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Carloni LE, Bezzu CG, Bonifazi D. Patterning Porous Networks through Self-Assembly of Programmed Biomacromolecules. Chemistry 2019; 25:16179-16200. [PMID: 31491049 DOI: 10.1002/chem.201902576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/11/2019] [Indexed: 11/08/2022]
Abstract
Two-dimensional (2D) porous networks are of great interest for the fabrication of complex organized functional materials for potential applications in nanotechnologies and nanoelectronics. This review aims at providing an overview of bottom-up approaches towards the engineering of 2D porous networks by using biomacromolecules, with a particular focus on nucleic acids and proteins. The first part illustrates how the advancements in DNA nanotechnology allowed for the attainment of complex ordered porous two-dimensional DNA nanostructures, thanks to a biomimetic approach based on DNA molecules self-assembly through specific hydrogen-bond base pairing. The second part focuses the attention on how polypeptides and proteins structural properties could be used to engineer organized networks templating the formation of multifunctional materials. The structural organization of all examples is discussed as revealed by scanning probe microscopy or transmission electron microscopy imaging techniques.
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Affiliation(s)
- Laure-Elie Carloni
- Department of Chemistry and Namur Research College (NARC), University of Namur, Rue de Bruxelles 61, Namur, 5000, Belgium
| | - C Grazia Bezzu
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
| | - Davide Bonifazi
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
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Stel B, Gunkel I, Gu X, Russell TP, De Yoreo JJ, Lingenfelder M. Contrasting Chemistry of Block Copolymer Films Controls the Dynamics of Protein Self-Assembly at the Nanoscale. ACS NANO 2019; 13:4018-4027. [PMID: 30917283 DOI: 10.1021/acsnano.8b08013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biological systems are able to control the assembly and positioning of proteins with nanoscale precision, as exemplified by the intricate molecular structures within cell membranes, virus capsids, and collagen matrices. Controlling the assembly of biomolecules is critical for the use of biomaterials in artificial systems such as antibacterial coatings, engineered tissue samples, and implanted medical devices. Furthermore, understanding the dynamics of protein assembly on heterogeneous templates will ultimately enable the control of protein crystallization in general. Here, we show a biomimetic, hierarchical bottom-up approach to direct the self-assembly of crystalline S-layers through nonspecific interactions with nanostructured block copolymer (BCP) thin-film templates. A comparison between physically and chemically patterned BCP substrates shows that chemical heterogeneity is required to confine the adhesion and self-assembly of S-layers to specific BCP domains. Furthermore, we show that this mechanism can be extended to direct the formation of collagen fibers along the principal direction of the underlying BCP substrate. The dynamics of protein self-assembly at the solid-liquid interface are followed using in situ high-resolution atomic force microscopy under continuous flow conditions, allowing the determination of the rate constants of the self-assembly. A pattern of alternating, chemically distinct nanoscale domains drastically increases the rate of self-assembly compared to non-patterned chemically homogeneous substrates.
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Affiliation(s)
- Bart Stel
- Max Planck-EPFL Lab for Molecular Nanoscience and Technology and Institute of Physics, EPFL , CH-1015 Lausanne , Switzerland
| | - Ilja Gunkel
- Polymer Science and Engineering Department , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Xiaodan Gu
- Polymer Science and Engineering Department , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | - Thomas P Russell
- Polymer Science and Engineering Department , University of Massachusetts at Amherst , Amherst , Massachusetts 01003 , United States
| | | | - Magalí Lingenfelder
- Max Planck-EPFL Lab for Molecular Nanoscience and Technology and Institute of Physics, EPFL , CH-1015 Lausanne , Switzerland
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Jorda J, Leibly DJ, Thompson MC, Yeates TO. Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein. Chem Commun (Camb) 2016; 52:5041-4. [PMID: 26988700 DOI: 10.1039/c6cc00851h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the crystal structure of a novel 60-subunit dodecahedral cage that results from self-assembly of a re-engineered version of a natural protein (PduA) from the Pdu microcompartment shell. Biophysical data illustrate the dependence of assembly on solution conditions, opening up new applications in microcompartment studies and nanotechnology.
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Affiliation(s)
- J Jorda
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
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Zan G, Wu Q. Biomimetic and Bioinspired Synthesis of Nanomaterials/Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:2099-147. [PMID: 26729639 DOI: 10.1002/adma.201503215] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/09/2015] [Indexed: 05/13/2023]
Abstract
In recent years, due to its unparalleled advantages, the biomimetic and bioinspired synthesis of nanomaterials/nanostructures has drawn increasing interest and attention. Generally, biomimetic synthesis can be conducted either by mimicking the functions of natural materials/structures or by mimicking the biological processes that organisms employ to produce substances or materials. Biomimetic synthesis is therefore divided here into "functional biomimetic synthesis" and "process biomimetic synthesis". Process biomimetic synthesis is the focus of this review. First, the above two terms are defined and their relationship is discussed. Next different levels of biological processes that can be used for process biomimetic synthesis are compiled. Then the current progress of process biomimetic synthesis is systematically summarized and reviewed from the following five perspectives: i) elementary biomimetic system via biomass templates, ii) high-level biomimetic system via soft/hard-combined films, iii) intelligent biomimetic systems via liquid membranes, iv) living-organism biomimetic systems, and v) macromolecular bioinspired systems. Moreover, for these five biomimetic systems, the synthesis procedures, basic principles, and relationships are discussed, and the challenges that are encountered and directions for further development are considered.
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Affiliation(s)
- Guangtao Zan
- Department of Chemistry, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092, P. R. China
- School of Materials Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Qingsheng Wu
- Department of Chemistry, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092, P. R. China
- School of Materials Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
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Abstract
At this post-genomic era, the focus of life science research has shifted from life genetic information to general biofunctions. Biomolecular sensors based on QDs will play an important role in the identification and detection of biomolecules.
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Affiliation(s)
| | - Jinzhi Lv
- Shanxi Normal University
- Linfen 041004
- PR China
| | - Yan Li
- Shanxi Normal University
- Linfen 041004
- PR China
| | - Guiqin Yan
- Shanxi Normal University
- Linfen 041004
- PR China
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Raff J, Matys S, Suhr M, Vogel M, Günther T, Pollmann K. S-Layer-Based Nanocomposites for Industrial Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 940:245-279. [PMID: 27677516 DOI: 10.1007/978-3-319-39196-0_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This chapter covers the fundamental aspects of bacterial S-layers: what are S-layers, what is known about them, and what are their main features that makes them so interesting for the production of nanostructures. After a detailed introduction of the paracrystalline protein lattices formed by S-layer systems in nature the chapter explores the engineering of S-layer-based materials. How can S-layers be used to produce "industry-ready" nanoscale bio-composite materials, and which kinds of nanomaterials are possible (e.g., nanoparticle synthesis, nanoparticle immobilization, and multifunctional coatings)? What are the advantages and disadvantages of S-layer-based composite materials? Finally, the chapter highlights the potential of these innovative bacterial biomolecules for future technologies in the fields of metal filtration, catalysis, and bio-functionalization.
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Affiliation(s)
- Johannes Raff
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Helmholtz Institute Freiberg for Resource Technology, 51 01 19, 01314, Dresden, Germany.
| | - Sabine Matys
- Department of Processing, Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, 51 01 19, 01314, Dresden, Germany
| | - Matthias Suhr
- Department of Processing, Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, 51 01 19, 01314, Dresden, Germany
| | - Manja Vogel
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Helmholtz Institute Freiberg for Resource Technology, 51 01 19, 01314, Dresden, Germany
| | - Tobias Günther
- Department of Processing, Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, 51 01 19, 01314, Dresden, Germany
| | - Katrin Pollmann
- Department of Processing, Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, 51 01 19, 01314, Dresden, Germany
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Miao Y, Zhang Z, Gong Y, Zhang Q, Yan G. Self-assembly of manganese doped zinc sulfide quantum dots/CTAB nanohybrids for detection of rutin. Biosens Bioelectron 2014; 52:271-6. [DOI: 10.1016/j.bios.2013.08.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/21/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022]
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Jayaram DT, Shankar BH, Ramaiah D. Photomorphogenesis of γ-globulin: effect on sequential ordering and knock out of gold nanoparticles array. RSC Adv 2013. [DOI: 10.1039/c3ra41844h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Howorka S. Rationally engineering natural protein assemblies in nanobiotechnology. Curr Opin Biotechnol 2011; 22:485-91. [PMID: 21664809 DOI: 10.1016/j.copbio.2011.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/06/2011] [Accepted: 05/10/2011] [Indexed: 01/07/2023]
Abstract
Multimeric protein assemblies are essential components in viruses, bacteria, eukaryotic cells, and organisms where they act as cytoskeletal scaffold, storage containers, or for directional transport. The bottom-up structures can be exploited in nanobiotechnology by harnessing their built-in properties and combining them with new functional modules. This review summarizes the design principles of natural protein assemblies, highlights recent progress in their structural elucidation, and shows how rational engineering can create new biomaterials for applications in vaccine development, biocatalysis, materials science, and synthetic biology.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, University College London, London WC1H 0AJ, UK.
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Kinns H, Badelt-Lichtblau H, Egelseer EM, Sleytr UB, Howorka S. Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus. J Mol Biol 2009; 395:742-53. [PMID: 19836402 DOI: 10.1016/j.jmb.2009.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 10/07/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
Abstract
Surface layer (S-layer) proteins self-assemble into two-dimensional crystalline lattices that cover the cell wall of all archaea and many bacteria. We have generated assembly-negative protein variants of high solubility that will facilitate high-resolution structure determination. Assembly-negative versions of the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 were obtained using an insertion mutagenesis screen. The haemagglutinin epitope tag was inserted at 23 amino acid positions known to be located on the monomer protein surface from a previous cysteine accessibility screen. Limited proteolysis, circular dichroism, and fluorescence were used to probe whether the epitope insertion affected the secondary and tertiary structures of the monomer, while electron microscopy and size-exclusion chromatography were employed to examine proteins' ability to self-assemble. The screen not only identified assembly-compromised mutants with native fold but also yielded correctly folded, self-assembling mutants suitable for displaying epitopes for biomedical and biophysical applications, as well as cryo-electron microscopy imaging. Our study marks an important step in the analysis of the S-layer structure. In addition, the approach of concerted insertion and cysteine mutagenesis can likely be applied for other supramolecular assemblies.
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Affiliation(s)
- Helen Kinns
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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Sharma N, Top A, Kiick K, Pochan D. One-Dimensional Gold Nanoparticle Arrays by Electrostatically Directed Organization Using Polypeptide Self-Assembly. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901621] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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He Y, Wang HF, Yan XP. Self-Assembly of Mn-Doped ZnS Quantum Dots/Octa(3-aminopropyl)octasilsequioxane Octahydrochloride Nanohybrids for Optosensing DNA. Chemistry 2009; 15:5436-40. [DOI: 10.1002/chem.200900432] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sharma N, Top A, Kiick KL, Pochan DJ. One-dimensional gold nanoparticle arrays by electrostatically directed organization using polypeptide self-assembly. Angew Chem Int Ed Engl 2009; 48:7078-82. [PMID: 19691075 PMCID: PMC2796555 DOI: 10.1002/anie.200901621] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Kristi L. Kiick
- Department of Materials Science & Engineering, University of Delaware, 201 DuPont Hall, Newark, DE 19716 (USA), Fax: (+1)302-831-4545
| | - Darrin J. Pochan
- Department of Materials Science & Engineering, University of Delaware, 201 DuPont Hall, Newark, DE 19716 (USA), Fax: (+1)302-831-4545
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Papapostolou D, Howorka S. Engineering and exploiting protein assemblies in synthetic biology. MOLECULAR BIOSYSTEMS 2009; 5:723-32. [DOI: 10.1039/b902440a] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kinge S, Crego-Calama M, Reinhoudt DN. Self-assembling nanoparticles at surfaces and interfaces. Chemphyschem 2008; 9:20-42. [PMID: 18080256 DOI: 10.1002/cphc.200700475] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nanoparticles are the focus of much attention due to their astonishing properties and numerous possibilities for applications in nanotechnology. For realising versatile functions, assembly of nanoparticles in regular patterns on surfaces and at interfaces is required. Assembling nanoparticles generates new nanostructures, which have unforeseen collective, intrinsic physical properties. These properties can be exploited for multipurpose applications in nanoelectronics, spintronics, sensors, etc. This review surveys different techniques, currently employed and being developed, for assembling nanoparticles in to ordered nanostructures. In this endeavour, the principles and methods involved in the development of assemblies are discussed. Subsequently, different possibilities of nanoparticle-based nanostructures, obtained in multi-dimensions, are presented.
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Affiliation(s)
- Sachin Kinge
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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Kinns H, Howorka S. The surface location of individual residues in a bacterial S-layer protein. J Mol Biol 2008; 377:589-604. [PMID: 18262545 DOI: 10.1016/j.jmb.2008.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 12/22/2007] [Accepted: 01/08/2008] [Indexed: 10/22/2022]
Abstract
Bacterial surface layer (S-layer) proteins self-assemble into large two-dimensional crystalline lattices that form the outermost cell-wall component of all archaea and many eubacteria. Despite being a large class of self-assembling proteins, little is known about their molecular architecture. We investigated the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 to identify residues located at the subunit-subunit interface and to determine the S-layer's topology. Twenty-three single cysteine mutants, which were previously mapped to the surface of the SbsB monomer, were subjected to a cross-linking screen using the photoactivatable, sulfhydryl-reactive reagent N-[4-(p-azidosalicylamido)butyl]-3'-(2'-pyridyldithio)propionamide. Gel electrophoretic analysis on the formation of cross-linked dimers indicated that 8 out of the 23 residues were located at the interface. In combination with surface accessibility data for the assembled protein, 10 residues were assigned to positions at the inner, cell-wall-facing lattice surface, while 5 residues were mapped to the outer, ambient-exposed lattice surface. In addition, the cross-linking screen identified six positions of intramolecular cross-linking within the assembled protein but not in the monomeric S-layer protein. Most likely, these intramolecular cross-links result from conformational changes upon self-assembly. The results are an important step toward the further structural elucidation of the S-layer protein via, for example, X-ray crystallography and cryo-electron microscopy. Our approach of identifying the surface location of residues is relevant to other planar supramolecular protein assemblies.
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Affiliation(s)
- Helen Kinns
- Department of Chemistry, University College London, Christopher Ingold Building, 20 Gordon Street, London WC1H 0AJ, England, UK
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Litschauer M, Neouze MA. Nanoparticles connected through an ionic liquid-like network. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b713442h] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Behrens SS. Synthesis of inorganic nanomaterials mediated by protein assemblies. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b806551a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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