to control the size, shape and internal structure of the resultant materials. Geometrical frustration may be envisioned as a possible mechanism to exert control over these structural parameters through rational design. While this objective has yet to be realized in practice, we discuss in this article the potential role of geometrical frustration as a principle to rationalize unusual self-assembly behaviour in several examples of two-dimensional peptide assemblies.
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Affiliation(s)
- Tao Jiang
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Elizabeth L Magnotti
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
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150
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Cascades in Compartments: En Route to Machine-Assisted Biotechnology. Angew Chem Int Ed Engl 2017; 56:13574-13589. [DOI: 10.1002/anie.201703806] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
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