1
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Chen S, Li K, Chen X, Lei S, Lin J, Huang P. Reversibly photoswitchable protein assemblies with collagen affinity for in vivo photoacoustic imaging of tumors. SCIENCE ADVANCES 2024; 10:eadn8274. [PMID: 39213344 PMCID: PMC11364091 DOI: 10.1126/sciadv.adn8274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Recent advancements in photoacoustic (PA) imaging have leveraged reversibly photoswitchable chromophores, known for their dual absorbance states, to enhance imaging sensitivity through differential techniques. Yet, their deployment in tumor imaging has faced obstacles in achieving targeted delivery with high efficiency and specificity. Addressing this challenge, we introduce innovative protein assemblies, DrBphP-CBD, by genetically fusing a photosensory module from Deinococcus radiodurans bacterial phytochrome (DrBphP) with a collagen-binding domain (CBD). These protein assemblies form sub-100-nanometer structures composed of 24 DrBphP dimers and 12 CBD trimers, presenting 24 protein subunits. Their affinity for collagens, combined with impressive photoswitching contrast, markedly improves PA imaging precision. In various tumor models, intravenous administration of DrBphP-CBD has demonstrated enhanced tumor targeting and retention, augmenting contrast in PA imaging by minimizing background noise. This strategy underscores the clinical potential of DrBphP-CBD as PA contrast agents, propelling photoswitchable chromoproteins to the forefront of precise cancer diagnosis.
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Affiliation(s)
| | | | - Xin Chen
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Shan Lei
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
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2
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Au CW, Manfield I, Webb ME, Paci E, Turnbull WB, Ross JF. The Mutagenic Plasticity of the Cholera Toxin B-Subunit Surface Residues: Stability and Affinity. Toxins (Basel) 2024; 16:133. [PMID: 38535799 PMCID: PMC10974167 DOI: 10.3390/toxins16030133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 04/01/2024] Open
Abstract
Mastering selective molecule trafficking across human cell membranes poses a formidable challenge in healthcare biotechnology while offering the prospect of breakthroughs in drug delivery, gene therapy, and diagnostic imaging. The cholera toxin B-subunit (CTB) has the potential to be a useful cargo transporter for these applications. CTB is a robust protein that is amenable to reengineering for diverse applications; however, protein redesign has mostly focused on modifications of the N- and C-termini of the protein. Exploiting the full power of rational redesign requires a detailed understanding of the contributions of the surface residues to protein stability and binding activity. Here, we employed Rosetta-based computational saturation scans on 58 surface residues of CTB, including the GM1 binding site, to analyze both ligand-bound and ligand-free structures to decipher mutational effects on protein stability and GM1 affinity. Complimentary experimental results from differential scanning fluorimetry and isothermal titration calorimetry provided melting temperatures and GM1 binding affinities for 40 alanine mutants among these positions. The results showed that CTB can accommodate diverse mutations while maintaining its stability and ligand binding affinity. These mutations could potentially allow modification of the oligosaccharide binding specificity to change its cellular targeting, alter the B-subunit intracellular routing, or impact its shelf-life and in vivo half-life through changes to protein stability. We anticipate that the mutational space maps presented here will serve as a cornerstone for future CTB redesigns, paving the way for the development of innovative biotechnological tools.
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Affiliation(s)
- Cheuk W. Au
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Iain Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michael E. Webb
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia “Augusto Righi”, Viale Berti Pichat 6/2, 40127 Bologna, Italy
| | - W. Bruce Turnbull
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - James F. Ross
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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3
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Barbosa Pereira PJ, Manso JA, Macedo-Ribeiro S. The structural plasticity of polyglutamine repeats. Curr Opin Struct Biol 2023; 80:102607. [PMID: 37178477 DOI: 10.1016/j.sbi.2023.102607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
From yeast to humans, polyglutamine (polyQ) repeat tracts are found frequently in the proteome and are particularly prominent in the activation domains of transcription factors. PolyQ is a polymorphic motif that modulates functional protein-protein interactions and aberrant self-assembly. Expansion of the polyQ repeated sequences beyond critical physiological repeat length thresholds triggers self-assembly and is linked to severe pathological implications. This review provides an overview of the current knowledge on the structures of polyQ tracts in the soluble and aggregated states and discusses the influence of neighboring regions on polyQ secondary structure, aggregation, and fibril morphologies. The influence of the genetic context of the polyQ-encoding trinucleotides is briefly discussed as a challenge for future endeavors in this field.
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Affiliation(s)
- Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
| | - José A Manso
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
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4
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Notova S, Imberty A. Tuning specificity and topology of lectins through synthetic biology. Curr Opin Chem Biol 2023; 73:102275. [PMID: 36796139 DOI: 10.1016/j.cbpa.2023.102275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/16/2023]
Abstract
Lectins are non-immunoglobulin and non-catalytic glycan binding proteins that are able to decipher the structure and function of complex glycans. They are widely used as biomarkers for following alteration of glycosylation state in many diseases and have application in therapeutics. Controlling and extending lectin specificity and topology is the key for obtaining better tools. Furthermore, lectins and other glycan binding proteins can be combined with additional domains, providing novel functionalities. We provide a view on the current strategy with a focus on synthetic biology approaches yielding to novel specificity, but other novel architectures with novel application in biotechnology or therapy.
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Affiliation(s)
- Simona Notova
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.
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5
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Notova S, Siukstaite L, Rosato F, Vena F, Audfray A, Bovin N, Landemarre L, Römer W, Imberty A. Extending Janus lectins architecture: characterization and application to protocells. Comput Struct Biotechnol J 2022; 20:6108-6119. [DOI: 10.1016/j.csbj.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
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6
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Tobola F, Wiltschi B. One, two, many: Strategies to alter the number of carbohydrate binding sites of lectins. Biotechnol Adv 2022; 60:108020. [PMID: 35868512 DOI: 10.1016/j.biotechadv.2022.108020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022]
Abstract
Carbohydrates are more than an energy-storage. They are ubiquitously found on cells and most proteins, where they encode biological information. Lectins bind these carbohydrates and are essential for translating the encoded information into biological functions and processes. Hundreds of lectins are known, and they are found in all domains of life. For half a century, researchers have been preparing variants of lectins in which the binding sites are varied. In this way, the traits of the lectins such as the affinity, avidity and specificity towards their ligands as well as their biological efficacy were changed. These efforts helped to unravel the biological importance of lectins and resulted in improved variants for biotechnological exploitation and potential medical applications. This review gives an overview on the methods for the preparation of artificial lectins and complexes thereof and how reducing or increasing the number of binding sites affects their function.
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Affiliation(s)
- Felix Tobola
- acib - Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
| | - Birgit Wiltschi
- acib - Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria.
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7
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Danielewicz N, Rosato F, Dai W, Römer W, Turnbull WB, Mairhofer J. Microbial carbohydrate-binding toxins – From etiology to biotechnological application. Biotechnol Adv 2022; 59:107951. [DOI: 10.1016/j.biotechadv.2022.107951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 02/06/2023]
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8
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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9
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Ramberg KO, Guagnini F, Engilberge S, Wrońska MA, Rennie ML, Pérez J, Crowley PB. Segregated Protein-Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons. Chemistry 2021; 27:14619-14627. [PMID: 34432924 PMCID: PMC8596587 DOI: 10.1002/chem.202103025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 12/30/2022]
Abstract
One approach to protein assembly involves water-soluble supramolecular receptors that act like glues. Bionanoarchitectures directed by these scaffolds are often system-specific, with few studies investigating their customization. Herein, the modulation of cucurbituril-mediated protein assemblies through the inclusion of peptide tectons is described. Three peptides of varying length and structural order were N-terminally appended to RSL, a β-propeller building block. Each fusion protein was incorporated into crystalline architectures mediated by cucurbit[7]uril (Q7). A trimeric coiled-coil served as a spacer within a Q7-directed sheet assembly of RSL, giving rise to a layered material of varying porosity. Within the spacer layers, the coiled-coils were dynamic. This result prompted consideration of intrinsically disordered peptides (IDPs) as modulatory tectons. Similar to the coiled-coil, a mussel adhesion peptide (Mefp) also acted as a spacer between protein-Q7 sheets. In contrast, the fusion of a nucleoporin peptide (Nup) to RSL did not recapitulate the sheet assembly. Instead, a Q7-directed cage was adopted, within which disordered Nup peptides were partially "captured" by Q7 receptors. IDP capture occurred by macrocycle recognition of an intrapeptide Phe-Gly motif in which the benzyl group was encapsulated by Q7. The modularity of these protein-cucurbituril architectures adds a new dimension to macrocycle-mediated protein assembly. Segregated protein crystals, with alternating layers of high and low porosity, could provide a basis for new types of materials.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Francesca Guagnini
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Małgorzata A Wrońska
- 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
| | - Javier Pérez
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91192, Gif-sur-Yvette Cedex, France
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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10
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Zapata-Cuellar L, Gaona-Bernal J, Manuel-Cabrera CA, Martínez-Velázquez M, Sánchez-Hernández C, Elizondo-Quiroga D, Camacho-Villegas TA, Gutiérrez-Ortega A. Development of a Platform for Noncovalent Coupling of Full Antigens to Tobacco Etch Virus-Like Particles by Means of Coiled-Coil Oligomerization Motifs. Molecules 2021; 26:molecules26154436. [PMID: 34361589 PMCID: PMC8348948 DOI: 10.3390/molecules26154436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/29/2022] Open
Abstract
Virus-like particles are excellent inducers of the adaptive immune response of humans and are presently being used as scaffolds for the presentation of foreign peptides and antigens derived from infectious microorganisms for subunit vaccine development. The most common approaches for peptide and antigen presentation are translational fusions and chemical coupling, but some alternatives that seek to simplify the coupling process have been reported recently. In this work, an alternative platform for coupling full antigens to virus-like particles is presented. Heterodimerization motifs inserted in both Tobacco etch virus coat protein and green fluorescent protein directed the coupling process by simple mixing, and the obtained complexes were easily taken up by a macrophage cell line.
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Affiliation(s)
- Lorena Zapata-Cuellar
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Unidad de Biotecnología Médica y Farmacéutica, Normalistas 800, Colinas de la Normal, Guadalajara 44270, Mexico; (L.Z.-C.); (C.A.M.-C.); (M.M.-V.); (D.E.-Q.)
| | - Jorge Gaona-Bernal
- Centro Universitario de Ciencias de la Salud, Departamento de Microbiología y Patología, Universidad de Guadalajara, Sierra Mojada 950, Independencia Oriente, Guadalajara 44340, Mexico;
| | - Carlos Alberto Manuel-Cabrera
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Unidad de Biotecnología Médica y Farmacéutica, Normalistas 800, Colinas de la Normal, Guadalajara 44270, Mexico; (L.Z.-C.); (C.A.M.-C.); (M.M.-V.); (D.E.-Q.)
| | - Moisés Martínez-Velázquez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Unidad de Biotecnología Médica y Farmacéutica, Normalistas 800, Colinas de la Normal, Guadalajara 44270, Mexico; (L.Z.-C.); (C.A.M.-C.); (M.M.-V.); (D.E.-Q.)
| | - Carla Sánchez-Hernández
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Departamento de Producción Agrícola, Universidad de Guadalajara, Carretera Guadalajara-Nogales km 15.5, Zapopan 45510, Mexico;
| | - Darwin Elizondo-Quiroga
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Unidad de Biotecnología Médica y Farmacéutica, Normalistas 800, Colinas de la Normal, Guadalajara 44270, Mexico; (L.Z.-C.); (C.A.M.-C.); (M.M.-V.); (D.E.-Q.)
| | - Tanya Amanda Camacho-Villegas
- CONACYT-CIATEJ, Unidad de Biotecnología Médica y Farmacéutica, Normalistas 800, Colinas de la Normal, Guadalajara 44270, Mexico;
| | - Abel Gutiérrez-Ortega
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Unidad de Biotecnología Médica y Farmacéutica, Normalistas 800, Colinas de la Normal, Guadalajara 44270, Mexico; (L.Z.-C.); (C.A.M.-C.); (M.M.-V.); (D.E.-Q.)
- Correspondence:
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11
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Lv C, Zhang X, Liu Y, Zhang T, Chen H, Zang J, Zheng B, Zhao G. Redesign of protein nanocages: the way from 0D, 1D, 2D to 3D assembly. Chem Soc Rev 2021; 50:3957-3989. [PMID: 33587075 DOI: 10.1039/d0cs01349h] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Compartmentalization is a hallmark of living systems. Through compartmentalization, ubiquitous protein nanocages such as viral capsids, ferritin, small heat shock proteins, and DNA-binding proteins from starved cells fulfill a variety of functions, while their shell-like structures hold great promise for various applications in the field of nanomedicine and nanotechnology. However, the number and structure of natural protein nanocages are limited, and these natural protein nanocages may not be suited for a given application, which might impede their further application as nanovehicles, biotemplates or building blocks. To overcome these shortcomings, different strategies have been developed by scientists to construct artificial protein nanocages, and 1D, 2D and 3D protein arrays with protein nanocages as building blocks through genetic and chemical modification to rival the size and functionality of natural protein nanocages. This review outlines the recent advances in the field of the design and construction of artificial protein nanocages and their assemblies with higher order, summarizes the strategies for creating the assembly of protein nanocages from zero-dimension to three dimensions, and introduces their corresponding applications in the preparation of nanomaterials, electrochemistry, and drug delivery. The review will highlight the roles of both the inter-subunit/intermolecular interactions at the key interface and the protein symmetry in constructing and controlling protein nanocage assemblies with different dimensions.
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Affiliation(s)
- Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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12
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Galloway JM, Bray HEV, Shoemark DK, Hodgson LR, Coombs J, Mantell JM, Rose RS, Ross JF, Morris C, Harniman RL, Wood CW, Arthur C, Verkade P, Woolfson DN. De Novo Designed Peptide and Protein Hairpins Self-Assemble into Sheets and Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100472. [PMID: 33590708 DOI: 10.1002/smll.202100472] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 06/12/2023]
Abstract
The design and assembly of peptide-based materials has advanced considerably, leading to a variety of fibrous, sheet, and nanoparticle structures. A remaining challenge is to account for and control different possible supramolecular outcomes accessible to the same or similar peptide building blocks. Here a de novo peptide system is presented that forms nanoparticles or sheets depending on the strategic placement of a "disulfide pin" between two elements of secondary structure that drive self-assembly. Specifically, homodimerizing and homotrimerizing de novo coiled-coil α-helices are joined with a flexible linker to generate a series of linear peptides. The helices are pinned back-to-back, constraining them as hairpins by a disulfide bond placed either proximal or distal to the linker. Computational modeling indicates, and advanced microscopy shows, that the proximally pinned hairpins self-assemble into nanoparticles, whereas the distally pinned constructs form sheets. These peptides can be made synthetically or recombinantly to allow both chemical modifications and the introduction of whole protein cargoes as required.
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Affiliation(s)
- Johanna M Galloway
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Harriet E V Bray
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Lorna R Hodgson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio/Bristol Biodesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Jennifer Coombs
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, HH Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Judith M Mantell
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Ruth S Rose
- School of Biological and Chemical Sciences, Fogg Building, Queen Mary University of London, Mile End Road, London, E1 4QD, UK
| | - James F Ross
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Caroline Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- BrisSynBio/Bristol Biodesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Chemistry, University of Glasgow, 0/1 125 Novar Drive, Glasgow, G12 9TA, UK
| | - Robert L Harniman
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Christopher W Wood
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- BrisSynBio/Bristol Biodesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Biological Sciences, Roger Land Building, King's Buildings, Edinburgh, EH9 3JQ, UK
| | - Christopher Arthur
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio/Bristol Biodesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, 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/Bristol Biodesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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13
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Kim S, Yun J, Yoo H, Kim S, Kim HM, Lee HS. Metal-Mediated Protein Assembly Using a Genetically Incorporated Metal-Chelating Amino Acid. Biomacromolecules 2020; 21:5021-5028. [PMID: 33253537 DOI: 10.1021/acs.biomac.0c01194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many natural proteins function in oligomeric forms, which are critical for their sophisticated functions. The construction of protein assemblies has great potential for biosensors, enzyme catalysis, and biomedical applications. In designing protein assemblies, a critical process is to create protein-protein interaction (PPI) networks at defined sites of a target protein. Although a few methods are available for this purpose, most of them are dependent on existing PPIs of natural proteins to some extent. In this report, a metal-chelating amino acid, 2,2'-bipyridylalanine (BPA), was genetically introduced into defined sites of a monomeric protein and used to form protein oligomers. Depending on the number of BPAs introduced into the protein and the species of metal ions (Ni2+ and Cu2+), dimers or oligomers with different oligomerization patterns were formed by complexation with a metal ion. Oligomer sizes could also be controlled by incorporating two BPAs at different locations with varied angles to the center of the protein. When three BPAs were introduced, the monomeric protein formed a large complex with Ni2+. In addition, when Cu2+ was used for complex formation with the protein containing two BPAs, a linear complex was formed. The method proposed in this report is technically simple and generally applicable to various proteins with interesting functions. Therefore, this method would be useful for the design and construction of functional protein assemblies.
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Affiliation(s)
- Sanggil Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Jeongwon Yun
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunjung Yoo
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Sooin Kim
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
| | - Ho Min Kim
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Biomolecular & Cellular Structure, Institution for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeomro Mapogu, Seoul 121-742, Republic of Korea
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14
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Winter DL, Iranmanesh H, Clark DS, Glover DJ. Design of Tunable Protein Interfaces Controlled by Post-Translational Modifications. ACS Synth Biol 2020; 9:2132-2143. [PMID: 32702241 DOI: 10.1021/acssynbio.0c00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design of protein interaction interfaces is a cornerstone of synthetic biology, where they can be used to promote the association of protein subunits into active molecular complexes or into protein nanostructures. In nature, protein interactions can be modulated by post-translational modifications (PTMs) that modify the protein interfaces with the addition and removal of various chemical groups. PTMs thus represent a means to gain control over protein interactions, yet they have seldom been considered in the design of synthetic proteins. Here, we explore the potential of a reversible PTM, serine phosphorylation, to modulate the interactions between peptides. We designed a series of interacting peptide pairs, including heterodimeric coiled coils, that contained one or more protein kinase A (PKA) recognition motifs. Our set of peptide pairs comprised interactions ranging from nanomolar to micromolar affinities. Mass spectrometry analyses showed that all peptides were excellent phosphorylation substrates of PKA, and subsequent phosphate removal could be catalyzed by lambda protein phosphatase. Binding kinetics measurements performed before and after treatment of the peptides with PKA revealed that phosphorylation of the target serines affected both the association and dissociation rates of the interacting peptides. We observed both the strengthening of interactions (up to an 11-fold decrease in Kd) and the weakening of interactions (up to a 180-fold increase in Kd). De novo-designed PTM-modulated interfaces will be useful to control the association of proteins in biological systems using protein-modifying enzymes, expanding the paradigm of self-assembly to encompass controlled assembly of engineerable protein complexes.
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Affiliation(s)
- Daniel L. Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Hasti Iranmanesh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Dominic J. Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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15
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Alex JM, Brancatelli G, Volpi S, Bonaccorso C, Casnati A, Geremia S, Crowley PB. Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene. Org Biomol Chem 2020; 18:211-214. [DOI: 10.1039/c9ob02275a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to sulfonato-calix[4]arene (sclx4), which mediates close-packed assemblies, the higher charge carboxylate-containing sclx4mc induced a crystalline framework of cytochrome c.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
| | - Giovanna Brancatelli
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Carmela Bonaccorso
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- Catania
- Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
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