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Travaglini L, Lam NT, Sawicki A, Cha HJ, Xu D, Micolich AP, Clark DS, Glover DJ. Fabrication of Electronically Conductive Protein-Heme Nanowires for Power Harvesting. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311661. [PMID: 38597694 DOI: 10.1002/smll.202311661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Electronically conductive protein-based materials can enable the creation of bioelectronic components and devices from sustainable and nontoxic materials, while also being well-suited to interface with biological systems, such as living cells, for biosensor applications. However, as proteins are generally electrical insulators, the ability to render protein assemblies electroactive in a tailorable manner can usher in a plethora of useful materials. Here, an approach to fabricate electronically conductive protein nanowires is presented by aligning heme molecules in proximity along protein filaments, with these nanowires also possessing charge transfer abilities that enable energy harvesting from ambient humidity. The heme-incorporated protein nanowires demonstrate electron transfer over micrometer distances, with conductive atomic force microscopy showing individual nanowires having comparable conductance to other previously characterized heme-based bacterial nanowires. Exposure of multilayer nanowire films to humidity produces an electrical current, presumably through water molecules ionizing carboxyl groups in the filament and creating an unbalanced total charge distribution that is enhanced by the heme. Incorporation of heme and potentially other metal-center porphyrin molecules into protein nanostructures could pave the way for structurally- and electrically-defined protein-based bioelectronic devices.
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Affiliation(s)
- Lorenzo Travaglini
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Nga T Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Artur Sawicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Hee-Jeong Cha
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Adam P Micolich
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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2
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Song CW, Ahn J, Yong I, Kim N, Park CE, Kim S, Chung S, Kim P, Kim I, Chang J. Metallization of Targeted Protein Assemblies in Cell-Derived Extracellular Matrix by Antibody-Guided Biotemplating. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302830. [PMID: 37852942 PMCID: PMC10724409 DOI: 10.1002/advs.202302830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/30/2023] [Indexed: 10/20/2023]
Abstract
Biological systems are composed of hierarchical structures made of a large number of proteins. These structures are highly sophisticated and challenging to replicate using artificial synthesis methods. To exploit these structures in materials science, biotemplating is used to achieve biocomposites that accurately mimic biological structures and impart functionality of inorganic materials, including electrical conductivity. However, the biological scaffolds used in previous studies are limited to stereotypical and simple morphologies with little synthetic diversity because of a lack of control over their morphologies. This study proposes that the specific protein assemblies within the cell-derived extracellular matrix (ECM), whose morphological features are widely tailorable, can be employed as versatile biotemplates. In a typical procedure, a fibrillar assembly of fibronectin-a constituent protein of the ECM-is metalized through an antibody-guided biotemplating approach. Specifically, the antibody-bearing nanogold is attached to the fibronectin through antibody-antigen interactions, and then metals are grown on the nanogold acting as a seed. The biomimetic structure can be adapted for hydrogen production and sensing after improving its electrical conductivity through thermal sintering or additional metal growth. This study demonstrates that cell-derived ECM can be an attractive option for addressing the diversity limitation of a conventional biotemplate.
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Affiliation(s)
- Chang Woo Song
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Jaewan Ahn
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Insung Yong
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Nakhyun Kim
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Chan E Park
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Sein Kim
- Department of Biomedical EngineeringSungkyunkwan University (SKKU)Suwon16419Republic of Korea
| | - Sung‐Yoon Chung
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Pilnam Kim
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Il‐Doo Kim
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
| | - Jae‐Byum Chang
- Department of Materials Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)291 Daehak‐roDaejeon34141Republic of Korea
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3
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Winter DL, Lebhar H, McCluskey JB, Glover DJ. A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates. J Nanobiotechnology 2023; 21:66. [PMID: 36829140 PMCID: PMC9960191 DOI: 10.1186/s12951-023-01817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Protein nanostructures produced through the self-assembly of individual subunits are attractive scaffolds to attach and position functional molecules for applications in biomaterials, metabolic engineering, tissue engineering, and a plethora of nanomaterials. However, the assembly of multicomponent protein nanomaterials is generally a laborious process that requires each protein component to be separately expressed and purified prior to assembly. Moreover, excess components not incorporated into the final assembly must be removed from the solution and thereby necessitate additional processing steps. RESULTS We developed an efficient approach to purify functionalized protein nanostructures directly from bacterial lysates through a type of multimodal chromatography (MMC) that combines size-exclusion, hydrophilic interaction, and ion exchange to separate recombinant protein assemblies from excess free subunits and bacterial proteins. We employed the ultrastable filamentous protein gamma-prefoldin as a material scaffold that can be functionalized with a variety of protein domains through SpyTag/SpyCatcher conjugation chemistry. The purification of recombinant gamma-prefoldin filaments from bacterial lysates using MMC was tested across a wide range of salt concentrations and pH, demonstrating that the MMC resin is robust, however the optimal choice of salt species, salt concentration, and pH is likely dependent on the protein nanostructure to be purified. In addition, we show that pre-processing of the samples with tangential flow filtration to remove nucleotides and metabolites improves resin capacity, and that post-processing with Triton X-114 phase partitioning is useful to remove lipids and any remaining lipid-associated protein. Subsequently, functionalized protein filaments were purified from bacterial lysates using MMC and shown to be free of unincorporated subunits. The assembly and purification of protein filaments with varying amounts of functionalization was confirmed using polyacrylamide gel electrophoresis, Förster resonance energy transfer, and transmission electron microscopy. Finally, we compared our MMC workflow to anion exchange chromatography with the purification of encapsulin nanocompartments containing a fluorescent protein as a cargo, demonstrating the versatility of the protocol and that the purity of the assembly is comparable to more traditional procedures. CONCLUSIONS We envision that the use of MMC will increase the throughput of protein nanostructure prototyping as well as enable the upscaling of the bioproduction of protein nanodevices.
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Affiliation(s)
- Daniel L. Winter
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hélène Lebhar
- grid.1005.40000 0004 4902 0432Recombinant Products Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Joshua B. McCluskey
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dominic J. Glover
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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4
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Sahoo JK, Xu D, Falcucci T, Choi J, Hasturk O, Clark DS, Kaplan DL. Horseradish Peroxidase Catalyzed Silk-Prefoldin Composite Hydrogel Networks. ACS APPLIED BIO MATERIALS 2023; 6:203-208. [PMID: 36580433 DOI: 10.1021/acsabm.2c00836] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein-based hydrogel biomaterials provide a platform for different biological applications, including the encapsulation and stabilization of different biomolecules. These hydrogel properties can be modulated by controlling the design parameters to match specific needs; thus, multicomponent hydrogels have distinct advantages over single-component hydrogels due to their enhanced versatility. Here, silk fibroin and γ-prefoldin chaperone protein based composite hydrogels were prepared and studied. Different ratios of the proteins were chosen, and the hydrogels were prepared by enzyme-assisted cross-linking. The secondary structure of the two proteins, dityrosine bond formation, and mechanical properties were assessed. The results obtained can be used as a platform for the rational design of composite thermostable hydrogel biomaterials to facilitate protection (due to hydrogel mechanics) and retention of bioactivity (e.g., of enzymes and other biomolecules) due to chaperone-like properties of γ-prefoldin.
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Affiliation(s)
- Jugal Kishore Sahoo
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States.,CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Thomas Falcucci
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Jaewon Choi
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Polymer Science and Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Onur Hasturk
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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5
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Lam NT, McCluskey JB, Glover DJ. Harnessing the Structural and Functional Diversity of Protein Filaments as Biomaterial Scaffolds. ACS APPLIED BIO MATERIALS 2022; 5:4668-4686. [PMID: 35766918 DOI: 10.1021/acsabm.2c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The natural ability of many proteins to polymerize into highly structured filaments has been harnessed as scaffolds to align functional molecules in a diverse range of biomaterials. Protein-engineering methodologies also enable the structural and physical properties of filaments to be tailored for specific biomaterial applications through genetic engineering or filaments built from the ground up using advances in the computational prediction of protein folding and assembly. Using these approaches, protein filament-based biomaterials have been engineered to accelerate enzymatic catalysis, provide routes for the biomineralization of inorganic materials, facilitate energy production and transfer, and provide support for mammalian cells for tissue engineering. In this review, we describe how the unique structural and functional diversity in natural and computationally designed protein filaments can be harnessed in biomaterials. In addition, we detail applications of these protein assemblies as material scaffolds with a particular emphasis on applications that exploit unique properties of specific filaments. Through the diversity of protein filaments, the biomaterial engineer's toolbox contains many modular protein filaments that will likely be incorporated as the main structural component of future biomaterials.
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Affiliation(s)
- Nga T Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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6
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Herranz-Montoya I, Park S, Djouder N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 2021; 24:103273. [PMID: 34761191 PMCID: PMC8567396 DOI: 10.1016/j.isci.2021.103273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Prefoldins (PFDNs) are evolutionary conserved co-chaperones, initially discovered in archaea but universally present in eukaryotes. PFDNs are prevalently organized into hetero-hexameric complexes. Although they have been overlooked since their discovery and their functions remain elusive, several reports indicate they act as co-chaperones escorting misfolded or non-native proteins to group II chaperonins. Unlike the eukaryotic PFDNs which interact with cytoskeletal components, the archaeal PFDNs can bind and stabilize a wide range of substrates, possibly due to their great structural diversity. The discovery of the unconventional RPB5 interactor (URI) PFDN-like complex (UPC) suggests that PFDNs have versatile functions and are required for different cellular processes, including an important role in cancer. Here, we summarize their functions across different species. Moreover, a comprehensive analysis of PFDNs genomic alterations across cancer types by using large-scale cancer genomic data indicates that PFDNs are a new class of non-mutated proteins significantly overexpressed in some cancer types.
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Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid 28029, Spain
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7
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Xu D, Lim S, Cao Y, Abad A, Kang AN, Clark DS. Filamentous chaperone protein-based hydrogel stabilizes enzymes against thermal inactivation. Chem Commun (Camb) 2021; 57:5511-5513. [PMID: 33988635 DOI: 10.1039/d1cc01288f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a filamentous chaperone-based protein hydrogel capable of stabilizing enzymes against thermal inactivation. The hydrogel backbone consists of a thermostable chaperone protein, the gamma-prefoldin (γPFD) from Methanocaldococcus jannaschii, which self-assembles into a fibrous structure. Specific coiled-coil interactions engineered into the wildtype γPFD trigger the formation of a cross-linked network of protein filaments. The structure of the filamentous chaperone is preserved through the designed coiled-coil interactions. The resulting hydrogel enables entrapped enzymes to retain greater activity after exposure to high temperatures, presumably by virtue of the inherent chaperone activity of the γPFD.
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Affiliation(s)
- Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Yuhong Cao
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Abner Abad
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Aubrey Nayeon Kang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA. and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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8
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Diamante A, Chaturbedy PK, Rowling PJE, Kumita JR, Eapen RS, McLaughlin SH, de la Roche M, Perez-Riba A, Itzhaki LS. Engineering mono- and multi-valent inhibitors on a modular scaffold. Chem Sci 2021; 12:880-895. [PMID: 33623657 PMCID: PMC7885266 DOI: 10.1039/d0sc03175e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Here we exploit the simple, ultra-stable, modular architecture of consensus-designed tetratricopeptide repeat proteins (CTPRs) to create a platform capable of displaying both single as well as multiple functions and with diverse programmable geometrical arrangements by grafting non-helical short linear binding motifs (SLiMs) onto the loops between adjacent repeats. As proof of concept, we built synthetic CTPRs to bind and inhibit the human tankyrase proteins (hTNKS), which play a key role in Wnt signaling and are upregulated in cancer. A series of mono-valent and multi-valent hTNKS binders was assembled. To fully exploit the modular scaffold and to further diversify the multi-valent geometry, we engineered the binding modules with two different formats, one monomeric and the other trimeric. We show that the designed proteins are stable, correctly folded and capable of binding to and inhibiting the cellular activity of hTNKS leading to downregulation of the Wnt pathway. Multivalency in both the CTPR protein arrays and the hTNKS target results in the formation of large macromolecular assemblies, which can be visualized both in vitro and in the cell. When delivered into the cell by nanoparticle encapsulation, the multivalent CTPR proteins displayed exceptional activity. They are able to inhibit Wnt signaling where small molecule inhibitors have failed to date. Our results point to the tremendous potential of the CTPR platform to exploit a range of SLiMs and assemble synthetic binding molecules with built-in multivalent capabilities and precise, pre-programmed geometries.
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Affiliation(s)
- Aurora Diamante
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Piyush K Chaturbedy
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Pamela J E Rowling
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Janet R Kumita
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Rohan S Eapen
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge Biomedical Campus , Cambridge , CB2 0QH , UK
| | - Marc de la Roche
- Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge CB2 1GA , UK
| | - Albert Perez-Riba
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
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9
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Synthesis and applications of anisotropic nanoparticles with precisely defined dimensions. Nat Rev Chem 2020; 5:21-45. [PMID: 37118104 DOI: 10.1038/s41570-020-00232-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
Shape and size play powerful roles in determining the properties of a material; controlling these aspects with precision is therefore an important, fundamental goal of the chemical sciences. In particular, the introduction of shape anisotropy at the nanoscale has emerged as a potent way to access new properties and functionality, enabling the exploration of complex nanomaterials across a range of applications. Recent advances in DNA and protein nanotechnology, inorganic crystallization techniques, and precision polymer self-assembly are now enabling unprecedented control over the synthesis of anisotropic nanoparticles with a variety of shapes, encompassing one-dimensional rods, dumbbells and wires, two-dimensional and three-dimensional platelets, rings, polyhedra, stars, and more. This has, in turn, enabled much progress to be made in our understanding of how anisotropy and particle dimensions can be tuned to produce materials with unique and optimized properties. In this Review, we bring these recent developments together to critically appraise the different methods for the bottom-up synthesis of anisotropic nanoparticles enabling exquisite control over morphology and dimensions. We highlight the unique properties of these materials in arenas as diverse as electron transport and biological processing, illustrating how they can be leveraged to produce devices and materials with otherwise inaccessible functionality. By making size and shape our focus, we aim to identify potential synergies between different disciplines and produce a road map for future research in this crucial area.
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10
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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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11
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Wi S, Hwang IS, Jo BH. Engineering a Plant Viral Coat Protein for In Vitro Hybrid Self-Assembly of CO2-Capturing Catalytic Nanofilaments. Biomacromolecules 2020; 21:3847-3856. [DOI: 10.1021/acs.biomac.0c00925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Suhan Wi
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Korea
| | - In Seong Hwang
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Korea
| | - Byung Hoon Jo
- Division of Life Science and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
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12
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Xing H, Peng C, Xue Y, Fan Y, Li J, Wang E. In Situ Formed Catalytic Interface for Boosting Chemiluminescence. Anal Chem 2020; 92:10108-10113. [PMID: 32545951 DOI: 10.1021/acs.analchem.0c02112] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Designing the catalytic interface that preferentially attracts reactants is highly desirable for amplifying chemiluminescence (CL) emission. Herein, to boost the generation of reactive oxygen species (ROS) from dissolved O2 molecule, flower-like cobalt hydroxide (f-Co(OH)2) based catalytic interface with hierarchical and porous architecture were in situ created in the coexistence of BSA and Co2+. Benefiting from the oxidase-like catalysis capability and the unique microstructure of f-Co(OH)2, ROS was efficiently produced. Meanwhile, the capping ligands of BSA endowed the interface with the capability of enriching functionality through the interaction between BSA and luminol. 100-fold CL enhancement was achieved using the as-prepared catalytic interface compared with the classical luminol-Co2+ or luminol-BSA system. Moreover, the proposed catalytic amplification mechanism could be extended to the different proteins such as lysozyme, protamine, thrombin, papain. Based on the quenching effect on CL, a sensitive sensing platform was constructed for the determination of ascorbic acid with satisfied results. Our finding provided a novel "all-in-one" route to design the catalytic interface for amplifying CL emission.
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Affiliation(s)
- Huanhuan Xing
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Chao Peng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yuan Xue
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yongchao Fan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jing Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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13
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Chen YX, Ing NL, Wang F, Xu D, Sloan NB, Lam NT, Winter DL, Egelman EH, Hochbaum AI, Clark DS, Glover DJ. Structural Determination of a Filamentous Chaperone to Fabricate Electronically Conductive Metalloprotein Nanowires. ACS NANO 2020; 14:6559-6569. [PMID: 32347705 PMCID: PMC8034818 DOI: 10.1021/acsnano.9b09405] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The transfer of electrons through protein complexes is central to cellular respiration. Exploiting proteins for charge transfer in a controllable fashion has the potential to revolutionize the integration of biological systems and electronic devices. Here we characterize the structure of an ultrastable protein filament and engineer the filament subunits to create electronically conductive nanowires under aqueous conditions. Cryoelectron microscopy was used to resolve the helical structure of gamma-prefoldin, a filamentous protein from a hyperthermophilic archaeon. Conjugation of tetra-heme c3-type cytochromes along the longitudinal axis of the filament created nanowires capable of long-range electron transfer. Electrochemical transport measurements indicated networks of the nanowires capable of conducting current between electrodes at the redox potential of the cytochromes. Functionalization of these highly engineerable nanowires with other molecules, such as redox enzymes, may be useful for bioelectronic applications.
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Affiliation(s)
- Yun X. Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicole L. Ing
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Nancy B. Sloan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Nga T. Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel L. Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Allon I. Hochbaum
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92697, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominic J. Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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14
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Brunette TJ, Bick MJ, Hansen JM, Chow CM, Kollman JM, Baker D. Modular repeat protein sculpting using rigid helical junctions. Proc Natl Acad Sci U S A 2020; 117:8870-8875. [PMID: 32245816 PMCID: PMC7183188 DOI: 10.1073/pnas.1908768117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ∼10-nm-diameter "L" and "V" shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.
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Affiliation(s)
- T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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15
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Peng Z, Peralta MDR, Cox DL, Toney MD. Bottom-up synthesis of protein-based nanomaterials from engineered β-solenoid proteins. PLoS One 2020; 15:e0229319. [PMID: 32084222 PMCID: PMC7034853 DOI: 10.1371/journal.pone.0229319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/02/2020] [Indexed: 02/04/2023] Open
Abstract
Biomolecular self-assembly is an emerging bottom-up approach for the synthesis of novel nanomaterials. DNA and viruses have both been used to create scaffolds but the former lacks chemical diversity and the latter lack spatial control. To date, the use of protein scaffolds to template materials on the nanoscale has focused on amyloidogenic proteins that are known to form fibrils or two-protein systems where a second protein acts as a cross-linker. We previously developed a unique approach for self-assembly of nanomaterials based on engineering β-solenoid proteins (BSPs) to polymerize into micrometer-length fibrils. BSPs have highly regular geometries, tunable lengths, and flat surfaces that are amenable to engineering and functionalization. Here, we present a newly engineered BSP based on the antifreeze protein of the beetle Rhagium inquisitor (RiAFP-m9), which polymerizes into stable fibrils under benign conditions. Gold nanoparticles were used to functionalize the RiAFP-m9 fibrils as well as those assembled from the previously described SBAFP-m1 protein. Cysteines incorporated into the sequences provide site-specific gold attachment. Additionally, silver was deposited on the gold-labelled fibrils by electroless plating to create nanowires. These results bolster prospects for programable self-assembly of BSPs to create scaffolds for functional nanomaterials.
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Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Maria D. R. Peralta
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Daniel L. Cox
- Department of Physics, University of California Davis, Davis, California, United States of America
| | - Michael D. Toney
- Department of Chemistry, University of California Davis, Davis, California, United States of America
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16
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Production of Multicomponent Protein Templates for the Positioning and Stabilization of Enzymes. Methods Mol Biol 2019. [PMID: 31612439 DOI: 10.1007/978-1-4939-9869-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Harnessing the ability of proteins to self-assemble into complex structures has enabled the creation of templates for applications in nanotechnology. Protein templates can be used to position functional molecules in regular patterns with nanometer precision over large surface areas. A difficult but successful approach to building customizable protein templates involves designing novel protein-protein interfaces to join protein building blocks into ordered arrangements. This approach was illustrated recently by engineering the protein interfaces of a molecular chaperone to produce filamentous templates composed of repeating subunits. In this chapter, we describe how these multicomponent protein templates can be produced recombinantly, assembled into filaments, and used as material templates. The templates enable the positioning and alignment of functional molecules at varying distances along the length of the filament, which can be demonstrated using a Förster resonance energy transfer (FRET) assay. In addition, we describe a method to quantify the chaperone ability of these filaments to stabilize and protect other proteins from thermal-induced aggregation-a useful property for bionanotechnology applications that involve molecular scaffolds for positioning and stabilizing enzymes.
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17
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Zottig X, Al-Halifa S, Babych M, Quittot N, Archambault D, Bourgault S. Guiding the Morphology of Amyloid Assemblies by Electrostatic Capping: from Polymorphic Twisted Fibrils to Uniform Nanorods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901806. [PMID: 31268238 DOI: 10.1002/smll.201901806] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Peptides that self-assemble into cross-β-sheet amyloid structures constitute promising building blocks to construct highly ordered proteinaceous materials and nanoparticles. Nevertheless, the intrinsic polymorphism of amyloids and the difficulty of controlling self-assembly currently limit their usage. In this study, the effect of electrostatic interactions on the supramolecular organization of peptide assemblies is investigated to gain insights into the structural basis of the morphological diversities of amyloids. Different charged capping units are introduced at the N-terminus of a potent β-sheet-forming sequence derived from the 20-29 segment of islet amyloid polypeptide, known to self-assemble into polymorphic fibrils. By tuning the charge and the electrostatic strength, different mesoscopic morphologies are obtained, including nanorods, rope-like fibrils, and twisted ribbons. Particularly, the addition of positive capping units leads to the formation of uniform rod-like assemblies, with lengths that can be modulated by the charge number. It is proposed that electrostatic repulsions between N-terminal positive charges hinder β-sheet tape twisting, leading to a unique control over the size of these cytocompatible nanorods by protofilament growth frustration. This study reveals the high susceptibility of amyloid formation to subtle chemical modifications and opens to promising strategies to control the final architecture of proteinaceous assemblies from the peptide sequence.
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Affiliation(s)
- Ximena Zottig
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Soultan Al-Halifa
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Margaryta Babych
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Noé Quittot
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, Québec, H2X 1Y4, Canada
- Swine and Poultry Infectious Diseases Research Center, CRIPA, Québec, J2S 2M2, Canada
| | - Steve Bourgault
- Chemistry Department, Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications PROTEO, Québec, G1V 0A6, Canada
- Swine and Poultry Infectious Diseases Research Center, CRIPA, Québec, J2S 2M2, Canada
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18
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Lim S, Jung GA, Glover DJ, Clark DS. Enhanced Enzyme Activity through Scaffolding on Customizable Self-Assembling Protein Filaments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805558. [PMID: 30920729 DOI: 10.1002/smll.201805558] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Precisely organized enzyme complexes are often found in nature to support complex metabolic reactions in a highly efficient and specific manner. Scaffolding enzymes on artificial materials has thus gained attention as a promising biomimetic strategy to design biocatalytic systems with enhanced productivity. Herein, a versatile scaffolding platform that can immobilize enzymes on customizable nanofibers is reported. An ultrastable self-assembling filamentous protein, the gamma-prefoldin (γ-PFD), is genetically engineered to display an array of peptide tags, which can specifically and stably bind enzymes containing the counterpart domain through simple in vitro mixing. Successful immobilization of proteins along the filamentous template in tunable density is first verified using fluorescent proteins. Then, two different model enzymes, glucose oxidase and horseradish peroxidase, are used to demonstrate that scaffold attachment could enhance the intrinsic catalytic activity of the immobilized enzymes. Considering the previously reported ability of γ-PFD to bind and stabilize a broad range of proteins, the filament's interaction with the bound enzymes may have created a favorable microenvironment for catalysis. It is envisioned that the strategy described here may provide a generally applicable methodology for the scaffolded assembly of multienzymatic complexes for use in biocatalysis.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Gi Ahn Jung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Dominic J Glover
- 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, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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19
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Wright JN, Wong WL, Harvey JA, Garnett JA, Itzhaki LS, Main ERG. Scalable Geometrically Designed Protein Cages Assembled via Genetically Encoded Split Inteins. Structure 2019; 27:776-784.e4. [PMID: 30879889 DOI: 10.1016/j.str.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 01/20/2023]
Abstract
Engineering proteins to assemble into user-defined structures is key in their development for biotechnological applications. However, designing generic rather than bespoke solutions is challenging. Here we describe an expandable recombinant assembly system that produces scalable protein cages via split intein-mediated native chemical ligation. Three types of component are used: two complementary oligomeric "half-cage" protein fusions and an extendable monomeric "linker" fusion. All are composed of modular protein domains chosen to fulfill the required geometries, with two orthogonal pairs of split intein halves to drive assembly when mixed. This combination enables both one-pot construction of two-component cages and stepwise assembly of larger three-component scalable cages. To illustrate the system's versatility, trimeric half-cages and linker constructs comprising consensus-designed repeat proteins were ligated in one-pot and stepwise reactions. Under mild conditions, rapid high-yielding ligations were obtained, from which discrete proteins cages were easily purified and shown to form the desired trigonal bipyramidal structures.
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Affiliation(s)
- James N Wright
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Wan Ling Wong
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Joseph A Harvey
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - James A Garnett
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ewan R G Main
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK.
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20
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Špakova A, Šimoliūnas E, Batiuškaitė R, Pajeda S, Meškys R, Petraitytė-Burneikienė R. Self-Assembly of Tail Tube Protein of Bacteriophage vB_EcoS_NBD2 into Extremely Long Polytubes in E. coli and S. cerevisiae. Viruses 2019; 11:E208. [PMID: 30832262 PMCID: PMC6466441 DOI: 10.3390/v11030208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 01/01/2023] Open
Abstract
Nucleotides, peptides and proteins serve as a scaffold material for self-assembling nanostructures. In this study, the production of siphovirus vB_EcoS_NBD2 (NBD2) recombinant tail tube protein gp39 reached approximately 33% and 27% of the total cell protein level in Escherichia coli and Saccharomyces cerevisiae expression systems, respectively. A simple purification protocol allowed us to produce a recombinant gp39 protein with 85%⁻90% purity. The yield of gp39 was 2.9 ± 0.36 mg/g of wet E. coli cells and 0.85 ± 0.33 mg/g for S. cerevisiae cells. The recombinant gp39 self-assembled into well-ordered tubular structures (polytubes) in vivo in the absence of other phage proteins. The diameter of these structures was the same as the diameter of the tail of phage NBD2 (~12 nm). The length of these structures varied from 0.1 µm to >3.95 µm, which is 23-fold the normal NBD2 tail length. Stability analysis demonstrated that the polytubes could withstand various chemical and physical conditions. These polytubes show the potential to be used as a nanomaterial in various fields of science.
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Affiliation(s)
- Aliona Špakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Eugenijus Šimoliūnas
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Raminta Batiuškaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Simonas Pajeda
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Rolandas Meškys
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Rasa Petraitytė-Burneikienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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21
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Controlled Assembly of the Filamentous Chaperone Gamma-Prefoldin into Defined Nanostructures. Methods Mol Biol 2019; 1798:293-306. [PMID: 29868968 DOI: 10.1007/978-1-4939-7893-9_22] [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] [Indexed: 04/25/2023]
Abstract
Self-assembling protein templates have enormous potential for the fabrication of multifunctional nanostructures that require precise positioning of individual molecules, such as enzymes and inorganic moieties, in regular patterns. A recently described approach uses ultrastable filaments composed of the gamma-prefoldin (γPFD) protein and engineered connector proteins to construct novel architectures useful for basic research and practical applications in nanobiotechnology. Here we describe the production of the γPFD and connector proteins from E. coli, and the assembly of γPFD with connector proteins into macromolecular structures with defined shapes.
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22
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Affiliation(s)
- Dominic J. Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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23
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Lim S, Jung GA, Muckom RJ, Glover DJ, Clark DS. Engineering bioorthogonal protein-polymer hybrid hydrogel as a functional protein immobilization platform. Chem Commun (Camb) 2019; 55:806-809. [PMID: 30574651 PMCID: PMC6370476 DOI: 10.1039/c8cc08720b] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate the synthesis of protein-polymer hybrid hydrogel that can be used as a platform for immobilizing functional proteins. Orthogonal chemistry was employed for cross-linking the hybrid network and conjugating proteins to the gel backbone, allowing for the convenient, one-pot formation of a functionalized hydrogel. The resulting hydrogel had tunable mechanical properties, was stable in solution, and biocompatible.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
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24
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The Robust Self-Assembling Tubular Nanostructures Formed by gp053 from Phage vB_EcoM_FV3. Viruses 2019; 11:v11010050. [PMID: 30641882 PMCID: PMC6357053 DOI: 10.3390/v11010050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 02/02/2023] Open
Abstract
The recombinant phage tail sheath protein, gp053, from Escherichia coli infecting myovirus vB_EcoM_FV3 (FV3) was able to self-assemble into long, ordered and extremely stable tubular structures (polysheaths) in the absence of other viral proteins. TEM observations revealed that those protein nanotubes varied in length (~10–1000 nm). Meanwhile, the width of the polysheaths (~28 nm) corresponded to the width of the contracted tail sheath of phage FV3. The formed protein nanotubes could withstand various extreme treatments including heating up to 100 °C and high concentrations of urea. To determine the shortest variant of gp053 capable of forming protein nanotubes, a set of N- or/and C-truncated as well as poly-His-tagged variants of gp053 were constructed. The TEM analysis of these mutants showed that up to 25 and 100 amino acid residues could be removed from the N and C termini, respectively, without disturbing the process of self-assembly. In addition, two to six copies of the gp053 encoding gene were fused into one open reading frame. All the constructed oligomers of gp053 self-assembled in vitro forming structures of different regularity. By using the modification of cysteines with biotin, the polysheaths were tested for exposed thiol groups. Polysheaths formed by the wild-type gp053 or its mutants possess physicochemical properties, which are very attractive for the construction of self-assembling nanostructures with potential applications in different fields of nanosciences.
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25
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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26
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Abstract
Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Douglas S Clark
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA.
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27
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Glover DJ, Lim S, Xu D, Sloan NB, Zhang Y, Clark DS. Assembly of Multicomponent Protein Filaments Using Engineered Subunit Interfaces. ACS Synth Biol 2018; 7:2447-2456. [PMID: 30234970 DOI: 10.1021/acssynbio.8b00241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Exploiting the ability of proteins to self-assemble into architectural templates may provide novel routes for the positioning of functional molecules in nanotechnology. Here we report the engineering of multicomponent protein templates composed of distinct monomers that assemble in repeating orders into a dynamic functional structure. This was achieved by redesigning the protein-protein interfaces of a molecular chaperone with helical sequences to create unique subunits that assemble through orthogonal coiled-coils into filaments up to several hundred nanometers in length. Subsequently, it was demonstrated that functional proteins could be fused to the subunits to achieve ordered alignment along filaments. Importantly, the multicomponent filaments had molecular chaperone activity and could prevent other proteins from thermal-induced aggregation, a potentially useful property for the scaffolding of enzymes. The design in this work is presented as proof-of-concept for the creation of modular templates that could potentially be used to position functional molecules, stabilize other proteins such as enzymes, and enable controlled assembly of nanostructures with unique topologies.
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Affiliation(s)
- Dominic J. Glover
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Nancy B. Sloan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ye Zhang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - 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
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Walsh TR, Knecht MR. Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials. Chem Rev 2017; 117:12641-12704. [DOI: 10.1021/acs.chemrev.7b00139] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Marc R. Knecht
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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Freeman A. Protein-Mediated Biotemplating on the Nanoscale. Biomimetics (Basel) 2017; 2:E14. [PMID: 31105177 PMCID: PMC6352702 DOI: 10.3390/biomimetics2030014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/18/2017] [Accepted: 08/01/2017] [Indexed: 12/26/2022] Open
Abstract
Purified proteins offer a homogeneous population of biological nanoparticles, equipped in many cases with specific binding sites enabling the directed self-assembly of envisaged one-, two- or three-dimensional arrays. These arrays may serve as nanoscale biotemplates for the preparation of novel functional composite materials, which exhibit potential applications, especially in the fields of nanoelectronics and optical devices. This review provides an overview of the field of protein-mediated biotemplating, focussing on achievements made throughout the past decade. It is comprised of seven sections designed according to the size and configuration of the protein-made biotemplate. Each section describes the design and size of the biotemplate, the resulting hybrid structures, the fabrication methodology, the analytical tools employed for the structural analysis of the hybrids obtained, and, finally, their claimed/intended applications and a feasibility demonstration (whenever available). In conclusion, a short assessment of the overall status of the achievements already made vs. the future challenges of this field is provided.
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Affiliation(s)
- Amihay Freeman
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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Abstract
Emerging protein design strategies are enabling the creation of diverse, self-assembling supramolecular structures with precision on the atomic scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally symmetric, and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications. For certain design approaches, a complete list of allowable symmetry combinations that can be used for construction has been articulated, opening a path to a rich diversity of geometrically defined protein materials. Future challenges include improving and elaborating on current strategies and endowing designed protein nanomaterials with properties useful in nanomedicine and material science applications.
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Affiliation(s)
- Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095.,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095;
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31
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Yeates TO, Liu Y, Laniado J. The design of symmetric protein nanomaterials comes of age in theory and practice. Curr Opin Struct Biol 2016; 39:134-143. [DOI: 10.1016/j.sbi.2016.07.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/02/2016] [Accepted: 07/03/2016] [Indexed: 12/25/2022]
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Glover DJ, Clark DS. Protein Calligraphy: A New Concept Begins To Take Shape. ACS CENTRAL SCIENCE 2016; 2:438-444. [PMID: 27504490 PMCID: PMC4965849 DOI: 10.1021/acscentsci.6b00067] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Indexed: 05/30/2023]
Abstract
The ability to assemble molecules into supramolecular architectures of controllable size and symmetry is a long sought after goal of nanotechnology and material engineering. Proteins are particularly attractive for molecular assembly due to their inherent molecular recognition and self-assembly capabilities. Advances in the computational prediction of protein folding and quaternary assembly have enabled the design of proteins that self-assemble into complex yet predictable shapes. These protein nanostructures are opening new possibilities in biomaterials, metabolic engineering, molecular delivery, tissue engineering, and a plethora of nanomaterials. Images of protein constructs assembled from simpler structures draw comparison to characters of calligraphy. In both cases, elaborate designs emerge from basic subunits, resulting in the translation of form into function with a high degree of artistry.
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