1
|
Liu B, Li X, Zhang JP, Li X, Yuan Y, Hou GH, Zhang HJ, Zhang H, Li Y, Mezzenga R. Protein Nanotubes as Advanced Material Platforms and Delivery Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307627. [PMID: 37921269 DOI: 10.1002/adma.202307627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/22/2023] [Indexed: 11/04/2023]
Abstract
Protein nanotubes (PNTs) as state-of-the-art nanocarriers are promising for various potential applications both in the food and pharmaceutical industries. Derived from edible starting sources like α-lactalbumin, lysozyme, and ovalbumin, PNTs bear properties of biocompatibility and biodegradability. Their large specific surface area and hydrophobic core facilitate chemical modification and loading of bioactive substances, respectively. Moreover, their enhanced permeability and penetration ability across biological barriers such as intestinal mucus, extracellular matrix, and thrombus clot, make it promising platforms for health-related applications. Most importantly, their simple preparation processes enable large-scale production, supporting applications in the biomedical and nanotechnological fields. Understanding the self-assembly principles is crucial for controlling their morphology, size, and shape, and thus provides the ground to a multitude of applications. Here, the current state-of-the-art of PNTs including their building materials, physicochemical properties, and self-assembly mechanisms are comprehensively reviewed. The advantages and limitations, as well as challenges and prospects for their successful applications in biomaterial and pharmaceutical sectors are then discussed and highlighted. Potential cytotoxicity of PNTs and the need of regulations as critical factors for enabling in vivo applications are also highlighted. In the end, a brief summary and future prospects for PNTs as advanced platforms and delivery systems are included.
Collapse
Affiliation(s)
- Bin Liu
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
- Department of Nutrition and Health, China Agricultural University, Beijing, 100091, P. R. China
| | - Xing Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Ji Peng Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xin Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Yu Yuan
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Guo Hua Hou
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Hui Juan Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Hui Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Yuan Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich, Zürich, 8092, Switzerland
- Department of Materials, ETH Zurich, Zürich, 8092, Switzerland
| |
Collapse
|
2
|
Kikuchi K, Date K, Ueno T. Design of a Hierarchical Assembly at a Solid-Liquid Interface Using an Asymmetric Protein Needle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2389-2397. [PMID: 36734675 DOI: 10.1021/acs.langmuir.2c03146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Design and control of processes for a hierarchical assembly of proteins remain challenging because it requires consideration of design principles with atomic-level accuracy. Previous studies have adopted symmetry-based strategies to minimize the complexity of protein-protein interactions and this has placed constraints on the structures of the resulting protein assemblies. In the present work, we used an anisotropic-shaped protein needle, gene product 5 (gp5) from bacteriophage T4 with a C-terminal hexahistidine-tag (His-tag) (gp5_CHis), to construct a hierarchical assembly with two distinct protein-protein interaction sites. High-speed atomic force microscopy (HS-AFM) measurements reveal that it forms unique tetrameric clusters through its N-terminal head on a mica surface. The clusters further self-assemble into a monolayer through the C-terminal His-tag. The HS-AFM images and displacement analyses show that the monolayer is a network-like structure rather than a crystalline lattice. Our results expand the toolbox for constructing hierarchical protein assemblies based on structural anisotropy.
Collapse
Affiliation(s)
- Kosuke Kikuchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Koki Date
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| |
Collapse
|
3
|
Kobayashi N, Arai R. Protein Cages and Nanostructures Constructed from Protein Nanobuilding Blocks. Methods Mol Biol 2023; 2671:79-94. [PMID: 37308639 DOI: 10.1007/978-1-0716-3222-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein cages and nanostructures are promising biocompatible medical materials, such as vaccines and drug carriers. Recent advances in designed protein nanocages and nanostructures have opened up cutting-edge applications in the fields of synthetic biology and biopharmaceuticals. A simple approach for constructing self-assembling protein nanocages and nanostructures is the design of a fusion protein composed of two different proteins forming symmetric oligomers. In this chapter, we describe the design and methods of protein nanobuilding blocks (PN-Blocks) using a dimeric de novo protein WA20 to construct self-assembling protein cages and nanostructures. A protein nanobuilding block (PN-Block), WA20-foldon, was developed by fusing an intermolecularly folded dimeric de novo protein WA20 and a trimeric foldon domain from bacteriophage T4 fibritin. The WA20-foldon self-assembled into several oligomeric nanoarchitectures in multiples of 6-mer. De novo extender protein nanobuilding blocks (ePN-Blocks) were also developed by fusing tandemly two WA20 with various linkers, to construct self-assembling cyclized and extended chain-like nanostructures. These PN-Blocks would be useful for the construction of self-assembling protein cages and nanostructures and their potential applications in the future.
Collapse
Affiliation(s)
- Naoya Kobayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Ueda, Nagano, Japan.
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, Japan.
| |
Collapse
|
4
|
Maity B, Taher M, Mazumdar S, Ueno T. Artificial metalloenzymes based on protein assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Kikuchi K, Fukuyama T, Uchihashi T, Furuta T, Maeda YT, Ueno T. Protein Needles Designed to Self-Assemble through Needle Tip Engineering. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106401. [PMID: 34989115 DOI: 10.1002/smll.202106401] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/01/2021] [Indexed: 06/14/2023]
Abstract
The dynamic process of formation of protein assemblies is essential to form highly ordered structures in biological systems. Advances in structural and synthetic biology have led to the construction of artificial protein assemblies. However, development of design strategies exploiting the anisotropic shape of building blocks of protein assemblies has not yet been achieved. Here, the 2D assembly pattern of protein needles (PNs) is controlled by regulating their tip-to-tip interactions. The PN is an anisotropic needle-shaped protein composed of β-helix, foldon, and His-tag. Three different types of tip-modified PNs are designed by deleting the His-tag and foldon to change the protein-protein interactions. Observing their assembly by high-speed atomic force microscopy (HS-AFM) reveals that PN, His-tag deleted PN, and His-tag and foldon deleted PN form triangular lattices, the monomeric state with nematic order, and fiber assemblies, respectively, on a mica surface. Their assembly dynamics are observed by HS-AFM and analyzed by the theoretical models. Monte Carlo (MC) simulations indicate that the mica-PN interactions and the flexible and multipoint His-tag interactions cooperatively guide the formation of the triangular lattice. This work is expected to provide a new strategy for constructing supramolecular protein architectures by controlling directional interactions of anisotropic shaped proteins.
Collapse
Affiliation(s)
- Kosuke Kikuchi
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Tatsuya Fukuyama
- Department of Physics, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Higashiyama 5-1, Myodaiji, Okazaki, 444-0864, Japan
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan
| |
Collapse
|
6
|
Nguyen QD, Kikuchi K, Kojima M, Ueno T. Dynamic Behavior of Cargo Proteins Regulated by Linker Peptides on a Protein Needle Scaffold. CHEM LETT 2022. [DOI: 10.1246/cl.210599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Que D. Nguyen
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, 4529-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Kikuchi
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, 4529-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Mariko Kojima
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, 4529-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takafumi Ueno
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, 4529-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| |
Collapse
|
7
|
Genome sequence analysis of Cronobacter phage PF-CE2 and proposal of a new species in the genus Pseudotevenvirus. Arch Virol 2021; 166:3467-3472. [PMID: 34601635 DOI: 10.1007/s00705-021-05255-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
The genome of a Cronobacter sakazakii M1 phage named PF-CE2 was characterized in this work, and a new species named "Cronobacter virus PF-CE2", in the genus Pseudotevenvirus of the subfamily Tevenvirinae of the family Myoviridae is proposed. The Gp190 gene of phage PF-CE2 is predicted to encode a bacteriophage-borne glycanase that is capable of degrading fucose-containing exopolysaccharides produced by C. sakazakii M1. Furthermore, we propose changing the taxonomic status of eight additional phages based on nucleotide sequence comparisons. This work provides a theoretical basis for subsequent heterologous expression of the phage PF-CE2 glycanase and provides an important reference for the preservation and sharing of these phages.
Collapse
|
8
|
Dhanker R, Hussain T, Tyagi P, Singh KJ, Kamble SS. The Emerging Trend of Bio-Engineering Approaches for Microbial Nanomaterial Synthesis and Its Applications. Front Microbiol 2021; 12:638003. [PMID: 33796089 PMCID: PMC8008120 DOI: 10.3389/fmicb.2021.638003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Micro-organisms colonized the world before the multi-cellular organisms evolved. With the advent of microscopy, their existence became evident to the mankind and also the vast processes they regulate, that are in direct interest of the human beings. One such process that intrigued the researchers is the ability to grow in presence of toxic metals. The process seemed to be simple with the metal ions being sequestrated into the inclusion bodies or cell surfaces enabling the conversion into nontoxic nanostructures. However, the discovery of genome sequencing techniques highlighted the genetic makeup of these microbes as a quintessential aspect of these phenomena. The findings of metal resistance genes (MRG) in these microbes showed a rather complex regulation of these processes. Since most of these MRGs are plasmid encoded they can be transferred horizontally. With the discovery of nanoparticles and their many applications from polymer chemistry to drug delivery, the demand for innovative techniques of nanoparticle synthesis increased dramatically. It is now established that microbial synthesis of nanoparticles provides numerous advantages over the existing chemical methods. However, it is the explicit use of biotechnology, molecular biology, metabolic engineering, synthetic biology, and genetic engineering tools that revolutionized the world of microbial nanotechnology. Detailed study of the micro and even nanolevel assembly of microbial life also intrigued biologists and engineers to generate molecular motors that mimic bacterial flagellar motor. In this review, we highlight the importance and tremendous hidden potential of bio-engineering tools in exploiting the area of microbial nanoparticle synthesis. We also highlight the application oriented specific modulations that can be done in the stages involved in the synthesis of these nanoparticles. Finally, the role of these nanoparticles in the natural ecosystem is also addressed.
Collapse
Affiliation(s)
- Raunak Dhanker
- Department of Basic and Applied Sciences, School of Engineering and Sciences, GD Goenka University, Gurugram, India
| | - Touseef Hussain
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Priyanka Tyagi
- Department of Basic and Applied Sciences, School of Engineering and Sciences, GD Goenka University, Gurugram, India
| | - Kawal Jeet Singh
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Shashank S. Kamble
- Department of Basic and Applied Sciences, School of Engineering and Sciences, GD Goenka University, Gurugram, India
| |
Collapse
|
9
|
The Versatile Manipulations of Self-Assembled Proteins in Vaccine Design. Int J Mol Sci 2021; 22:ijms22041934. [PMID: 33669238 PMCID: PMC7919822 DOI: 10.3390/ijms22041934] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Abstract
Protein assemblies provide unique structural features which make them useful as carrier molecules in biomedical and chemical science. Protein assemblies can accommodate a variety of organic, inorganic and biological molecules such as small proteins and peptides and have been used in development of subunit vaccines via display parts of viral pathogens or antigens. Such subunit vaccines are much safer than traditional vaccines based on inactivated pathogens which are more likely to produce side-effects. Therefore, to tackle a pandemic and rapidly produce safer and more effective subunit vaccines based on protein assemblies, it is necessary to understand the basic structural features which drive protein self-assembly and functionalization of portions of pathogens. This review highlights recent developments and future perspectives in production of non-viral protein assemblies with essential structural features of subunit vaccines.
Collapse
|
10
|
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.
Collapse
|
11
|
Cai Y, Yu Q, Zhao H. Electrostatic assisted fabrication and dissociation of multi-component proteinosomes. J Colloid Interface Sci 2020; 576:90-98. [PMID: 32408164 DOI: 10.1016/j.jcis.2020.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 01/17/2023]
Abstract
Self-assembly of proteins into well-organized proteinosomes has attracted great interest due to the potential medical and biological applications of the structures. Herein, a new concept of electrostatic assisted fabrication of proteinosomes is proposed. The self-assembly is performed by using multi-step dialysis approach, where negatively charged bovine serum albumin-poly(N-isopropylacrylamide) (BSA-PNIPAM) bioconjugate and positively charged enzyme (lysozyme or trypsin) are initially dissolved in phosphate buffer (PB) solution at a high salt concentration, and subsequently the protein solution is dialyzed against PB solutions at low salt concentrations, resulting in the formation of biofunctional proteinosomes. Transmission electron microscopy (TEM), cryo-TEM and light scattering results all demonstrate the formation of hollow structures. The wall of a proteinosome is composed of BSA and enzyme (lysozyme or trypsin), and PNIPAM chains of the bioconjugate are in the corona stabilizing the structure. In comparison with the native enzymes, the enzyme molecules in the assemblies basically retain their bioactivities. The proteinosomes formed by BSA-PNIPAM and lysozyme can be dissociated in the presence of trypsin, and those self-assembled by BSA-PNIPAM and trypsin are able to be self-hydrolyzed, resulting in the dissociation of the structures in aqueous solution. The size and morphology changes of the proteinosomes in the hydrolysis are studied.
Collapse
Affiliation(s)
- Yaqian Cai
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Qianyu Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Hanying Zhao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China.
| |
Collapse
|
12
|
Ueno T, Niwase K, Tsubokawa D, Kikuchi K, Takai N, Furuta T, Kawano R, Uchihashi T. Dynamic behavior of an artificial protein needle contacting a membrane observed by high-speed atomic force microscopy. NANOSCALE 2020; 12:8166-8173. [PMID: 32239053 DOI: 10.1039/d0nr01121e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacteriophage T4 and other bacteriophages have a protein component known as a molecular needle which is used for the transmembrane reaction in the infection process. In this paper, the transmembrane reaction mechanisms of artificial protein needles (PNs) constructed by protein engineering of the component protein of bacteriophage T4 are elucidated by observation of single-molecules by high-speed atomic force microscopy (HS-AFM) and molecular dynamics (MD) simulations. The HS-AFM images indicate that the tip of the needle structure stabilizes the interaction of the needle with the membrane surface and is involved in controlling the contact angle and angular velocity with respect to the membrane. The MD simulations indicate that the dynamic behavior of PN is governed by hydrogen bonds between the membrane phosphate fragments and the tip. Moreover, quartz crystal microbalance (QCM) and electrophysiological experiments indicate that the tip structure of PN affects its kinetic behavior and membrane potential. These results demonstrate that protein assemblies derived from natural biosupramolecules can be used to create nanomaterials with rationally-designed functionality.
Collapse
Affiliation(s)
- Takafumi Ueno
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
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.
Collapse
|
14
|
Hyodo F, Sho T, Maity B, Fujita K, Tachibana Y, Akashi S, Mano M, Hishikawa Y, Matsuo M, Ueno T. Photoinduced in Vivo Magnetic Resonance Imaging (MRI) with Rapid CO Release from an MnCO‐Protein Needle Composite. Chemistry 2018; 24:11578-11583. [DOI: 10.1002/chem.201802445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Fuminori Hyodo
- Innovation Center for Medical Redox NavigationKyushu University 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
- Department of radiologySchool of MedicineGifu University 1-1 Yanagido Gifu 501-1194 Japan
| | - Takeya Sho
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Basudev Maity
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Kenta Fujita
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Yoko Tachibana
- Innovation Center for Medical Redox NavigationKyushu University 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Satoko Akashi
- Graduate School of Medical Life ScienceYokohama City University 1-7-29 Suehiro-cho, Tsurumi-ku Yokohama Kanagawa 230-0045 Japan
| | - Megumi Mano
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Yuki Hishikawa
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| | - Masayuki Matsuo
- Department of radiologySchool of MedicineGifu University 1-1 Yanagido Gifu 501-1194 Japan
| | - Takafumi Ueno
- School of Life Science and TechnologyTokyo Institute of Technology B55-4259 Nagatsuta-cho Midori-ku Yokohama 226-8501 Japan
| |
Collapse
|
15
|
Hall D, Takagi J, Nakamura H. Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday. Biophys Rev 2018; 10:105-129. [PMID: 29500796 PMCID: PMC5899743 DOI: 10.1007/s12551-018-0401-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.
Collapse
Affiliation(s)
- Damien Hall
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
- Research School of Chemistry, Australian National University, Acton, ACT 2601 Australia
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
| |
Collapse
|
16
|
Inaba H, Ueno T. Artificial bio-nanomachines based on protein needles derived from bacteriophage T4. Biophys Rev 2017; 10:641-658. [PMID: 29147941 DOI: 10.1007/s12551-017-0336-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
Bacteriophage T4 is a natural bio-nanomachine which achieves efficient infection of host cells via cooperative motion of specific three-dimensional protein architectures. The relationships between the protein structures and their dynamic functions have recently been clarified. In this review we summarize the design principles for fabrication of nanomachines using the component proteins of bacteriophage T4 based on these recent advances. We focus on the protein needle known as gp5, which is located at the center of the baseplate at the end of the contractile tail of bacteriophage T4. This protein needle plays a critical role in directly puncturing host cells, and analysis has revealed that it contains a common motif used for cell puncture in other known injection systems, such as T6SS. Our artificial needle based on the β-helical domain of gp5 retains the ability to penetrate cells and can be engineered to deliver various cargos into living cells. Thus, the unique components of bacteriophage T4 and other natural nanomachines have great potential for use as molecular scaffolds in efforts to fabricate new bio-nanomachines.
Collapse
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
| |
Collapse
|
17
|
Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 500] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
Collapse
Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| |
Collapse
|
18
|
Maity B, Ueno T. Design of Bioinorganic Materials at the Interface of Coordination and Biosupramolecular Chemistry. CHEM REC 2016; 17:383-398. [PMID: 28028896 DOI: 10.1002/tcr.201600122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Indexed: 12/22/2022]
Abstract
Protein assemblies have recently become known as potential molecular scaffolds for applications in materials science and bio-nanotechnology. Efforts to design protein assemblies for construction of protein-based hybrid materials with metal ions, metal complexes, nanomaterials and proteins now represent a growing field with a common aim of providing novel functions and mimicking natural functions. However, the important roles of protein assemblies in coordination and biosupramolecular chemistry have not been systematically investigated and characterized. In this personal account, we focus on our recent progress in rational design of protein assemblies using bioinorganic chemistry for (1) exploration of unnatural reactions, (2) construction of functional protein architectures, and (3) in vivo applications.
Collapse
Affiliation(s)
- Basudev Maity
- Department of Life Science anad Technology, Tokyo Institute of Technology, B55-Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Takafumi Ueno
- Department of Life Science anad Technology, Tokyo Institute of Technology, B55-Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| |
Collapse
|
19
|
Karimi M, Mirshekari H, Moosavi Basri SM, Bahrami S, Moghoofei M, Hamblin MR. Bacteriophages and phage-inspired nanocarriers for targeted delivery of therapeutic cargos. Adv Drug Deliv Rev 2016; 106:45-62. [PMID: 26994592 PMCID: PMC5026880 DOI: 10.1016/j.addr.2016.03.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 02/08/2023]
Abstract
The main goal of drug delivery systems is to target therapeutic cargoes to desired cells and to ensure their efficient uptake. Recently a number of studies have focused on designing bio-inspired nanocarriers, such as bacteriophages, and synthetic carriers based on the bacteriophage structure. Bacteriophages are viruses that specifically recognize their bacterial hosts. They can replicate only inside their host cell and can act as natural gene carriers. Each type of phage has a particular shape, a different capacity for loading cargo, a specific production time, and their own mechanisms of supramolecular assembly, that have enabled them to act as tunable carriers. New phage-based technologies have led to the construction of different peptide libraries, and recognition abilities provided by novel targeting ligands. Phage hybridization with non-organic compounds introduces new properties to phages and could be a suitable strategy for construction of bio-inorganic carriers. In this review we try to cover the major phage species that have been used in drug and gene delivery systems, and the biological application of phages as novel targeting ligands and targeted therapeutics.
Collapse
Affiliation(s)
- Mahdi Karimi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirshekari
- Advanced Nanobiotechnology & Nanomedicine Research Group [ANNRG], Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Masoud Moosavi Basri
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; Civil & Environmental Engineering Department, Shahid Beheshti University, Tehran, Iran
| | - Sajad Bahrami
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Mohsen Moghoofei
- Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran; Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
20
|
Luo Q, Hou C, Bai Y, Wang R, Liu J. Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. Chem Rev 2016; 116:13571-13632. [PMID: 27587089 DOI: 10.1021/acs.chemrev.6b00228] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.
Collapse
Affiliation(s)
- Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR 999078, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| |
Collapse
|
21
|
White EM, Miranker AD. A solenoid design for assessing determinants of parallel β-sheet registration. Protein Eng Des Sel 2015; 28:577-83. [PMID: 26487712 DOI: 10.1093/protein/gzv053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/17/2015] [Indexed: 11/12/2022] Open
Abstract
A novel protein construct is presented that combines a homotrimeric, triple-stranded β-helix as a guest to a homotrimeric foldon unit from bacteriophage T4 fibritin. The β-helical solenoid selected is short (46 residues) and is part of a subdomain of the T4 cell-puncturing device. The resultant design is trimeric and displays greatly enhanced stability over each sub-component alone. The intended goal is a design that will enable evaluation of sequence determinants that promote in-register versus out-of-register parallel β-sheet homotrimerization. Towards that end, the importance of a set of three buried salt-bridges was evaluated by converting them to residues otherwise consistently found throughout the natural solenoid at the same positions. The critical role of the charged residues in the salt-bridges was evident in that their elimination resulted in amyloid-like aggregation.
Collapse
Affiliation(s)
- Ellen M White
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Andrew D Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
| |
Collapse
|
22
|
Inaba H, Sanghamitra NJM, Fujita K, Sho T, Kuchimaru T, Kitagawa S, Kizaka-Kondoh S, Ueno T. A metal carbonyl-protein needle composite designed for intracellular CO delivery to modulate NF-κB activity. MOLECULAR BIOSYSTEMS 2015; 11:3111-8. [PMID: 26360102 DOI: 10.1039/c5mb00327j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbon monoxide (CO) has been recognized as a messenger for signal transduction in living cells and tissues. For intracellular CO delivery, several metal carbonyl complexes have been used as CO-releasing molecules (CO-RMs). To improve the properties of CO-RMs, such as the stability and the CO release rate, ligands and carriers of the metal complexes have been exploited. Here we report the development of an efficient intracellular CO delivery system using a protein scaffold. We used a protein needle reconstructed from gene product 5 of bacteriophage T4, which has high cellular permeability and stability. When ruthenium carbonyl complexes are conjugated to the needle using a His-tag triad at the C-terminus, the resulting composite has a significantly higher cellular uptake efficiency of Ru carbonyl and a 12-fold prolonged CO release rate relative to Ru(CO)3Cl(glycinate), a widely used CO-RM. We demonstrate that CO delivered by the composite activates the transcriptional factor nuclear factor-kappaB (NF-κB), which in turn leads to significant induction of expression of its target genes, HO1, NQO1, and IL6, through generation of reactive oxygen species (ROS). The signaling pathway is distinct from that of tumor necrosis factor (TNF)-α-induced activation of NF-κB. The protein needle-based CO-RM can be exploited to elucidate the biological functions of CO and used in the development of protein-based organometallic tools for modulation of cellular signaling.
Collapse
Affiliation(s)
- Hiroshi Inaba
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Buth SA, Menin L, Shneider MM, Engel J, Boudko SP, Leiman PG. Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4. Viruses 2015; 7:4676-706. [PMID: 26295253 PMCID: PMC4576200 DOI: 10.3390/v7082839] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 12/22/2022] Open
Abstract
Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.
Collapse
Affiliation(s)
- Sergey A Buth
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
| | - Laure Menin
- Service de Spectrométrie de Masse, ISIC, EPFL, BCH 1520, 1015 Lausanne, Switzerland.
| | - Mikhail M Shneider
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Jürgen Engel
- Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
| | - Sergei P Boudko
- Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
- The Research Department, Shriner's Hospital for Children, 3101 Sam Jackson Park Road, Portland, OR 97239, USA.
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Petr G Leiman
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
| |
Collapse
|
24
|
Kobayashi N, Yanase K, Sato T, Unzai S, Hecht MH, Arai R. Self-Assembling Nano-Architectures Created from a Protein Nano-Building Block Using an Intermolecularly Folded Dimeric de Novo Protein. J Am Chem Soc 2015; 137:11285-93. [PMID: 26120734 DOI: 10.1021/jacs.5b03593] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design of novel proteins that self-assemble into supramolecular complexes is an important step in the development of synthetic biology and nanotechnology. Recently, we described the three-dimensional structure of WA20, a de novo protein that forms an intermolecularly folded dimeric 4-helix bundle (PDB code 3VJF ). To harness the unusual intertwined structure of WA20 for the self-assembly of supramolecular nanostructures, we created a protein nanobuilding block (PN-Block), called WA20-foldon, by fusing the dimeric structure of WA20 to the trimeric foldon domain of fibritin from bacteriophage T4. The WA20-foldon fusion protein was expressed in the soluble fraction in Escherichia coli, purified, and shown to form several homooligomeric forms. The stable oligomeric forms were further purified and characterized by a range of biophysical techniques. Size exclusion chromatography, multiangle light scattering, analytical ultracentrifugation, and small-angle X-ray scattering (SAXS) analyses indicate that the small (S form), middle (M form), and large (L form) forms of the WA20-foldon oligomers exist as hexamer (6-mer), dodecamer (12-mer), and octadecamer (18-mer), respectively. These findings suggest that the oligomers in multiples of 6-mer are stably formed by fusing the interdigitated dimer of WA20 with the trimer of foldon domain. Pair-distance distribution functions obtained from the Fourier inversion of the SAXS data suggest that the S and M forms have barrel- and tetrahedron-like shapes, respectively. These results demonstrate that the de novo WA20-foldon is an effective building block for the creation of self-assembling artificial nanoarchitectures.
Collapse
Affiliation(s)
- Naoya Kobayashi
- Japan Society for the Promotion of Science , Chiyoda, Tokyo 102-8471, Japan
| | | | | | - Satoru Unzai
- Graduate School of Medical Life Science, Yokohama City University , Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Michael H Hecht
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Ryoichi Arai
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University , Matsumoto, Nagano 390-8621, Japan
| |
Collapse
|
25
|
Sanghamitra NJM, Inaba H, Arisaka F, Ohtan Wang D, Kanamaru S, Kitagawa S, Ueno T. Plasma membrane translocation of a protein needle based on a triple-stranded β-helix motif. MOLECULAR BIOSYSTEMS 2015; 10:2677-83. [PMID: 25082560 DOI: 10.1039/c4mb00293h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Plasma membrane translocation is challenging due to the barrier of the cell membrane. Contrary to the synthetic cell-penetrating materials, tailed bacteriophages use cell-puncturing protein needles to puncture the cell membranes as an initial step of the DNA injection process. Cell-puncturing protein needles are thought to remain functional in the native phages. In this paper, we found that a bacteriophage T4 derived protein needle of 16 nm length spontaneously translocates through the living cell membrane. The β-helical protein needle (β-PN) internalizes into human red blood cells that lack endocytic machinery. By comparing the cellular uptake of β-PNs with modified surface charge, it is shown that the uptake efficiency is maximum when it has a negative charge corresponding to a zeta potential value of -16 mV. In HeLa cells, uptake of β-PN incorporates endocytosis independent mechanisms with partial macropinocytosis dependence. The endocytosis dependence of the uptake increases when the surface charges of β-PNs are modified to positive or negative. Thus, these results suggest that natural DNA injecting machinery can serve as an inspiration to design new class of cell-penetrating materials with a tailored mechanism.
Collapse
Affiliation(s)
- Nusrat J M Sanghamitra
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.
| | | | | | | | | | | | | |
Collapse
|
26
|
Use of the confined spaces of apo-ferritin and virus capsids as nanoreactors for catalytic reactions. Curr Opin Chem Biol 2015; 25:88-97. [DOI: 10.1016/j.cbpa.2014.12.026] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 01/17/2023]
|
27
|
Abstract
![]()
Homomeric self-assembly of peptides
into amyloid fibers is a feature of many diseases. A central role
has been suggested for the lateral fiber surface affecting gains of
toxic function. To investigate this, a protein scaffold that presents
a discrete, parallel β-sheet surface for amyloid subdomains
up to eight residues in length has been designed. Scaffolds that present
the fiber surface of islet amyloid polypeptide (IAPP) were prepared.
The designs show sequence-specific surface effects apparent in that
they gain the capacity to attenuate rates of IAPP self-assembly in
solution and affect IAPP-induced toxicity in insulin-secreting cells.
Collapse
Affiliation(s)
- Marisa A Rubio
- Department of Molecular Biophysics and Biochemistry, Yale University , 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
| | | | | | | |
Collapse
|
28
|
Inaba H, Kitagawa S, Ueno T. Protein Needles as Molecular Templates for Artificial Metalloenzymes. Isr J Chem 2014. [DOI: 10.1002/ijch.201400097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
29
|
Inaba H, Sanghamitra NJM, Fukai T, Matsumoto T, Nishijo K, Kanamaru S, Arisaka F, Kitagawa S, Ueno T. Intracellular Protein Delivery System with Protein Needle–GFP Construct. CHEM LETT 2014. [DOI: 10.1246/cl.140481] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroshi Inaba
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | | | - Toshihiro Fukai
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Takahiro Matsumoto
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Kaname Nishijo
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Shuji Kanamaru
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Fumio Arisaka
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Susumu Kitagawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Takafumi Ueno
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| |
Collapse
|
30
|
Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | |
Collapse
|
31
|
Ding Y, Shi L, Wei H. Protein-directed approaches to functional nanomaterials: a case study of lysozyme. J Mater Chem B 2014; 2:8268-8291. [DOI: 10.1039/c4tb01235f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using lysozyme as a model, protein-directed approaches to functional nanomaterials were reviewed, making rational materials design possible in the future.
Collapse
Affiliation(s)
- Yubin Ding
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Leilei Shi
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Hui Wei
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| |
Collapse
|
32
|
Artificial Metalloenzymes Constructed From Hierarchically-Assembled Proteins. Chem Asian J 2013; 8:1646-60. [DOI: 10.1002/asia.201300347] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 01/20/2023]
|
33
|
|
34
|
Sanghamitra NJM, Ueno T. Expanding coordination chemistry from protein to protein assembly. Chem Commun (Camb) 2013; 49:4114-26. [DOI: 10.1039/c2cc36935d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
35
|
Inaba H, Kanamaru S, Arisaka F, Kitagawa S, Ueno T. Semi-synthesis of an artificial scandium(iii) enzyme with a β-helical bio-nanotube. Dalton Trans 2012; 41:11424-7. [DOI: 10.1039/c2dt31030a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
36
|
Kato R, Komatsu T. Protein Nanotube Arrays Immobilized on Solid Substrates: Molecular Trap in Aqueous Medium. CHEM LETT 2011. [DOI: 10.1246/cl.2011.1338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
37
|
Yokoi N, Miura Y, Huang CY, Takatani N, Inaba H, Koshiyama T, Kanamaru S, Arisaka F, Watanabe Y, Kitagawa S, Ueno T. Dual modification of a triple-stranded β-helix nanotube with Ru and Re metal complexes to promote photocatalytic reduction of CO2. Chem Commun (Camb) 2011; 47:2074-6. [DOI: 10.1039/c0cc03015e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|