201
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Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DAA, Baker D. De novo design of a homo-trimeric amantadine-binding protein. eLife 2019; 8:e47839. [PMID: 31854299 PMCID: PMC6922598 DOI: 10.7554/elife.47839] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2022] Open
Abstract
The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.
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Affiliation(s)
- Jooyoung Park
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| | - Brinda Selvaraj
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
| | - Andrew C McShan
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Scott E Boyken
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| | - Kathy Y Wei
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
- Department of BioengineeringUniversity of California, BerkeleyBerkeleyUnited States
| | | | - William DeGrado
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Nikolaos G Sgourakis
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Matthew J Cuneo
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
- Department of Structural BiologySt. Jude Children’s Research HospitalMemphisUnited States
| | - Dean AA Myles
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
| | - David Baker
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
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202
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Engineering protein assemblies with allosteric control via monomer fold-switching. Nat Commun 2019; 10:5703. [PMID: 31836707 PMCID: PMC6911049 DOI: 10.1038/s41467-019-13686-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
The macromolecular machines of life use allosteric control to self-assemble, dissociate and change shape in response to signals. Despite enormous interest, the design of nanoscale allosteric assemblies has proven tremendously challenging. Here we present a proof of concept of allosteric assembly in which an engineered fold switch on the protein monomer triggers or blocks assembly. Our design is based on the hyper-stable, naturally monomeric protein CI2, a paradigm of simple two-state folding, and the toroidal arrangement with 6-fold symmetry that it only adopts in crystalline form. We engineer CI2 to enable a switch between the native and an alternate, latent fold that self-assembles onto hexagonal toroidal particles by exposing a favorable inter-monomer interface. The assembly is controlled on demand via the competing effects of temperature and a designed short peptide. These findings unveil a remarkable potential for structural metamorphosis in proteins and demonstrate key principles for engineering protein-based nanomachinery. The design of protein assemblies is a major thrust for biomolecular engineering and nanobiotechnology. Here the authors demonstrate a general mechanism for designing allosteric macromolecular assemblies and showcase a proof of concept for engineered allosteric protein assembly.
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203
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Li H, Gao S, Qiu Y, Liang C, Zhu S, Zheng G. Genome mining integrating semi-rational protein engineering and nanoreactor design: roadmap for a robust biocatalyst for industrial resolution of Vince lactam. Appl Microbiol Biotechnol 2019; 104:1109-1123. [PMID: 31828408 DOI: 10.1007/s00253-019-10275-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/13/2019] [Accepted: 11/23/2019] [Indexed: 11/25/2022]
Abstract
Biomanufacturing of chemicals using biocatalysts is an attractive strategy for the production of valuable pharmaceuticals since it is usually more economical and has a much-reduced environmental impact. However, there are often challenges such as their thermal instability that should be overcome before a newly discovered enzyme is eventually translated into industrial processes. In this work, we describe a roadmap for the development of a robust catalyst for industrial resolution of Vince lactam, a key intermediate for the synthesis of carbocyclic-nucleoside-related pharmaceuticals. By a genome mining strategy, a new (+)-γ-lactamase (MiteL) from Microbacterium testaceum was successfully discovered and biochemically characterized. In vitro studies showed that the enzyme exhibited high activity but poor enantioselectivity (E = 6.3 ± 0.2) toward racemic Vince lactam, and thus, it is not suitable for industrial applications. Based on structural modeling and docking studies, a semi-rational engineering strategy combined with an efficient screening method was then applied to improve the enantioselectivity of MiteL. Several mutants with significant shifting stereoselectivity toward (-)-γ-lactam were obtained by site-saturation mutagenesis. Synergy effects led to the final mutant F14D/Q114R/M117L, which enabled efficient acquisition of (-)-γ-lactam with a high E value (> 200). The mutant was biochemically characterized, and the docking studies suggested a plausible mechanism for its improved selectivity. Finally, a sunflower-like nanoreactor was successfully constructed to improve the mutant's robustness via protein supramolecular self-assembly. Thus, the synergism between semi-rational protein engineering and self-assembling immobilization enabled construction of a nanoreactor with superior properties, which can be used for resolution of Vince lactam in large scale.
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Affiliation(s)
- Hongxia Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shuaihua Gao
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yan Qiu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Chaoqun Liang
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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204
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Li Y, An Y, Fan J, Liu X, Li X, Hahn FE, Wang Y, Han Y. Strategy for the Construction of Diverse Poly‐NHC‐Derived Assemblies and Their Photoinduced Transformations. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yang Li
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
| | - Yuan‐Yuan An
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
| | - Jian‐Zhong Fan
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
| | - Xiao‐Xu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
| | - Xin Li
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
| | - F. Ekkehardt Hahn
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
- Institut für Anorganische und Analytische ChemieWestfälische Wilhelms- Universität Münster, Corrensstraße 39 48149 Münster Germany
| | - Yao‐Yu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
| | - Ying‐Feng Han
- Key Laboratory of Synthetic and Natural Functional Molecule ChemistryCollege of Chemistry and Materials ScienceNorthwest University Xi'an 710127 P. R. China
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205
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Li Y, An YY, Fan JZ, Liu XX, Li X, Hahn FE, Wang YY, Han YF. Strategy for the Construction of Diverse Poly-NHC-Derived Assemblies and Their Photoinduced Transformations. Angew Chem Int Ed Engl 2019; 59:10073-10080. [PMID: 31589799 DOI: 10.1002/anie.201912322] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Indexed: 12/14/2022]
Abstract
A series of supramolecular assemblies of types [Ag8 (L)4 ](PF6 )8 and [Ag4 (L)2 ](PF6 )4 , obtained from the tetraphenylethylene (TPE) bridged tetrakis(1,2,4-triazolium) salts H4 -L(PF6 )4 and AgI ions, is described. The assembly type obtained dependends on the N-wingtip substituents of H4 -L(PF6 )4 . Changes in the lengths of the N4-wingtip substituents enables controlled formation of assemblies with either [Ag4 (L)2 ](PF6 )4 or [Ag8 (L)4 ](PF6 )8 stoichiometry. The molecular structures of selected [Ag8 (L)4 ](PF6 )8 and [Ag4 (L)2 ](PF6 )4 assemblies were determined by X-ray diffraction analyses. While H4 -L(PF6 )4 does not exhibit fluorescence in solution, their tetra-NHC (NHC=N-heterocyclic carbene) assemblies do upon NHC-metal coordination. Upon irradiation, all assemblies undergo a light-induced, supramolecule-to-supramolecule structural transformation by an oxidative photocyclization involving phenyl groups of the TPE core, resulting in a significant change of the luminescence properties.
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Affiliation(s)
- Yang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Yuan-Yuan An
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Jian-Zhong Fan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Xiao-Xu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Xin Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - F Ekkehardt Hahn
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China.,Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-, Universität Münster, Corrensstraße 39, 48149, Münster, Germany
| | - Yao-Yu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Ying-Feng Han
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
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206
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Affiliation(s)
- Aleksei Solomonov
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
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207
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Engilberge S, Rennie ML, Dumont E, Crowley PB. Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. ACS NANO 2019; 13:10343-10350. [PMID: 31490058 DOI: 10.1021/acsnano.9b04115] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein crystals with their precise, periodic array of functional building blocks have potential applications in biomaterials, sensing, and catalysis. This paper describes how a highly porous crystalline framework of a cationic redox protein and an anionic macrocycle can be modulated by a small cationic effector. Ternary composites of protein (∼13 kDa), calix[8]arene (∼1.5 kDa), and effector (∼0.2 kDa) formed distinct crystalline architectures, dependent on the effector concentration and the crystallization technique. A combination of X-ray crystallography and density functional theory (DFT) calculations was used to decipher the framework variations, which appear to be dependent on a calixarene conformation change mediated by the effector. This "switch" calixarene was observed in three states, each of which is associated with a different interaction network. Two structures obtained by co-crystallization with the effector contained an additional protein "pillar", resulting in framework duplication and decreased porosity. These results suggest how protein assembly can be engineered by supramolecular host-guest interactions.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Martin L Rennie
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , 69342 Lyon , France
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
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208
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Brouwer PJM, Antanasijevic A, Berndsen Z, Yasmeen A, Fiala B, Bijl TPL, Bontjer I, Bale JB, Sheffler W, Allen JD, Schorcht A, Burger JA, Camacho M, Ellis D, Cottrell CA, Behrens AJ, Catalano M, Del Moral-Sánchez I, Ketas TJ, LaBranche C, van Gils MJ, Sliepen K, Stewart LJ, Crispin M, Montefiori DC, Baker D, Moore JP, Klasse PJ, Ward AB, King NP, Sanders RW. Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle. Nat Commun 2019; 10:4272. [PMID: 31537780 PMCID: PMC6753213 DOI: 10.1038/s41467-019-12080-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
The development of native-like HIV-1 envelope (Env) trimer antigens has enabled the induction of neutralizing antibody (NAb) responses against neutralization-resistant HIV-1 strains in animal models. However, NAb responses are relatively weak and narrow in specificity. Displaying antigens in a multivalent fashion on nanoparticles (NPs) is an established strategy to increase their immunogenicity. Here we present the design and characterization of two-component protein NPs displaying 20 stabilized SOSIP trimers from various HIV-1 strains. The two-component nature permits the incorporation of exclusively well-folded, native-like Env trimers into NPs that self-assemble in vitro with high efficiency. Immunization studies show that the NPs are particularly efficacious as priming immunogens, improve the quality of the Ab response over a conventional one-component nanoparticle system, and are most effective when SOSIP trimers with an apex-proximate neutralizing epitope are displayed. Their ability to enhance and shape the immunogenicity of SOSIP trimers make these NPs a promising immunogen platform.
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Affiliation(s)
- Philip J M Brouwer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Zachary Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Tom P L Bijl
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Jacob B Bale
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.,Arzeda Corporation, Seattle, Washington, 98119, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Joel D Allen
- Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Anna Schorcht
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Judith A Burger
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Miguel Camacho
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Anna-Janina Behrens
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK.,New England Biolabs, Inc., Ipswich, Massachussetts, 01938, USA
| | - Marco Catalano
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Iván Del Moral-Sánchez
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Marit J van Gils
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
| | - Lance J Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA
| | - Max Crispin
- Biological Sciences and Institute of Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK.,Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, OX1 3QU, Oxford, UK
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98105, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, 10065, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, Washington, 98195, USA.
| | - Rogier W Sanders
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands.
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209
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Wang T, Fan X, Xu J, Li R, Yan X, Liu S, Jiang X, Li F, Liu J. Giant Proteinosomes As Scaffolds for Light Harvesting. ACS Macro Lett 2019; 8:1128-1132. [PMID: 35619446 DOI: 10.1021/acsmacrolett.9b00545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on an interfacial assembly strategy, a giant proteinosome was successfully fabricated by using protein-surfactant as building blocks, which formed a thin protein layer as a membrane. This approach of making protein assemblies was very facile, and it was very convenient to remove the templates of oil and get water-filled proteinosomes by dialysis. Through modifying acceptor and donor chromophores on the protein monomers, an efficient artificial light-harvesting system was successfully fabricated on the proteinosome, which was a scaffold for efficient light harvesting. Furthermore, the on-off switchable energy transfer was realized by protein folding and unfolding. The efficient artificial light-harvesting systems we designed as the potential platforms could be utilized for biomaterials.
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Affiliation(s)
- Tingting Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xiaotong Fan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Ruyu Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xu Yan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shengda Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xiaojia Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
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210
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Barros EP, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:5703-5715. [PMID: 31442033 DOI: 10.1021/acs.jctc.9b00483] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Custom-designed ligand-binding proteins represent a promising class of macromolecules with exciting applications toward the design of new enzymes or the engineering of antibodies and small-molecule recruited proteins for therapeutic interventions. However, several challenges remain in designing a protein sequence such that the binding site organization results in high affinity interaction with a bound ligand. Here, we study the dynamics of explicitly solvated designed proteins through all-atom molecular dynamics (MD) simulations to gain insight into the causes that lead to the low affinity or instability of most of these designs, despite the prediction of their success by the computational design methodology. Simulations ranging from 500 to 1000 ns per replicate were conducted on 37 designed protein variants encompassing two distinct folds and a range of ligand affinities, resulting in more than 180 μs of combined sampling. The simulations provide retrospective insights into the properties affecting ligand affinity that can prove useful in guiding further steps of design optimization. Features indicate that entropic components are particularly important for affinity, which are not easily incorporated in the empirical models often used in design protocols. Additionally, we demonstrate that the application of machine learning approaches built upon the output from the simulations can help discriminate between successful and failed binders, such that MD could act as a screening step in protein design, resulting in a more efficient process.
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Affiliation(s)
| | - Jamie M Schiffer
- Janssen Pharmaceuticals, Inc. , San Diego , California 92121 , United States
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211
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212
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Cristie‐David AS, Marsh ENG. Metal-dependent assembly of a protein nano-cage. Protein Sci 2019; 28:1620-1629. [PMID: 31278804 PMCID: PMC6699099 DOI: 10.1002/pro.3676] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022]
Abstract
Short, alpha-helical coiled coils provide a simple, modular method to direct the assembly of proteins into higher order structures. We previously demonstrated that by genetically fusing de novo-designed coiled coils of the appropriate oligomerization state to a natural trimeric protein, we could direct the assembly of this protein into various geometrical cages. Here, we have extended this approach by appending a coiled coil designed to trimerize in response to binding divalent transition metal ions and thereby achieve metal ion-dependent assembly of a tetrahedral protein cage. Ni2+ , Co2+ , Cu2+ , and Zn2+ ions were evaluated, with Ni2+ proving the most effective at mediating protein assembly. Characterization of the assembled protein indicated that the metal ion-protein complex formed discrete globular structures of the diameter expected for a complex containing 12 copies of the protein monomer. Protein assembly could be reversed by removing metal ions with ethylenediaminetetraacetic acid or under mildly acidic conditions.
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Affiliation(s)
| | - E. Neil G. Marsh
- Department of ChemistryUniversity of MichiganAnn ArborMichigan
- Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
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213
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Covalently-assembled single-chain protein nanostructures with ultra-high stability. Nat Commun 2019; 10:3317. [PMID: 31346167 PMCID: PMC6658521 DOI: 10.1038/s41467-019-11285-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022] Open
Abstract
Protein nanostructures with precisely defined geometries have many potential applications in catalysis, sensing, signal processing, and drug delivery. While many de novo protein nanostructures have been assembled via non-covalent intramolecular and intermolecular interactions, a largely unexplored strategy is to construct nanostructures by covalently linking multiple individually folded proteins through site-specific ligations. Here, we report the synthesis of single-chain protein nanostructures with triangular and square shapes made using multiple copies of a three-helix bundle protein and split intein chemistry. Coarse-grained simulations confirm the experimentally observed flexibility of these nanostructures, which is optimized to produce triangular structures with high regularity. These single-chain nanostructures also display ultra-high thermostability, resist denaturation by chaotropes and organic solvents, and have applicability as scaffolds for assembling materials with nanometer resolution. Our results show that site-specific covalent ligation can be used to assemble individually folded proteins into single-chain nanostructures with bespoke architectures and high stabilities. De novo protein nanostructures are typically assembled via top-down approaches. Here, the authors developed a bottom-up approach, using split inteins to ligate multiple copies of a three-helix bundle to create 2D triangular and square-shaped structures with high stability.
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214
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Romanov V, McCullough J, Gale BK, Frost A. A Tunable Microfluidic Device Enables Cargo Encapsulation by Cell- or Organelle-Sized Lipid Vesicles Comprising Asymmetric Lipid Bilayers. ADVANCED BIOSYSTEMS 2019; 3:1900010. [PMID: 31428671 PMCID: PMC6699779 DOI: 10.1002/adbi.201900010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 01/14/2023]
Abstract
Cellular membranes play host to a wide variety of morphologically and chemically complex processes. Although model membranes, like liposomes, are already widely used to reconstitute and study these processes, better tools are needed for making model bilayers that faithfully mimic cellular membranes. Existing methods for fabricating cell-sized (μm) or organelle-sized (tens to hundreds of nanometers) lipid vesicles have distinctly different requirements. Of particular note for biology, it remains challenging for any technique to efficiently encapsulate fragile cargo molecules or to generate liposomes with stable, asymmetric lipid leaflets within the bilayer. Here a tunable microfluidic device and protocol for fabricating liposomes with desired diameters ranging from ≈10 μm to ≈100 nm are described. Lipid vesicle size is templated by the simple inclusion of a polycarbonate filter within the microfluidic system and tuned with flow rate. It is shown that the vesicles made with this device are stable, unilamellar, lipid asymmetric, and capable of supporting transmembrane protein assembly, peripheral membrane protein binding, as well as soluble cargo encapsulation (including designer nanocages for biotechnology applications). These fabricated vesicles provide a new platform for studying the biophysically rich processes found within lipid-lipid and lipid-protein systems typically associated with cellular membranes.
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Affiliation(s)
- Valentin Romanov
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - John McCullough
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Bruce K Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Adam Frost
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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215
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Stimulus-responsive self-assembly of protein-based fractals by computational design. Nat Chem 2019; 11:605-614. [DOI: 10.1038/s41557-019-0277-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/29/2019] [Indexed: 11/09/2022]
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216
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Edwardson TGW, Hilvert D. Virus-Inspired Function in Engineered Protein Cages. J Am Chem Soc 2019; 141:9432-9443. [PMID: 31117660 DOI: 10.1021/jacs.9b03705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structural and functional diversity of proteins combined with their genetic programmability has made them indispensable modern materials. Well-defined, hollow protein capsules have proven to be particularly useful due to their ability to compartmentalize macromolecules and chemical processes. To this end, viral capsids are common scaffolds and have been successfully repurposed to produce a suite of practical protein-based nanotechnologies. Recently, the recapitulation of viromimetic function in protein cages of nonviral origin has emerged as a strategy to both complement physical studies of natural viruses and produce useful scaffolds for diverse applications. In this perspective, we review recent progress toward generation of virus-like behavior in nonviral protein cages through rational engineering and directed evolution. These artificial systems can aid our understanding of the emergence of viruses from existing cellular components, as well as provide alternative approaches to tackle current problems, and open up new opportunities, in medicine and biotechnology.
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Affiliation(s)
| | - Donald Hilvert
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
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217
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Abstract
Capsid of tomato bushy stunt virus consists of an outer coat protein shell decorated on an internal skeleton comprising a β-annulus motif. We mimicked this capsid structure with our artificial viral capsid dressed up with protein. We synthesized the β-annulus peptide bearing a Cys at the C-terminal side and linked it with Cys34 of the human serum albumin (HSA) via a bismaleimide linker. The β-annulus peptide-HSA conjugate self-assembled into spherical structures of a 50-70 nm size range in the Tris-HCl buffer, with the ζ-potential of assemblies of such conjugate revealing that HSA proteins were displayed on the outer surface of the artificial viral capsid. Interestingly, the critical aggregation concentration (CAC) of the conjugate in the Tris-HCl buffer at 25 °C was approximately 0.01 μM, or 1/2500 lower than that of the unmodified β-annulus peptides, suggesting that the artificial viral capsids were stabilized via HSA modification. The present strategy of constructing protein nanocapsule by self-assembly of a β-annulus peptide-protein conjugate is simpler than that of previously reported protein nanocapsules.
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218
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Cristie-David AS, Chen J, Nowak DB, Bondy AL, Sun K, Park SI, Banaszak Holl MM, Su M, Marsh ENG. Coiled-Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability. J Am Chem Soc 2019; 141:9207-9216. [PMID: 31117640 DOI: 10.1021/jacs.8b13604] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Furthermore, the stabilization of enzyme activity has many practical applications in biotechnology and medicine. Here we describe the symmetry-directed design of an extremely stable, enzymatically active, hollow protein cage of Mr ≈ 2.1 MDa with dimensions similar to those of a small icosahedral virus. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain, and cryo-EM and by atomic force and IR-photoinduced force microscopy established that Ico8 assembles into a flexible hollow cage comprising 20 copies of the esterase trimer, 60 protein subunits in total, with overall icosahedral geometry. Notably, the cages formed by Ico8 proved to be extremely stable toward thermal and chemical denaturation: whereas TriEst was unfolded by heating ( Tm ≈ 75 °C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 °C or in 8 M guanidine hydrochloride. The increased stability of the cages is a new property that emerges from the higher-order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.
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Affiliation(s)
- Ajitha S Cristie-David
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Junjie Chen
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Derek B Nowak
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Amy L Bondy
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Kai Sun
- Michigan Center for Materials Characterization , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Sung I Park
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Mark M Banaszak Holl
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - E Neil G Marsh
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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219
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Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S. Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins. ACS Synth Biol 2019; 8:1112-1120. [PMID: 30966743 DOI: 10.1021/acssynbio.9b00019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Self-assembled protein nanostructures have gained interest, owing to their potential applications in biomaterials; however, successful design and construction of protein nanostructures are limited. Herein, we constructed fusion protein 1 by linking the C-terminus of a dimerization domain and the N-terminus of another dimerization domain with a three-helix bundle protein, where it self-assembled mainly into tetramers. By replacing the C-terminal dimerization domain of 1 with a trimerization domain (fusion protein 2), hexamers were mainly obtained. According to ab initio structural models reconstructed from the small-angle X-ray scattering data, the tetramer of 1 and hexamer of 2 adopted quadrangle and cage-like structures, respectively, although they were combinations of different conformations. High-speed atomic force microscopy observations indicated that the tetramer and hexamer exhibit conformational dynamics. These results show that the present method utilizing three-helix bundle-linked fusion proteins is useful in the construction of protein nanostructures.
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Affiliation(s)
- Takaaki Miyamoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yugo Hayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keito Yoshida
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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220
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Beesley JL, Woolfson DN. The de novo design of α-helical peptides for supramolecular self-assembly. Curr Opin Biotechnol 2019; 58:175-182. [PMID: 31039508 DOI: 10.1016/j.copbio.2019.03.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
One approach to designing de novo proteinaceous assemblies and materials is to develop simple, standardised building blocks and then to combine these symmetrically to construct more-complex higher-order structures. This has been done extensively using β-structured peptides to produce peptide fibres and hydrogels. Here, we focus on building with de novo α-helical peptides. Because of their self-contained, well-defined structures and clear sequence-to-structure relationships, α helices are highly programmable making them robust building blocks for biomolecular construction. The progress made with this approach over the past two decades is astonishing and has led to a variety of de novo assemblies, including discrete nanoscale objects, and fibrous, nanotube, sheet and colloidal materials. This body of work provides an exceptionally strong foundation for advancing the field beyond in vitro design and into in vivo applications including what we call protein design in cells.
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Affiliation(s)
- Joseph L Beesley
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK; BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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221
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Cannon KA, Ochoa JM, Yeates TO. High-symmetry protein assemblies: patterns and emerging applications. Curr Opin Struct Biol 2019; 55:77-84. [PMID: 31005680 DOI: 10.1016/j.sbi.2019.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/06/2019] [Indexed: 12/28/2022]
Abstract
The accelerated elucidation of three-dimensional structures of protein complexes, both natural and designed, is providing new examples of large supramolecular assemblies with intriguing shapes. Those with high symmetry - based on the geometries of the Platonic solids - are particularly notable as their innately closed forms create interior spaces with varying degrees of enclosure. We survey known protein assemblies of this type and discuss their geometric features. The results bear on issues of protein function and evolution, while also guiding novel bioengineering applications. Recent successes using high-symmetry protein assemblies for applications in interior encapsulation and exterior display are highlighted.
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Affiliation(s)
- Kevin A Cannon
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States
| | - Jessica M Ochoa
- UCLA Department of Chemistry and Biochemistry, United States; UCLA Molecular Biology Institute, United States
| | - Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States; UCLA Molecular Biology Institute, United States.
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222
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Abstract
![]()
Ordered
protein assemblies are attracting interest as next-generation
biomaterials with a remarkable range of structural and functional
properties, leading to potential applications in biocatalysis, materials
templating, drug delivery and vaccine development. This Review covers
ordered protein assemblies including protein nanowires/nanofibrils,
nanorings, nanotubes, designed two- and three-dimensional ordered
protein lattices and protein-like cages including polyhedral virus-like
cage structures. The main focus is on designed ordered protein assemblies,
in which the spatial organization of the proteins is controlled by
tailored noncovalent interactions (including metal ion binding interactions,
electrostatic interactions and ligand–receptor interactions
among others) or by careful design of modified (mutant) proteins or de novo constructs. The modification of natural protein
assemblies including bacterial S-layers and cage-like and rod-like
viruses to impart novel function, e.g. enzymatic activity, is also
considered. A diversity of structures have been created using distinct
approaches, and this Review provides a summary of the state-of-the-art
in the development of these systems, which have exceptional potential
as advanced bionanomaterials for a diversity of applications.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
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223
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Sokolov AV, Kostin NN, Ovchinnikova LA, Lomakin YA, Kudriaeva AA. Targeted Drug Delivery in Lipid-like Nanocages and Extracellular Vesicles. Acta Naturae 2019; 11:28-41. [PMID: 31413877 PMCID: PMC6643341 DOI: 10.32607/20758251-2019-11-2-28-41] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 12/12/2022] Open
Abstract
The possibility of targeted drug delivery to a specific tissue, organ, or cell has opened new promising avenues in treatment development. The technology of targeted delivery aims to create multifunctional carriers that are capable of long circulation in the patient's organism and possess low toxicity at the same time. The surface of modern synthetic carriers has high structural similarity to the cell membrane, which, when combined with additional modifications, also promotes the transfer of biological properties in order to penetrate physiological barriers effectively. Along with artificial nanocages, further efforts have recently been devoted to research into extracellular vesicles that could serve as natural drug delivery vehicles. This review provides a detailed description of targeted delivery systems that employ lipid and lipid-like nanocages, as well as extracellular vesicles with a high level of biocompatibility, highlighting genetically encoded drug delivery vehicles.
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Affiliation(s)
- A. V. Sokolov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16 /10, Moscow, 117997, Russia
| | - N. N. Kostin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16 /10, Moscow, 117997, Russia
| | - L. A. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16 /10, Moscow, 117997, Russia
| | - Y. A. Lomakin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16 /10, Moscow, 117997, Russia
| | - A. A. Kudriaeva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16 /10, Moscow, 117997, Russia
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224
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Attachment of flagellin enhances the immunostimulatory activity of a hemagglutinin-ferritin nano-cage. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 17:223-235. [DOI: 10.1016/j.nano.2019.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 10/31/2018] [Accepted: 01/11/2019] [Indexed: 12/15/2022]
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225
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Xu Y, Jiang S, Simmons CR, Narayanan RP, Zhang F, Aziz AM, Yan H, Stephanopoulos N. Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks. ACS NANO 2019; 13:3545-3554. [PMID: 30835439 DOI: 10.1021/acsnano.8b09798] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Three-dimensional (3D) cages are one of the most important targets for nanotechnology. Both proteins and DNA have been used as building blocks to create tunable nanoscale cages for a wide range of applications, but each molecular type has its own limitations. Here, we report a cage constructed from both protein and DNA building blocks through the use of covalent protein-DNA conjugates. We modified a homotrimeric protein (KDPG aldolase) with three identical single-stranded DNA handles by functionalizing a reactive cysteine residue introduced via site-directed mutagenesis. This protein-DNA building block was coassembled with a triangular DNA structure bearing three complementary arms to the handles, resulting in tetrahedral cages comprising six DNA sides capped by the protein trimer. The dimensions of the cage could be tuned through the number of turns per DNA arm (3 turns ∼ 10 nm, 4 turns ∼ 14 nm), and the hybrid structures were purified and characterized to confirm the three-dimensional structure. Cages were also modified with DNA using click chemistry and using aldolase trimers bearing the noncanonical amino acid 4-azidophenylalanine, demonstrating the generality of the method. Our approach will allow for the construction of nanomaterials that possess the advantages of both protein and DNA nanotechnology and find applications in fields such as targeted delivery, structural biology, biomedicine, and catalytic materials.
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226
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Ross JF, Wildsmith GC, Johnson M, Hurdiss DL, Hollingsworth K, Thompson RF, Mosayebi M, Trinh CH, Paci E, Pearson AR, Webb ME, Turnbull WB. Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages. J Am Chem Soc 2019; 141:5211-5219. [PMID: 30856321 PMCID: PMC6449800 DOI: 10.1021/jacs.8b11480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The self-assembly
of proteins into higher order structures is ubiquitous
in living systems. It is also an essential process for the bottom-up
creation of novel molecular architectures and devices for synthetic
biology. However, the complexity of protein–protein interaction
surfaces makes it challenging to mimic natural assembly processes
in artificial systems. Indeed, many successful computationally designed
protein assemblies are prescreened for “designability”,
limiting the choice of components. Here, we report a simple and pragmatic
strategy to assemble chosen multisubunit proteins into more complex
structures. A coiled-coil domain appended to one face of the pentameric
cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular
supra-molecular complexes. Analysis of a tubular structure determined
by X-ray crystallography has revealed a hierarchical assembly process
that displays features reminiscent of the polymorphic assembly of
polyomavirus proteins. The approach provides a simple and straightforward
method to direct the assembly of protein building blocks which present
either termini on a single face of an oligomer. This scaffolding approach
can be used to generate bespoke supramolecular assemblies of functional
proteins. Additionally, structural resolution of the scaffolded assemblies
highlight “native-state” forced protein–protein
interfaces, which may prove useful as starting conformations for future
computational design.
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Affiliation(s)
- James F Ross
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Gemma C Wildsmith
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Michael Johnson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Daniel L Hurdiss
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Kristian Hollingsworth
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Majid Mosayebi
- School of Mathematics , University of Bristol , Bristol BS8 1TW , United Kingdom.,BrisSynBio, Life Sciences Building , University of Bristol , Bristol BS8 1TQ , United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics , Universität Hamburg , Hamburg D-22761 , Germany
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - W Bruce Turnbull
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
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227
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Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein. Proc Natl Acad Sci U S A 2019; 116:6806-6811. [PMID: 30877249 DOI: 10.1073/pnas.1818744116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The successful de novo design of proteins can provide insights into the physical chemical basis of stability, the role of evolution in constraining amino acid sequences, and the production of customizable platforms for engineering applications. Previous guanidine hydrochloride (GdnHCl; an ionic denaturant) experiments of a designed, naturally occurring βα fold, Di-III_14, revealed a cooperative, two-state unfolding transition and a modest stability. Continuous-flow mixing experiments in our laboratory revealed a simple two-state reaction in the microsecond to millisecond time range and consistent with the thermodynamic results. In striking contrast, the protein remains folded up to 9.25 M in urea, a neutral denaturant, and hydrogen exchange (HDX) NMR analysis in water revealed the presence of numerous high-energy states that interconvert on a time scale greater than seconds. The complex protection pattern for HDX corresponds closely with a pair of electrostatic networks on the surface and an extensive network of hydrophobic side chains in the interior of the protein. Mutational analysis showed that electrostatic and hydrophobic networks contribute to the resistance to urea denaturation for the WT protein; remarkably, single charge reversals on the protein surface restore the expected urea sensitivity. The roughness of the energy surface reflects the densely packed hydrophobic core; the removal of only two methyl groups eliminates the high-energy states and creates a smooth surface. The design of a very stable βα fold containing electrostatic and hydrophobic networks has created a complex energy surface rarely observed in natural proteins.
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228
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Oohora K, Kajihara R, Jiromaru M, Kitagishi H, Hayashi T. Arginine Residues Provide a Multivalent Effect for Cellular Uptake of a Hemoprotein Assembly. CHEM LETT 2019. [DOI: 10.1246/cl.180897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Ryota Kajihara
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Misa Jiromaru
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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229
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Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization. Nat Commun 2019; 10:1006. [PMID: 30824698 PMCID: PMC6397255 DOI: 10.1038/s41467-019-09004-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/21/2019] [Indexed: 12/12/2022] Open
Abstract
Formation of biological filaments via intracellular supramolecular polymerization of proteins or protein/nucleic acid complexes is under programmable and spatiotemporal control to maintain cellular and genomic integrity. Here we devise a bioinspired, catassembly-like isothermal chain-growth approach to copolymerize DNA hairpin tiles (DHTs) into nanofilaments with desirable composition, chain length and function. By designing metastable DNA hairpins with shape-defining intramolecular hydrogen bonds, we generate two types of DHT monomers for copolymerization with high cooperativity and low dispersity indexes. Quantitative single-molecule dissection methods reveal that catalytic opening of a DHT motif harbouring a toehold triggers successive branch migration, which autonomously propagates to form copolymers with alternate tile units. We find that these shape-defined supramolecular nanostructures become substrates for efficient endocytosis by living mammalian cells in a stiffness-dependent manner. Hence, this catassembly-like in-vitro reconstruction approach provides clues for understanding structure-function relationship of biological filaments under physiological and pathological conditions.
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230
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Morris C, Glennie SJ, Lam HS, Baum HE, Kandage D, Williams NA, Morgan DJ, Woolfson DN, Davidson AD. A Modular Vaccine Platform Combining Self-Assembled Peptide Cages and Immunogenic Peptides. ADVANCED FUNCTIONAL MATERIALS 2019; 29:1807357. [PMID: 32313545 PMCID: PMC7161841 DOI: 10.1002/adfm.201807357] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/18/2018] [Indexed: 05/11/2023]
Abstract
Subunit vaccines use delivery platforms to present minimal antigenic components for immunization. The benefits of such systems include multivalency, self-adjuvanting properties, and more specific immune responses. Previously, the design, synthesis, and characterization of self-assembling peptide cages (SAGEs) have been reported. In these, de novo peptides are combined to make hubs that assemble into nanoparticles when mixed in aqueous solution. Here it is shown that SAGEs are nontoxic particles with potential as accessible synthetic peptide scaffolds for the delivery of immunogenic components. To this end, SAGEs functionalized with the model antigenic peptides tetanus toxoid632-651 and ovalbumin323-339 drive antigen-specific responses both in vitro and in vivo, eliciting both CD4+ T cell and B cell responses. Additionally, SAGEs functionalized with the antigenic peptide hemagglutinin518-526 from the influenza virus are also able to drive a CD8+ T cell response in vivo. This work demonstrates the potential of SAGEs to act as a modular scaffold for antigen delivery, capable of inducing and boosting specific and tailored immune responses.
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Affiliation(s)
- Caroline Morris
- BrisSynBioUniversity of BristolBristolBS8 1TQUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Sarah J. Glennie
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Hon S. Lam
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Holly E. Baum
- BrisSynBioUniversity of BristolBristolBS8 1TQUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Dhinushi Kandage
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Neil A. Williams
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - David J. Morgan
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Derek N. Woolfson
- BrisSynBioUniversity of BristolBristolBS8 1TQUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | - Andrew D. Davidson
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
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231
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Hirabayashi J, Arai R. Lectin engineering: the possible and the actual. Interface Focus 2019; 9:20180068. [PMID: 30842871 DOI: 10.1098/rsfs.2018.0068] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Lectins are a widespread group of sugar-binding proteins occurring in all types of organisms including animals, plants, bacteria, fungi and even viruses. According to a recent report, there are more than 50 lectin scaffolds (∼Pfam), for which three-dimensional structures are known and sugar-binding functions have been confirmed in the literature, which far exceeds our view in the twentieth century (Fujimoto et al. 2014 Methods Mol. Biol. 1200, 579-606 (doi:10.1007/978-1-4939-1292-6_46)). This fact suggests that new lectins will be discovered either by a conventional screening approach or just by chance. It is also expected that new lectin domains including those found in enzymes as carbohydrate-binding modules will be generated in the future through evolution, although this has never been attempted on an experimental level. Based on the current state of the art, various methods of lectin engineering are available, by which lectin specificity and/or stability of a known lectin scaffold can be improved. However, the above observation implies that any protein scaffold, including those that have never been described as lectins, may be modified to acquire a sugar-binding function. In this review, possible approaches to confer sugar-binding properties on synthetic proteins and peptides are described.
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Affiliation(s)
- Jun Hirabayashi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Central-2, 1-1-1, Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan.,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, 8304, Minamiminowa, Kamiina, Nagano 399-4598, Japan
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232
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Oohora K, Kajihara R, Fujimaki N, Uchihashi T, Hayashi T. A ring-shaped hemoprotein trimer thermodynamically controlled by the supramolecular heme-heme pocket interaction. Chem Commun (Camb) 2019; 55:1544-1547. [PMID: 30565588 DOI: 10.1039/c8cc09314h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Engineered cytochrome b562, a small hemoprotein, with an externally-attached heme moiety via a moderately long linker at a suitable position predominantly forms a thermodynamically stable ring-shaped trimer in dilute solution. In an equilibrium between supramolecular polymerization and depolymerization, the ring-shaped trimer is kinetically trapped even in a concentrated solution.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan.
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233
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Sasaki E, Hilvert D. Structure and Self-assembly of Negatively Supercharged Protein Cages. YAKUGAKU ZASSHI 2019; 139:199-208. [DOI: 10.1248/yakushi.18-00169-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Eita Sasaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich
| | - Donald Hilvert
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich
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234
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Nanoreactor Design Based on Self-Assembling Protein Nanocages. Int J Mol Sci 2019; 20:ijms20030592. [PMID: 30704048 PMCID: PMC6387247 DOI: 10.3390/ijms20030592] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/18/2022] Open
Abstract
Self-assembling proteins that form diverse architectures are widely used in material science and nanobiotechnology. One class belongs to protein nanocages, which are compartments with nanosized internal spaces. Because of the precise nanoscale structures, proteinaceous compartments are ideal materials for use as general platforms to create distinct microenvironments within confined cellular environments. This spatial organization strategy brings several advantages including the protection of catalyst cargo, faster turnover rates, and avoiding side reactions. Inspired by diverse molecular machines in nature, bioengineers have developed a variety of self-assembling supramolecular protein cages for use as biosynthetic nanoreactors that mimic natural systems. In this mini-review, we summarize current progress and ongoing efforts creating self-assembling protein based nanoreactors and their use in biocatalysis and synthetic biology. We also highlight the prospects for future research on these versatile nanomaterials.
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235
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Simon AJ, Zhou Y, Ramasubramani V, Glaser J, Pothukuchy A, Gollihar J, Gerberich JC, Leggere JC, Morrow BR, Jung C, Glotzer SC, Taylor DW, Ellington AD. Supercharging enables organized assembly of synthetic biomolecules. Nat Chem 2019; 11:204-212. [DOI: 10.1038/s41557-018-0196-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 11/09/2022]
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236
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Magic number colloidal clusters as minimum free energy structures. Nat Commun 2018; 9:5259. [PMID: 30532018 PMCID: PMC6288123 DOI: 10.1038/s41467-018-07600-4] [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: 07/11/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022] Open
Abstract
Clusters in systems as diverse as metal atoms, virus proteins, noble gases, and nucleons have properties that depend sensitively on the number of constituent particles. Certain numbers are termed ‘magic’ because they grant the system with closed shells and exceptional stability. To this point, magic number clusters have been exclusively found with attractive interactions as present between atoms. Here we show that magic number clusters exist in a confined soft matter system with negligible interactions. Colloidal particles in an emulsion droplet spontaneously organize into a series of clusters with precisely defined shell structures. Crucially, free energy calculations demonstrate that colloidal clusters with magic numbers possess higher thermodynamic stability than those off magic numbers. A complex kinetic pathway is responsible for the efficiency of this system in finding its minimum free energy configuration. Targeting similar magic number states is a strategy towards unique configurations in finite self-organizing systems across the scales. Magic number cluster with closed shells and increased stability often result from potential energy minimization between attractive atoms or particles. Here, Wang et al. show that such magic number clusters can also result from entropy maximization in colloidal systems with negligible interactions.
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237
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Dimou E, Cosentino K, Platonova E, Ros U, Sadeghi M, Kashyap P, Katsinelos T, Wegehingel S, Noé F, García-Sáez AJ, Ewers H, Nickel W. Single event visualization of unconventional secretion of FGF2. J Cell Biol 2018; 218:683-699. [PMID: 30470711 PMCID: PMC6363455 DOI: 10.1083/jcb.201802008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/07/2018] [Accepted: 11/08/2018] [Indexed: 12/29/2022] Open
Abstract
FGF2 is a cell survival factor secreted by unconventional means. Dimou et al. visualize individual FGF2 translocation events at the plasma membrane by live cell TIRF microscopy, providing insight into the kinetics and the mechanism of this process. FGF2 is exported from cells by an unconventional secretory mechanism. Here, we directly visualized individual FGF2 membrane translocation events at the plasma membrane using live cell TIRF microscopy. This process was dependent on both PI(4,5)P2–mediated recruitment of FGF2 at the inner leaflet and heparan sulfates capturing FGF2 at the outer plasma membrane leaflet. By simultaneous imaging of both FGF2 membrane recruitment and the appearance of FGF2 at the cell surface, we revealed the kinetics of FGF2 membrane translocation in living cells with an average duration of ∼200 ms. Furthermore, we directly demonstrated FGF2 oligomers at the inner leaflet of living cells with a FGF2 dimer being the most prominent species. We propose this dimer to represent a key intermediate in the formation of higher FGF2 oligomers that form membrane pores and put forward a kinetic model explaining the mechanism by which membrane-inserted FGF2 oligomers serve as dynamic translocation intermediates during unconventional secretion of FGF2.
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Affiliation(s)
- Eleni Dimou
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Katia Cosentino
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Evgenia Platonova
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Uris Ros
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Mohsen Sadeghi
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Purba Kashyap
- Institute for Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | | | | | - Frank Noé
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Helge Ewers
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK .,Institute for Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
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238
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Liu X, Kang F, Hu C, Wang L, Xu Z, Zheng D, Gong W, Lu Y, Ma Y, Wang J. A genetically encoded photosensitizer protein facilitates the rational design of a miniature photocatalytic CO 2-reducing enzyme. Nat Chem 2018; 10:1201-1206. [PMID: 30397317 DOI: 10.1038/s41557-018-0150-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/30/2018] [Indexed: 12/31/2022]
Abstract
Photosensitizers, which harness light energy to upgrade weak reductants to strong reductants, are pivotal components of the natural and artificial photosynthesis machineries. However, it has proved difficult to enhance and expand their functions through genetic engineering. Here we report a genetically encoded, 27 kDa photosensitizer protein (PSP), which facilitates the rational design of miniature photocatalytic CO2-reducing enzymes. Visible light drives PSP efficiently into a long-lived triplet excited state (PSP*), which reacts rapidly with reduced nicotinamide adenine dinucleotide to generate a super-reducing radical (PSP•), which is strong enough to reduce many CO2-reducing catalysts. We determined the three-dimensional structure of PSP• at 1.8 Å resolution by X-ray crystallography. Genetic engineering enabled the site-specific attachment of a nickel-terpyridine complex and the modular optimization of the photochemical properties of PSP, the chromophore/catalytic centre distance and the catalytic centre microenvironment, which culminated in a miniature photocatalytic CO2-reducing enzyme that has a CO2/CO conversion quantum efficiency of 2.6%.
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Affiliation(s)
- Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China
| | - Fuying Kang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China.,College of Life Sciences and School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China.,College of Life Sciences and School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China.,College of Life Sciences and School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Xu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China
| | - Dandan Zheng
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China
| | - Weimin Gong
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science & Technology of China, Hefei, Anhui, China
| | - Yi Lu
- Center of Chemical Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, Chaoyang District, Beijing, China. .,College of Life Sciences and School of Future Technology, University of Chinese Academy of Sciences, Beijing, China. .,Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China.
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239
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He L, Kumar S, Allen JD, Huang D, Lin X, Mann CJ, Saye-Francisco KL, Copps J, Sarkar A, Blizard GS, Ozorowski G, Sok D, Crispin M, Ward AB, Nemazee D, Burton DR, Wilson IA, Zhu J. HIV-1 vaccine design through minimizing envelope metastability. SCIENCE ADVANCES 2018; 4:eaau6769. [PMID: 30474059 PMCID: PMC6248932 DOI: 10.1126/sciadv.aau6769] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/19/2018] [Indexed: 05/17/2023]
Abstract
Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41ECTO) is the main source of envelope metastability by replacing wild-type gp41ECTO with BG505 gp41ECTO of the uncleaved prefusion-optimized (UFO) design. These gp41ECTO-swapped trimers can be produced in CHO cells with high yield and high purity. The crystal structure of a gp41ECTO-swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder viruses and UFO trimers containing a consensus-based ancestral gp41ECTO suggest an evolutionary root of metastability. The gp41ECTO-stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer, I3-01. In mice and rabbits, these gp140 nanoparticles induced tier 2 neutralizing antibody responses more effectively than soluble trimers.
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Affiliation(s)
- Linling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joel D. Allen
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin J. Mann
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen L. Saye-Francisco
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabrielle S. Blizard
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139-3583, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Corresponding author. (I.A.W.); (J.Z.)
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Corresponding author. (I.A.W.); (J.Z.)
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240
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Cristie‐David AS, Koldewey P, Meinen BA, Bardwell JCA, Marsh ENG. Elaborating a coiled-coil-assembled octahedral protein cage with additional protein domains. Protein Sci 2018; 27:1893-1900. [PMID: 30113093 PMCID: PMC6201728 DOI: 10.1002/pro.3497] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/07/2018] [Accepted: 08/07/2018] [Indexed: 01/28/2023]
Abstract
De novo design of protein nano-cages has potential applications in medicine, synthetic biology, and materials science. We recently developed a modular, symmetry-based strategy for protein assembly in which short, coiled-coil sequences mediate the assembly of a protein building block into a cage. The geometry of the cage is specified by the combination of rotational symmetries associated with the coiled-coil and protein building block. We have used this approach to design well-defined octahedral and tetrahedral cages. Here, we show that the cages can be further elaborated and functionalized by the addition of another protein domain to the free end of the coiled-coil: in this case by fusing maltose-binding protein to an octahedral protein cage to produce a structure with a designed molecular weight of ~1.8 MDa. Importantly, the addition of the maltose binding protein domain dramatically improved the efficiency of assembly, resulting in ~ 60-fold greater yield of purified protein compared to the original cage design. This study shows the potential of using small, coiled-coil motifs as off-the-shelf components to design MDa-sized protein cages to which additional structural or functional elements can be added in a modular manner.
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Affiliation(s)
| | - Philipp Koldewey
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109
| | - Ben A. Meinen
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109
| | - James C. A. Bardwell
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109
- Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan48109
- Howard Hughes Medical InstituteChevy ChaseMaryland
| | - E. Neil G. Marsh
- Department of ChemistryUniversity of MichiganAnn ArborMichigan48109
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241
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Inaba H, Matsuura K. Peptide Nanomaterials Designed from Natural Supramolecular Systems. CHEM REC 2018; 19:843-858. [PMID: 30375148 DOI: 10.1002/tcr.201800149] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/07/2018] [Indexed: 12/22/2022]
Abstract
Natural supramolecular assemblies exhibit unique structural and functional properties that have been optimized over the course of evolution. Inspired by these natural systems, various bio-nanomaterials have been developed using peptides, proteins, and nucleic acids as components. Peptides are attractive building blocks because they enable the important domains of natural protein assemblies to be isolated and optimized while retaining the original structures and functions. Furthermore, the peptide subunits can be conjugated with exogenous molecules such as peptides, proteins, nucleic acids, and metal nanoparticles to generate advanced functions. In this personal account, we summarize recent progress in the construction of peptide-based nanomaterial designed from natural supramolecular systems, including (1) artificial viral capsids, (2) self-assembled nanofibers, and (3) protein-binding motifs. The peptides inspired by nature should provide new design principles for bio-nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
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242
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Gadzuk-Shea MM, Bush MF. Effects of Charge State on the Structures of Serum Albumin Ions in the Gas Phase: Insights from Cation-to-Anion Proton-Transfer Reactions, Ion Mobility, and Mass Spectrometry. J Phys Chem B 2018; 122:9947-9955. [DOI: 10.1021/acs.jpcb.8b08427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Meagan M. Gadzuk-Shea
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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243
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Tian Y, Polzer FB, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides. Biomacromolecules 2018; 19:4286-4298. [DOI: 10.1021/acs.biomac.8b01163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Frank B. Polzer
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kristi L. Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J. Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
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244
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Maita N. Crystal Structure Determination of Ubiquitin by Fusion to a Protein That Forms a Highly Porous Crystal Lattice. J Am Chem Soc 2018; 140:13546-13549. [DOI: 10.1021/jacs.8b07512] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nobuo Maita
- Division of Disease Proteomics, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
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245
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Sandanaraj BS, Reddy MM, Bhandari PJ, Kumar S, Aswal VK. Rational Design of Supramolecular Dynamic Protein Assemblies by Using a Micelle-Assisted Activity-Based Protein-Labeling Technology. Chemistry 2018; 24:16085-16096. [DOI: 10.1002/chem.201802824] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Britto S. Sandanaraj
- Department of Chemistry & Biology; Indian Institute of Science Education and Research (IISER); Pune 411 008 India
| | - Mullapudi Mohan Reddy
- Department of Chemistry & Biology; Indian Institute of Science Education and Research (IISER); Pune 411 008 India
| | | | - Sugam Kumar
- Solid State Physics Division; Bhabha Atomic Research Centre (BARC); Mumbai 400085 India
| | - Vinod K. Aswal
- Solid State Physics Division; Bhabha Atomic Research Centre (BARC); Mumbai 400085 India
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246
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Bruun TJ, Andersson AMC, Draper SJ, Howarth M. Engineering a Rugged Nanoscaffold To Enhance Plug-and-Display Vaccination. ACS NANO 2018; 12:8855-8866. [PMID: 30028591 PMCID: PMC6158681 DOI: 10.1021/acsnano.8b02805] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/20/2018] [Indexed: 05/24/2023]
Abstract
Nanoscale organization is crucial to stimulating an immune response. Using self-assembling proteins as multimerization platforms provides a safe and immunogenic system to vaccinate against otherwise weakly immunogenic antigens. Such multimerization platforms are generally based on icosahedral viruses and have led to vaccines given to millions of people. It is unclear whether synthetic protein nanoassemblies would show similar potency. Here we take the computationally designed porous dodecahedral i301 60-mer and rationally engineer this particle, giving a mutated i301 (mi3) with improved particle uniformity and stability. To simplify the conjugation of this nanoparticle, we employ a SpyCatcher fusion of mi3, such that an antigen of interest linked to the SpyTag peptide can spontaneously couple through isopeptide bond formation (Plug-and-Display). SpyCatcher-mi3 expressed solubly to high yields in Escherichia coli, giving more than 10-fold greater yield than a comparable phage-derived icosahedral nanoparticle, SpyCatcher-AP205. SpyCatcher-mi3 nanoparticles showed high stability to temperature, freeze-thaw, lyophilization, and storage over time. We demonstrate approximately 95% efficiency coupling to different transmission-blocking and blood-stage malaria antigens. Plasmodium falciparum CyRPA was conjugated to SpyCatcher-mi3 nanoparticles and elicited a high avidity antibody response, comparable to phage-derived virus-like particles despite their higher valency and RNA cargo. The simple production, precise derivatization, and exceptional ruggedness of this nanoscaffold should facilitate broad application for nanobiotechnology and vaccine development.
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Affiliation(s)
- Theodora
U. J. Bruun
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anne-Marie C. Andersson
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Simon J. Draper
- Jenner
Institute, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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247
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Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K. Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Norifumi Kawakami
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Hiroki Kondo
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Yuki Matsuzawa
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kaoru Hayasaka
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Erika Nasu
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kenji Sasahara
- Department of Applied Biology; Faculty of Textile Science and Technology; Shinshu University; Ueda Nagano 386-8567 Japan
| | - 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
| | - Kenji Miyamoto
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
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248
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Beyeh N, Nonappa, Liljeström V, Mikkilä J, Korpi A, Bochicchio D, Pavan GM, Ikkala O, Ras RHA, Kostiainen MA. Crystalline Cyclophane-Protein Cage Frameworks. ACS NANO 2018; 12:8029-8036. [PMID: 30028590 PMCID: PMC6150715 DOI: 10.1021/acsnano.8b02856] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/13/2018] [Indexed: 10/13/2023]
Abstract
Cyclophanes are macrocyclic supramolecular hosts famous for their ability to bind atomic or molecular guests via noncovalent interactions within their well-defined cavities. In a similar way, porous crystalline networks, such as metal-organic frameworks, can create microenvironments that enable controlled guest binding in the solid state. Both types of materials often consist of synthetic components, and they have been developed within separate research fields. Moreover, the use of biomolecules as their structural units has remained elusive. Here, we have synthesized a library of organic cyclophanes and studied their electrostatic self-assembly with biological metal-binding protein cages (ferritins) into ordered structures. We show that cationic pillar[5]arenes and ferritin cages form biohybrid cocrystals with an open protein network structure. Our cyclophane-protein cage frameworks bridge the gap between molecular frameworks and colloidal nanoparticle crystals and combine the versatility of synthetic supramolecular hosts with the highly selective recognition properties of biomolecules. Such host-guest materials are interesting for porous material applications, including water remediation and heterogeneous catalysis.
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Affiliation(s)
- Ngong
Kodiah Beyeh
- HYBER
Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
- Department
of Chemistry and Biochemistry, University
of Windsor, N9B 3P4 Windsor, Canada
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309-4479, United States
| | - Nonappa
- HYBER
Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
| | - Ville Liljeström
- HYBER
Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
| | - Joona Mikkilä
- Department
of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland
| | - Antti Korpi
- Department
of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland
| | - Davide Bochicchio
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, CH-6928 Manno, Switzerland
| | - Giovanni M. Pavan
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, CH-6928 Manno, Switzerland
| | - Olli Ikkala
- HYBER
Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
| | - Robin H. A. Ras
- HYBER
Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
- Department
of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland
| | - Mauri A. Kostiainen
- HYBER
Centre of Excellence, Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
- Department
of Bioproducts and Biosystems, Aalto University, FI-00076 Aalto, Finland
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249
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Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K. Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Angew Chem Int Ed Engl 2018; 57:12400-12404. [DOI: 10.1002/anie.201805565] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/03/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Norifumi Kawakami
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Hiroki Kondo
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Yuki Matsuzawa
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kaoru Hayasaka
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Erika Nasu
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kenji Sasahara
- Department of Applied Biology; Faculty of Textile Science and Technology; Shinshu University; Ueda Nagano 386-8567 Japan
| | - 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
| | - Kenji Miyamoto
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
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250
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Timmermans SBPE, Vervoort DFM, Schoonen L, Nolte RJM, van Hest JCM. Self-Assembly and Stabilization of Hybrid Cowpea Chlorotic Mottle Virus Particles under Nearly Physiological Conditions. Chem Asian J 2018; 13:3518-3525. [PMID: 29975459 DOI: 10.1002/asia.201800842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Capsids of the cowpea chlorotic mottle virus (CCMV) hold great promise for use as nanocarriers in vivo. A major drawback, however, is the lack of stability of the empty wild-type virus particles under physiological conditions. Herein, the assembly behavior and stability under nearly physiological conditions of protein-based block copolymers composed of the CCMV capsid protein and two hydrophobic elastin-like polypeptides are reported. UV/Vis spectroscopy studies, dynamic light-scattering analysis, and TEM measurements demonstrate that both hybrid variants form stable capsids at pH 7.5, physiological NaCl concentration, and 37 °C. The more hydrophobic variant also remains stable in a cell culture medium. These engineered, hybrid CCMV capsid particles can therefore be regarded as suitable candidates for in vivo applications.
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Affiliation(s)
- Suzanne B P E Timmermans
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
| | - Daan F M Vervoort
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
| | - Lise Schoonen
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jan C M van Hest
- Bio-Organic Chemistry research group, Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513 (STO3.41), 5600 MB, Eindhoven, The Netherlands
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