1
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Wang BP, Yin X, Huang MY, Li TY, Long XF, Li Y, Niu FX. A Self-Assembling γPFD-SpyCatcher Hydrogel Scaffold for the Coimmobilization of SpyTag-Enzymes to Facilitate the Catalysis of Regulated Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39194331 DOI: 10.1021/acs.jafc.4c03403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
In this study, a γPFD-SpyCatcher hydrogel scaffold with the capacity for spontaneous assembly was established. With a maximum loading capacity of a 1:1 molar ratio with SpyTag-enzymes, the immobilized proteins can not only rapidly provide pure enzymes but also exhibit improved thermal and pH stability. The results of the transmission electron microscopic analysis and the traits they present indicated that SpyCatcher promotes the aggregation of γPFD and the formation of hydrogels. In the cell-free pyruvate synthesis system, the γPFD-SpyCatcher coimmobilized SpyTag-hexokinase (HK), SpyTag-phosphofructokinase (PFK) and SpyTag-pyruvate kinase (PK) were employed, and the production of pyruvate increased by 43, 78 and 47% respectively. In in vitro experiments, the oxidative deamination activity of glutamate dehydrogenase (GDH) coimmobilized with γPFD-SpyCatcher was 38% higher than that of purified enzymes. These findings indicate that the γPFD-SpyCatcher-based hydrogels play an important role in breaking the barrier of regulatory enzymes and will provide more strategies for the development of synthetic biology.
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Affiliation(s)
- Bei-Ping Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Xue Yin
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Ming-Yue Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Tian-Yan Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Xiu-Feng Long
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Ya Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Fu-Xing Niu
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
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2
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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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3
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Cha HJ, He C, Glover DJ, Xu K, Clark DS. STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii. NANO LETTERS 2024; 24:6078-6083. [PMID: 38723608 PMCID: PMC11117396 DOI: 10.1021/acs.nanolett.4c01043] [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: 03/01/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ∼20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.
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Affiliation(s)
- Hee-Jeong Cha
- Department
of Chemical and Biomolecular Engineering, University of California—Berkeley, Berkeley, California 94720, United States
| | - Changdong He
- Department
of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
| | - Dominic J. Glover
- School
of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ke Xu
- Department
of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department
of Chemical and Biomolecular Engineering, University of California—Berkeley, 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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4
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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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5
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Gad S, Ayakar S. Protein scaffolds: A tool for multi-enzyme assembly. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00670. [PMID: 34824995 PMCID: PMC8605239 DOI: 10.1016/j.btre.2021.e00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
The synthesis of complex molecules using multiple enzymes simultaneously in one reaction vessel has rapidly emerged as a new frontier in the field of bioprocess technology. However, operating different enzymes together in a single vessel limits their operational performance which needs to be addressed. With this respect, scaffolding proteins play an immense role in bringing different enzymes together in a specific manner. The scaffolding improves the catalytic performance, enzyme stability and provides an optimal micro-environment for biochemical reactions. This review describes the components of protein scaffolds, different ways of constructing a protein scaffold-based multi-enzyme complex, and their effects on enzyme kinetics. Moreover, different conjugation strategies viz; dockerin-cohesin interaction, SpyTag-SpyCatcher system, peptide linker-based ligation, affibody, and sortase-mediated ligation are discussed in detail. Various analytical and characterization tools that have enabled the development of these scaffolding strategies are also reviewed. Such mega-enzyme complexes promise wider applications in the field of biotechnology and bioengineering.
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Affiliation(s)
- Shubhada Gad
- Department of Biotechnology, Institute of Chemical Technology - IndianOil Odisha Campus Bhubaneswar, Odisha 751013, India
| | - Sonal Ayakar
- Department of Biotechnology, Institute of Chemical Technology - IndianOil Odisha Campus Bhubaneswar, Odisha 751013, India
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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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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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Fernández-Fernández MR, Sot B, Valpuesta JM. Molecular chaperones: functional mechanisms and nanotechnological applications. NANOTECHNOLOGY 2016; 27:324004. [PMID: 27363314 DOI: 10.1088/0957-4484/27/32/324004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular chaperones are a group of proteins that assist in protein homeostasis. They not only prevent protein misfolding and aggregation, but also target misfolded proteins for degradation. Despite differences in structure, all types of chaperones share a common general feature, a surface that recognizes and interacts with the misfolded protein. This and other, more specialized properties can be adapted for various nanotechnological purposes, by modification of the original biomolecules or by de novo design based on artificial structures.
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Affiliation(s)
- M Rosario Fernández-Fernández
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de la Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
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15
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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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16
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Geometrical assembly of ultrastable protein templates for nanomaterials. Nat Commun 2016; 7:11771. [PMID: 27249579 PMCID: PMC4895442 DOI: 10.1038/ncomms11771] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 04/28/2016] [Indexed: 11/15/2022] Open
Abstract
The fabrication of nanoscale devices requires architectural templates on which to position functional molecules in complex arrangements. Protein scaffolds are particularly promising templates for nanomaterials due to inherent molecular recognition and self-assembly capabilities combined with genetically encoded functionalities. However, difficulties in engineering protein quaternary structure into stable and well-ordered shapes have hampered progress. Here we report the development of an ultrastable biomolecular construction kit for the assembly of filamentous proteins into geometrically defined templates of controllable size and symmetry. The strategy combines redesign of protein–protein interaction specificity with the creation of tunable connector proteins that govern the assembly and projection angles of the filaments. The functionality of these nanoarchitectures is illustrated by incorporation of nanoparticles at specific locations and orientations to create hybrid materials such as conductive nanowires. These new structural components facilitate the manufacturing of nanomaterials with diverse shapes and functional properties over a wide range of processing conditions. Protein nanotechnology for the fabrication of protein-based nanoscale devices is gaining momentum but assembling well-defined three-dimensional shapes is still challenging. Here, the authors use an existing prefoldin assembled system to design a template for the construction of geometrically constrained structures.
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Rother M, Nussbaumer MG, Renggli K, Bruns N. Protein cages and synthetic polymers: a fruitful symbiosis for drug delivery applications, bionanotechnology and materials science. Chem Soc Rev 2016; 45:6213-6249. [DOI: 10.1039/c6cs00177g] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein cages have become essential tools in bionanotechnology due to their well-defined, monodisperse, capsule-like structure. Combining them with synthetic polymers greatly expands their application, giving rise to novel nanomaterials fore.g.drug-delivery, sensing, electronic devices and for uses as nanoreactors.
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Affiliation(s)
- Martin Rother
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Martin G. Nussbaumer
- Wyss Institute for Biologically Inspired Engineering
- Harvard University
- Cambridge
- USA
| | - Kasper Renggli
- Department of Biosystems Science and Engineering
- ETH Zürich
- 4058 Basel
- Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute
- University of Fribourg
- CH-1700 Fribourg
- Switzerland
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Glover DJ, Clark DS. Oligomeric assembly is required for chaperone activity of the filamentous γ-prefoldin. FEBS J 2015; 282:2985-97. [DOI: 10.1111/febs.13341] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/17/2015] [Accepted: 06/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Dominic J. Glover
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley CA USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley CA USA
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Exceptionally stable, redox-active supramolecular protein assemblies with emergent properties. Proc Natl Acad Sci U S A 2014; 111:2897-902. [PMID: 24516140 DOI: 10.1073/pnas.1319866111] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The designed assembly of proteins into well-defined supramolecular architectures not only tests our understanding of protein-protein interactions, but it also provides an opportunity to tailor materials with new physical and chemical properties. Previously, we described that RIDC3, a designed variant of the monomeric electron transfer protein cytochrome cb562, could self-assemble through Zn(2+) coordination into uniform 1D nanotubes or 2D arrays with crystalline order. Here we show that these 1D and 2D RIDC3 assemblies display very high chemical stabilities owing to their metal-mediated frameworks, maintaining their structural order in ≥90% (vol/vol) of several polar organic solvents including tetrahydrofuran (THF) and isopropanol (iPrOH). In contrast, the unassembled RIDC3 monomers denature in ∼30% THF and 50% iPrOH, indicating that metal-mediated self-assembly also leads to considerable stabilization of the individual building blocks. The 1D and 2D RIDC3 assemblies are highly thermostable as well, remaining intact at up to ∼70 °C and ∼90 °C, respectively. The 1D nanotubes cleanly convert into the 2D arrays on heating above 70 °C, a rare example of a thermal crystalline-to-crystalline conversion in a biomolecular assembly. Finally, we demonstrate that the Zn-directed RIDC3 assemblies can be used to spatiotemporally control the templated growth of small Pt(0) nanocrystals. This emergent function is enabled by and absolutely dependent on both the supramolecular assembly of RIDC3 molecules (to form a periodically organized structural template) and their innate redox activities (to direct Pt(2+) reduction).
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Abstract
Nanobio versus Bionano--what's in a name? This special Issue of Biotechnology Journal includes two sections, one featuring articles on nanobio, the other articles on bionano. The editors of the issue, François Baneyx and Je-Kyun Park, discuss the similarities and differences between the two in their editorial.
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