1
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Kordys M, Urbanowicz A. 3D Puzzle at the Nanoscale-How do RNA Viruses Self-Assemble their Capsids into Perfectly Ordered Structures. Macromol Biosci 2024:e2400088. [PMID: 38864315 DOI: 10.1002/mabi.202400088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/03/2024] [Indexed: 06/13/2024]
Abstract
The phenomenon of RNA virus self-organization, first observed in the mid-20th century in tobacco mosaic virus, is the subject of extensive research. Efforts to comprehend this process intensify due to its potential for producing vaccines or antiviral compounds as well as nanocarriers and nanotemplates. However, direct observation of the self-assembly is hindered by its prevalence within infected host cells. One of the approaches involves in vitro and in silico research using model viruses featuring a ssRNA(+) genome enclosed within a capsid made up of a single type protein. While various pathways are proposed based on these studies, their relevance in vivo remains uncertain. On the other hand, the development of advanced microscopic methods provide insights into the events within living cells, where following viral infection, specialized compartments form to facilitate the creation of nascent virions. Intriguingly, a growing body of evidence indicates that the primary function of packaging signals in viral RNA is to effectively initiate the virion self-assembly. This is in contrast to earlier opinions suggesting a role in marking RNA for encapsidation. Another noteworthy observation is that many viruses undergo self-assembly within membraneless liquid organelles, which are specifically induced by viral proteins.
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Affiliation(s)
- Martyna Kordys
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego Str. 12/14, Poznan, 61-704, Poland
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego Str. 12/14, Poznan, 61-704, Poland
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2
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De Sá Magalhães S, De Santis E, Hussein-Gore S, Colomb-Delsuc M, Keshavarz-Moore E. Quality assessment of virus-like particle: A new transmission electron microscopy approach. Front Mol Biosci 2022; 9:975054. [PMID: 36504719 PMCID: PMC9732438 DOI: 10.3389/fmolb.2022.975054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/15/2022] [Indexed: 11/26/2022] Open
Abstract
Transmission electron microscopy (TEM) is a gold standard analytical method for nanoparticle characterization and is playing a valuable role in virus-like particle (VLP) characterization extending to other biological entities such as viral vectors. A dedicated TEM facility is a challenge to both small and medium-sized enterprises (SMEs) and companies operating in low-and-middle income countries (LMICs) due to high start-up and running costs. A low-voltage TEM solution with assisted image acquisition and analysis such as the MiniTEM system, coupled with Vironova Imaging and Analysis Software (VIAS) could provide an affordable and practical alternative. The MiniTEM system has a small footprint and software that enables semi-automated data collection and image analysis workflows using built-in deep learning methods (convolutional neural networks) for automation in analysis, increasing speed of information processing and enabling scaling to larger datasets. In this perspective we outline the potential and challenges in the use of TEM as mainstream analytical tool in manufacturing settings. We highlight the rationale and preliminary findings from our proof-of-concept study aiming to develop a method to assess critical quality attributes (CQAs) of VLPs and facilitate adoption of TEM in manufacturing settings. In our study we explored all the steps, from sample preparation to data collection and analysis using synthetic VLPs as model systems. The applicability of the method in product development was verified at pilot-scale during the technology transfer of dengue VLPs development from a university setting to an LMIC- based vaccine manufacturing company, demonstrating the applicability of this analytical technique to VLP vaccine characterization.
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Affiliation(s)
- Salomé De Sá Magalhães
- Department of Biochemical Engineering, University College London, UCL, London, United Kingdom
| | - Emiliana De Santis
- National Physical Laboratory, NPL, Teddington, United Kingdom,*Correspondence: Eli Keshavarz-Moore, ; Emiliana De Santis,
| | | | | | - Eli Keshavarz-Moore
- Department of Biochemical Engineering, University College London, UCL, London, United Kingdom,*Correspondence: Eli Keshavarz-Moore, ; Emiliana De Santis,
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3
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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4
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Cao M, Zhang Z, Zhang X, Wang Y, Wu J, Liu Z, Sun L, Wang D, Yue T, Han Y, Wang Y, Wang Y, Wang M. Peptide Self-assembly into stable Capsid-Like nanospheres and Co-assembly with DNA to produce smart artificial viruses. J Colloid Interface Sci 2022; 615:395-407. [PMID: 35150952 DOI: 10.1016/j.jcis.2022.01.181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 01/28/2023]
Abstract
Smart artificial viruses have been successfully developed by co-assembly of de novo designed peptides with DNA, which achieved stimuli-responsibility and efficient gene transfection in cancer cells. The peptides were designed to incorporate several functional segments, including a hydrophobic aromatic segment to drive self-assembly, two or more cysteines to regulate the assemblage shape and stabilize the assembled nanostructures via forming disulfide bonds, several lysines to facilitate co-assembly with DNA and binding to cell membranes, and an enzyme-cleavable segment to introduce cancer sensitivity. The rationally designed peptides self-assembled into stable nanospheres with a uniform diameter of < 10 nm, which worked as capsid-like subunits to further interact with DNA to produce hierarchical virus-mimicking structures by encapsulating DNA in the interior. Such artificial viruses can effectively protect DNA from nuclease digestion and achieve efficient genome release by enzyme-triggered structure disassembly, which ensured a high level of gene transfection in tumor cells. The system emulates very well the structural and functional properties of natural viruses from the aspects of capsid formation, genome package and gene transfection, which is highly promising for application as efficient gene vectors.
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Affiliation(s)
- Meiwen Cao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China.
| | - Zijin Zhang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Xiaoyang Zhang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yu Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Jingjing Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhihong Liu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Li Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China.
| | - Yuchun Han
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid and Interface Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yingxiong Wang
- Institute of Coal Chemistry, Chinese Academy of Sciences, 27 South Taoyuan Road, Taiyuan 030001, China
| | - Yilin Wang
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid and Interface Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Wang
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China.
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5
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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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6
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Rey S, Faruqui N, Hoose A, Dondi C, Ryadnov MG. Designer protein pseudo-capsids targeting intracellular bacteria. Biomater Sci 2021; 9:6807-6812. [PMID: 34491257 DOI: 10.1039/d1bm01235e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of multidrug-resistant bacteria stimulates the search for antimicrobial materials capable of addressing challenges conventional antibiotics fail to address. The ability to target intracellular bacteria remains one of the most fundamental tasks for contemporary antimicrobial treatments. Here we report engineered protein pseudo-capsids targeting bacteria internalised in macrophages. Using a combination of live-cell imaging and single-cell electron microscopy analysis we show that these materials effectively disrupt the bacteria without affecting the host cells. The study offers a disruptive antimicrobial strategy demonstrating potential for developing principally more challenging mechanisms for bacteria to overcome.
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Affiliation(s)
- Stephanie Rey
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Nilofar Faruqui
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Camilla Dondi
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK. .,Department of Physics, King's College London, London, WC2R 2LS, UK
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7
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Cruz CHB, Marzuoli I, Fraternali F. Virus-inspired designs of antimicrobial nanocapsules. Faraday Discuss 2021; 232:448-462. [PMID: 34596638 DOI: 10.1039/d1fd00041a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antimicrobial resistance is becoming a serious burden for drug design. The challenges are in finding novel approaches for effectively targeting a number of different bacterial strains, and in delivering these to the site of action. We propose here a novel approach that exploits the assembly of antimicrobial peptidic units in nanocapsules that can penetrate and rupture the bacterial membrane. Additionally, the chemical versatility of the designed units can be tailored to specific targets and to the delivery of genetic material in the cell. The proposed design exploits a β-annulus (sequence ITHVGGVGGSIMAPVAVSRQLVGS) triskelion unit from the Tomato Bushy Stunt Virus, able to self assemble in solution, and functionalised with antimicrobial sequences to form dodecahedral antimicrobial nanocapsules. The stability and the activity of the antimicrobial β-annulus capsule is measured by molecular dynamics simulations in water and in the presence of model membranes.
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Affiliation(s)
- Carlos H B Cruz
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
| | - Irene Marzuoli
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
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8
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Janković P, Šantek I, Pina AS, Kalafatovic D. Exploiting Peptide Self-Assembly for the Development of Minimalistic Viral Mimetics. Front Chem 2021; 9:723473. [PMID: 34395387 PMCID: PMC8355586 DOI: 10.3389/fchem.2021.723473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/15/2021] [Indexed: 12/03/2022] Open
Abstract
Viruses are natural supramolecular nanostructures that form spontaneously by molecular self-assembly of complex biomolecules. Peptide self-assembly is a versatile tool that allows mimicking viruses by creating their simplified versions through the design of functional, supramolecular materials with modularity, tunability, and responsiveness to chemical and physical stimuli. The main challenge in the design and fabrication of peptide materials is related to the precise control between the peptide sequence and its resulting supramolecular morphology. We provide an overview of existing sequence patterns employed for the development of spherical and fibrillar peptide assemblies that can act as viral mimetics, offering the opportunity to tackle the challenges of viral infections.
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Affiliation(s)
| | - Iva Šantek
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Ana Sofia Pina
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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9
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Marzuoli I, Cruz CHB, Lorenz CD, Fraternali F. Nanocapsule designs for antimicrobial resistance. NANOSCALE 2021; 13:10342-10355. [PMID: 34137751 DOI: 10.1039/d0nr08146a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections. The recent coronavirus pandemic has dramatically highlighted the necessity of effective antibacterial and antiviral protection. This work explores at the molecular level the mechanism of action of antibacterial nanocapsules assembled in virus-like particles, their stability and their interaction with mammal and antimicrobial model membranes. We use Molecular Dynamics with force-fields of different granularity and protein design strategies to study the stability, self-assembly and membrane poration properties of these nanocapsules.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | - Carlos H B Cruz
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | | | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
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10
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Long K, Liu Y, Li Y, Wang W. Self-assembly of trigonal building blocks into nanostructures: molecular design and biomedical applications. J Mater Chem B 2021; 8:6739-6752. [PMID: 32686806 DOI: 10.1039/d0tb01128b] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Trigonal molecules have a special triskelion structure similar to clathrin protein, providing great inspiration for constructing artificial nanoassemblies. To date, various synthetic trigonal conjugates have been designed for supramolecular self-assembly, which have demonstrated versatile and controllable self-assembly ability in materials science. Here we will review the design of trigonal (sometimes called three-legged, tripodal, C3-symmetric, or triskelion) building blocks that can self-assemble into various nanostructures and discuss the biomedical applications of the self-assembled nanomaterials.
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Affiliation(s)
- Kaiqi Long
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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11
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Inaba H, Matsuura K. Functional Peptide Nanocapsules Self-Assembled from β-Annulus Peptides. Methods Mol Biol 2021; 2208:101-121. [PMID: 32856258 DOI: 10.1007/978-1-0716-0928-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Spherical viruses are unique nanocapsules formed by self-assembly of coat proteins (capsids). By mimicking natural spherical capsids, various artificial viral capsids are developed by using self-assembled proteins and peptides as building blocks. We developed an artificial viral capsid consisting of a β-annulus peptide designed from natural viruses. The "β-annulus capsid" can be functionalized by encapsulating guest molecules to the inside and decoration of exogenous molecules on the outside. Here, we describe the encapsulation and decoration on the β-annulus capsids by connecting additional sequences to the β-annulus peptide, conjugation with objective molecules, and subsequent self-assembly in aqueous solutions.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.
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12
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Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes. Methods Mol Biol 2021. [PMID: 32856257 DOI: 10.1007/978-1-0716-0928-6_6] [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
In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.
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13
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Abstract
Nanoscale systems encapsulating biomacromolecules hold promise for cell and gene therapies. Common issues hampering progress include polydispersity, heterogeneity in size and shape, agglomeration, and poor stability. Much attention is given to the search of novel designs. However, reliable protocols for the validation of encapsulating systems in the continuum of their physicochemical properties, from design to ultrastructure, are lacking. Herein, we report electron microscopy protocols for biologically functional shell-like peptide capsids, which exhibit the physical characteristics of viruses including folding-mediated self-assembly, hollow shell morphology, and uniformity in size.
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14
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Vila-Gómez P, Noble JE, Ryadnov MG. Peptide Nanoparticles for Gene Packaging and Intracellular Delivery. Methods Mol Biol 2021; 2208:33-48. [PMID: 32856254 DOI: 10.1007/978-1-0716-0928-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Efficient gene transfer is necessary for advanced biotechnologies ranging from gene therapy to synthetic biology. Peptide nanoparticles provide suitable packaging systems promoting targeted gene expression or silencing. Though these systems have yet to match the transfection efficacy of viruses, they are typically devoid of drawbacks characteristic of virus-based vectors, including insertional mutagenesis, low packaging capacities, and strong immune responses. Given the promise nanoparticle formulations hold for gene delivery, methods of their preparation and accurate analysis of their physicochemical and biological properties become indispensable for progress toward systems that seek to outperform viral vectors. Herein, we report a comprehensive protocol for the preparation and characterization of archetypal peptide nanoparticles resulting from nonspecific and noncovalent complexation with RNA and DNA.
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Affiliation(s)
| | - James E Noble
- National Physical Laboratory, Teddington, Middlesex, UK
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15
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Abstract
Electron microscopy offers necessary precision for the characterization of peptide materials at the nanoscale. Analysis is typically performed for acellular material specimens, whereas measurements in more complex, cellular environments prompt additional considerations for sample processing. Herein, we describe a protocol for the ultramicrotomy analysis of peptide-treated bacterial and mammalian cells. An emphasis is made on cell analysis following peptide treatment, as opposed to peptide analysis in cells, and focuses on sample processing, including fixation and staining procedures, resin embedding, sectioning, and imaging. The application of the protocol is demonstrated for intracellular measurements using antimicrobial peptide materials.
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Affiliation(s)
- Stephanie Rey
- National Physical Laboratory, Teddington, Middlesex, UK
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16
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Hammond K, Ryadnov MG, Hoogenboom BW. Atomic force microscopy to elucidate how peptides disrupt membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183447. [PMID: 32835656 DOI: 10.1016/j.bbamem.2020.183447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022]
Abstract
Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.
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Affiliation(s)
- Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; Department of Physics, King's College London, Strand Lane, London WC2R 2LS, UK.
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
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17
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Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy. MICROMACHINES 2020; 11:mi11030251. [PMID: 32120860 PMCID: PMC7143348 DOI: 10.3390/mi11030251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022]
Abstract
Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification.
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18
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Kepiro IE, Marzuoli I, Hammond K, Ba X, Lewis H, Shaw M, Gunnoo SB, De Santis E, Łapińska U, Pagliara S, Holmes MA, Lorenz CD, Hoogenboom BW, Fraternali F, Ryadnov MG. Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters. ACS NANO 2020; 14:1609-1622. [PMID: 31794180 DOI: 10.1021/acsnano.9b06814] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance stimulates the search for antimicrobial forms that may be less subject to acquired resistance. Here we report a conceptual design of protein pseudocapsids exhibiting a broad spectrum of antimicrobial activities. Unlike conventional antibiotics, these agents are effective against phenotypic bacterial variants, while clearing "superbugs" in vivo without toxicity. The design adopts an icosahedral architecture that is polymorphic in size, but not in shape, and that is available in both l and d epimeric forms. Using a combination of nanoscale and single-cell imaging we demonstrate that such pseudocapsids inflict rapid and irreparable damage to bacterial cells. In phospholipid membranes they rapidly convert into nanopores, which remain confined to the binding positions of individual pseudocapsids. This mechanism ensures precisely delivered influxes of high antimicrobial doses, rendering the design a versatile platform for engineering structurally diverse and functionally persistent antimicrobial agents.
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Affiliation(s)
- Ibolya E Kepiro
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Irene Marzuoli
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Randall Centre for Cell and Molecular Biophysics , King's College London , London , SE1 1UL , U.K
| | - Katharine Hammond
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Physics and Astronomy , University College London , London , WC1E 6BT , U.K
- London Centre for Nanotechnology , University College London , London , WC1H 0AH , U.K
| | - Xiaoliang Ba
- Department of Veterinary Medicine , University of Cambridge , Cambridge , CB3 0ES , U.K
| | - Helen Lewis
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Michael Shaw
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Computer Science , University College London , London , WC1 6BT , U.K
| | - Smita B Gunnoo
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Emiliana De Santis
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
| | - Urszula Łapińska
- Living Systems Institute , University of Exeter , Exeter , EX4 4QD , U.K
| | - Stefano Pagliara
- Living Systems Institute , University of Exeter , Exeter , EX4 4QD , U.K
| | - Mark A Holmes
- Department of Veterinary Medicine , University of Cambridge , Cambridge , CB3 0ES , U.K
| | - Christian D Lorenz
- Department of Physics , King's College London , Strand Lane , London , WC2R 2LS , U.K
| | - Bart W Hoogenboom
- Department of Physics and Astronomy , University College London , London , WC1E 6BT , U.K
- London Centre for Nanotechnology , University College London , London , WC1H 0AH , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics , King's College London , London , SE1 1UL , U.K
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington , TW11 0LW , U.K
- Department of Physics , King's College London , Strand Lane , London , WC2R 2LS , U.K
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19
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Datta LP, Manchineella S, Govindaraju T. Biomolecules-derived biomaterials. Biomaterials 2020; 230:119633. [DOI: 10.1016/j.biomaterials.2019.119633] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022]
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20
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Vaezi Z, Bortolotti A, Luca V, Perilli G, Mangoni ML, Khosravi-Far R, Bobone S, Stella L. Aggregation determines the selectivity of membrane-active anticancer and antimicrobial peptides: The case of killerFLIP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183107. [PMID: 31678022 DOI: 10.1016/j.bbamem.2019.183107] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 07/19/2019] [Accepted: 09/19/2019] [Indexed: 01/02/2023]
Abstract
Host defense peptides selectively kill bacterial and cancer cells (including those that are drug-resistant) by perturbing the permeability of their membranes, without being significantly toxic to the host. Coulombic interactions between these cationic and amphipathic peptides and the negatively charged membranes of pathogenic cells contribute to the selective toxicity. However, a positive charge is not sufficient for selectivity, which can be achieved only by a finely tuned balance of electrostatic and hydrophobic driving forces. A common property of amphipathic peptides is the formation of aggregated structures in solution, but the role of this phenomenon in peptide activity and selectivity has received limited attention. Our data on the anticancer peptide killerFLIP demonstrate that aggregation strongly increases peptide selectivity, by reducing the effective peptide hydrophobicity and thus the affinity towards membranes composed of neutral lipids (like the outer layer of healthy eukaryotic cell membranes). Aggregation is therefore a useful tool to modulate the selectivity of membrane active peptides and peptidomimetics.
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Affiliation(s)
- Zahra Vaezi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Annalisa Bortolotti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Vincenzo Luca
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Giulia Perilli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Maria Luisa Mangoni
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Roya Khosravi-Far
- BiomaRx Inc, Cambridge, MA, USA; Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy.
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy.
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21
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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22
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Lou S, Wang X, Yu Z, Shi L. Peptide Tectonics: Encoded Structural Complementarity Dictates Programmable Self-Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802043. [PMID: 31380179 PMCID: PMC6662064 DOI: 10.1002/advs.201802043] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/20/2019] [Indexed: 05/23/2023]
Abstract
Programmable self-assembly of peptides into well-defined nanostructures represents one promising approach for bioinspired and biomimetic synthesis of artificial complex systems and functional materials. Despite the progress made over the past two decades in the development of strategies for precise manipulation of the self-assembly of peptides, there is a remarkable gap between current peptide assemblies and biological systems in terms of structural complexity and functions. Here, the concept of peptide tectonics for the creation of well-defined nanostructures predominately driven by the complementary association at the interacting interfaces of tectons is introduced. Peptide tectons are defined as peptide building blocks exhibiting structural complementarity at the interacting interfaces of commensurate domains and undergoing programmable self-assembly into defined supramolecular structures promoted by complementary interactions. Peptide tectons are categorized based on their conformational entropy and the underlying mechanism for the programmable self-assembly of peptide tectons is highlighted focusing on the approaches for incorporating the structural complementarity within tectons. Peptide tectonics not only provides an alternative perspective to understand the self-assembly of peptides, but also allows for precise manipulation of peptide interactions, thus leading to artificial systems with advanced complexity and functions and paves the way toward peptide-related functional materials resembling natural systems.
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Affiliation(s)
- Shaofeng Lou
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Xinmou Wang
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
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23
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Abstract
![]()
Ordered
protein assemblies are attracting interest as next-generation
biomaterials with a remarkable range of structural and functional
properties, leading to potential applications in biocatalysis, materials
templating, drug delivery and vaccine development. This Review covers
ordered protein assemblies including protein nanowires/nanofibrils,
nanorings, nanotubes, designed two- and three-dimensional ordered
protein lattices and protein-like cages including polyhedral virus-like
cage structures. The main focus is on designed ordered protein assemblies,
in which the spatial organization of the proteins is controlled by
tailored noncovalent interactions (including metal ion binding interactions,
electrostatic interactions and ligand–receptor interactions
among others) or by careful design of modified (mutant) proteins or de novo constructs. The modification of natural protein
assemblies including bacterial S-layers and cage-like and rod-like
viruses to impart novel function, e.g. enzymatic activity, is also
considered. A diversity of structures have been created using distinct
approaches, and this Review provides a summary of the state-of-the-art
in the development of these systems, which have exceptional potential
as advanced bionanomaterials for a diversity of applications.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
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24
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Wu G, Liu X, Zhou P, Wang L, Hegazy M, Huang X, Huang Y. A facile approach for the reduction of 4‑nitrophenol and degradation of congo red using gold nanoparticles or laccase decorated hybrid inorganic nanoparticles/polymer-biomacromolecules vesicles. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 94:524-533. [DOI: 10.1016/j.msec.2018.09.061] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/13/2018] [Accepted: 09/30/2018] [Indexed: 02/03/2023]
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25
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Inaba H, Matsuura K. Peptide Nanomaterials Designed from Natural Supramolecular Systems. CHEM REC 2018; 19:843-858. [PMID: 30375148 DOI: 10.1002/tcr.201800149] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/07/2018] [Indexed: 12/22/2022]
Abstract
Natural supramolecular assemblies exhibit unique structural and functional properties that have been optimized over the course of evolution. Inspired by these natural systems, various bio-nanomaterials have been developed using peptides, proteins, and nucleic acids as components. Peptides are attractive building blocks because they enable the important domains of natural protein assemblies to be isolated and optimized while retaining the original structures and functions. Furthermore, the peptide subunits can be conjugated with exogenous molecules such as peptides, proteins, nucleic acids, and metal nanoparticles to generate advanced functions. In this personal account, we summarize recent progress in the construction of peptide-based nanomaterial designed from natural supramolecular systems, including (1) artificial viral capsids, (2) self-assembled nanofibers, and (3) protein-binding motifs. The peptides inspired by nature should provide new design principles for bio-nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Koyama-Minami 4-101, Tottori, 680-8552, Japan
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26
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Sánchez JM, Sánchez-García L, Pesarrodona M, Serna N, Sánchez-Chardi A, Unzueta U, Mangues R, Vázquez E, Villaverde A. Conformational Conversion during Controlled Oligomerization into Nonamylogenic Protein Nanoparticles. Biomacromolecules 2018; 19:3788-3797. [PMID: 30052033 DOI: 10.1021/acs.biomac.8b00924] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein materials are rapidly gaining interest in materials sciences and nanomedicine because of their intrinsic biocompatibility and full biodegradability. The controlled construction of supramolecular entities relies on the controlled oligomerization of individual polypeptides, achievable through different strategies. Because of the potential toxicity of amyloids, those based on alternative molecular organizations are particularly appealing, but the structural bases on nonamylogenic oligomerization remain poorly studied. We have applied spectrofluorimetry and spectropolarimetry to identify the conformational conversion during the oligomerization of His-tagged cationic stretches into regular nanoparticles ranging around 11 nm, useful for tumor-targeted drug delivery. We demonstrate that the novel conformation acquired by the proteins, as building blocks of these supramolecular assemblies, shows different extents of compactness and results in a beta structure enrichment that enhances their structural stability. The conformational profiling presented here offers clear clues for understanding and tailoring the process of nanoparticle formation through the use of cationic and histidine rich stretches in the context of protein materials usable in advanced nanomedical strategies.
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Affiliation(s)
- Julieta M Sánchez
- Institut de Biotecnologia i de Biomedicina , Universitat Autònoma de Barcelona , Bellaterra 08193 Barcelona , Spain.,Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Córdoba, Argentina, CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Córdoba, Argentina , Av. Velez Sarsfield 1611 , X5016GCA Córdoba , Argentina
| | - Laura Sánchez-García
- Departament de Genètica i de Microbiologia , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain
| | - Mireia Pesarrodona
- Institut de Biotecnologia i de Biomedicina , Universitat Autònoma de Barcelona , Bellaterra 08193 Barcelona , Spain.,Departament de Genètica i de Microbiologia , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina , Universitat Autònoma de Barcelona , Bellaterra 08193 Barcelona , Spain.,Departament de Genètica i de Microbiologia , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain
| | | | - Ugutz Unzueta
- Institut de Biotecnologia i de Biomedicina , Universitat Autònoma de Barcelona , Bellaterra 08193 Barcelona , Spain.,Departament de Genètica i de Microbiologia , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain.,Biomedical Research Institute Sant Pau (IIB-Sant Pau) and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau , 08025 Barcelona , Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain.,Biomedical Research Institute Sant Pau (IIB-Sant Pau) and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau , 08025 Barcelona , Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina , Universitat Autònoma de Barcelona , Bellaterra 08193 Barcelona , Spain.,Departament de Genètica i de Microbiologia , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina , Universitat Autònoma de Barcelona , Bellaterra 08193 Barcelona , Spain.,Departament de Genètica i de Microbiologia , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , Bellaterra, 08193 Barcelona , Spain
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27
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Abstract
A synthetic topology for everted viruses is reported. The topology is a single-stranded virion DNA assembled into a hollow cube with exterior decorated with HIV-Tat transduction domains. The cube incorporates a pH-responsive lid allowing for the controlled encapsulation of functional proteins and their transfer and release into live cells. Unlike viruses, which are protein shells with a [3,5]-fold rotational symmetry that encase nucleic acids, these cubes are [3, 4]-fold DNA boxes encapsulating proteins. Like viruses, such everted DNA-built viruses are monodisperse nanoscale assemblies that infect human cells with a specialist cargo. The design offers a bespoke bottom-up platform for engineering nonpolyhedral, nonprotein synthetic viruses.
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Affiliation(s)
- Jonathan R. Burns
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
- Department of Chemistry, University College London, London, WC1E 6BT, U.K
| | - Baptiste Lamarre
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - Alice L. B. Pyne
- London Centre for Nanotechnology, University College London, London, WC1E 6BT, U.K
| | - James E. Noble
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - Maxim G. Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
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28
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Matsuura K. Synthetic approaches to construct viral capsid-like spherical nanomaterials. Chem Commun (Camb) 2018; 54:8944-8959. [DOI: 10.1039/c8cc03844a] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This feature article describes recent progress in synthetic strategies to construct viral capsid-like spherical nanomaterials using the self-assembly of peptides and/or proteins.
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Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biotechnology
- Graduate School of Engineering
- Tottori University
- Tottori 680-8552
- Japan
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29
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Abstract
The spread of bacterial resistance to antibiotics poses the need for antimicrobial discovery. With traditional search paradigms being exhausted, approaches that are altogether different from antibiotics may offer promising and creative solutions. Here, we introduce a de novo peptide topology that—by emulating the virus architecture—assembles into discrete antimicrobial capsids. Using the combination of high-resolution and real-time imaging, we demonstrate that these artificial capsids assemble as 20-nm hollow shells that attack bacterial membranes and upon landing on phospholipid bilayers instantaneously (seconds) convert into rapidly expanding pores causing membrane lysis (minutes). The designed capsids show broad antimicrobial activities, thus executing one primary function—they destroy bacteria on contact. With the growing threat of antibiotic resistance, unconventional approaches to antimicrobial discovery are needed. Here, the authors present a peptide topology that mimics virus architecture and assembles into antimicrobial capsids that disrupt bacterial membranes upon contact.
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30
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Datta LP, Mukherjee R, Biswas S, Das TK. Peptide-Based Polymer-Polyoxometalate Supramolecular Structure with a Differed Antimicrobial Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14195-14208. [PMID: 29135264 DOI: 10.1021/acs.langmuir.7b02916] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Because of the increasing prevalence of multidrug resistance feature, several investigations have been so far reported regarding the antibiotic alternative supramolecular bioactive agents made of hybrid assemblies. In this regard, it is well-established that combinational therapy inherited by assembled supramolecular structures can improve the bioactivity to some extent, but their mode of action has not been studied in detail. We provide first direct evidence that the improved mechanism of action of antimicrobial supra-amphiphilic nanocomposites differs largely from their parent antimicrobial peptide-based polymers. For the construction of a hybrid combinational system, we have synthesized side-chain peptide-based antimicrobial polymers via RAFT polymerization and exploited their cationic nature to decorate supra-amphiphilic nanocomposites via interaction with anionic polyoxometalates. Because of cooperative antimicrobial properties of both the polymer and polyoxometalate, the nanocomposites show an enhanced antimicrobial activity with a different antimicrobial mechanism. The cationic stimuli-responsive peptide-based polymers attack bacteria via membrane disruption mechanism, whereas free radical-mediated cell damage is the likely mechanism of polymer-polyoxometalate-based supra-amphiphilic nanocomposites. Thus, our study highlights the different antimicrobial mechanism of combinational systems in detail, which improves our understanding of enhanced antimicrobial efficacy.
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Affiliation(s)
- Lakshmi Priya Datta
- Department of Biochemistry & Biophysics, University of Kalyani , Kalyani 741235, Nadia, West Bengal, India
| | - Riya Mukherjee
- Department of Biochemistry & Biophysics, University of Kalyani , Kalyani 741235, Nadia, West Bengal, India
| | - Subharanjan Biswas
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata , Mohanpur 741246, Nadia, West Bengal, India
| | - Tapan Kumar Das
- Department of Biochemistry & Biophysics, University of Kalyani , Kalyani 741235, Nadia, West Bengal, India
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31
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Beter M, Kara HK, Topal AE, Dana A, Tekinay AB, Guler MO. Multivalent Presentation of Cationic Peptides on Supramolecular Nanofibers for Antimicrobial Activity. Mol Pharm 2017; 14:3660-3668. [DOI: 10.1021/acs.molpharmaceut.7b00434] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mustafa Beter
- Institute
of Materials Science and Nanotechnology, National Nanotechnology Research
Center (UNAM), Bilkent University, Ankara 06800, Turkey
| | - Hatice K. Kara
- Institute
of Materials Science and Nanotechnology, National Nanotechnology Research
Center (UNAM), Bilkent University, Ankara 06800, Turkey
| | - Ahmet E. Topal
- Institute
of Materials Science and Nanotechnology, National Nanotechnology Research
Center (UNAM), Bilkent University, Ankara 06800, Turkey
| | - Aykutlu Dana
- Institute
of Materials Science and Nanotechnology, National Nanotechnology Research
Center (UNAM), Bilkent University, Ankara 06800, Turkey
| | - Ayse B. Tekinay
- Institute
of Materials Science and Nanotechnology, National Nanotechnology Research
Center (UNAM), Bilkent University, Ankara 06800, Turkey
- Neuroscience
Graduate Program, Bilkent University, Ankara 06800, Turkey
| | - Mustafa O. Guler
- Institute
for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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32
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Brea RJ, Devaraj NK. Continual reproduction of self-assembling oligotriazole peptide nanomaterials. Nat Commun 2017; 8:730. [PMID: 28959049 PMCID: PMC5620040 DOI: 10.1038/s41467-017-00849-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 08/01/2017] [Indexed: 01/24/2023] Open
Abstract
Autocatalytic chemical reactions, whereby a molecule is able to catalyze its own formation from a set of precursors, mimic nature’s ability to generate identical copies of relevant biomolecules, and are thought to have been crucial for the origin of life. While several molecular autocatalysts have been previously reported, coupling autocatalytic behavior to macromolecular self-assembly has been challenging. Here, we report a non-enzymatic and chemoselective methodology capable of autocatalytically producing triskelion peptides that self-associate into spherical bioinspired nanostructures. Serial transfer experiments demonstrate that oligotriazole autocatalysis successfully leads to continual self-assembly of three-dimensional nanospheres. Triskelion-based spherical architectures offer an opportunity to organize biomolecules and chemical reactions in unique, nanoscale compartments. The use of peptide-based autocatalysts that are capable of self-assembly represents a promising method for the development of self-synthesizing biomaterials, and may shed light on understanding life’s chemical origins. Molecules that act as both autocatalysts and material precursors offer exciting prospects for self-synthesizing materials. Here, the authors design a triazole peptide that self-replicates and then self-assembles into nanostructures, coupling autocatalytic and assembly pathways to realize a reproducing supramolecular system.
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Affiliation(s)
- Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, San Diego, CA, 92093, USA.
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33
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Ross JF, Bridges A, Fletcher JM, Shoemark D, Alibhai D, Bray HEV, Beesley JL, Dawson WM, Hodgson LR, Mantell J, Verkade P, Edge CM, Sessions RB, Tew D, Woolfson DN. Decorating Self-Assembled Peptide Cages with Proteins. ACS NANO 2017; 11:7901-7914. [PMID: 28686416 DOI: 10.1021/acsnano.7b02368] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
An ability to organize and encapsulate multiple active proteins into defined objects and spaces at the nanoscale has potential applications in biotechnology, nanotechnology, and synthetic biology. Previously, we have described the design, assembly, and characterization of peptide-based self-assembled cages (SAGEs). These ≈100 nm particles comprise thousands of copies of de novo designed peptide-based hubs that array into a hexagonal network and close to give caged structures. Here, we show that, when fused to the designed peptides, various natural proteins can be co-assembled into SAGE particles. We call these constructs pSAGE for protein-SAGE. These particles tolerate the incorporation of multiple copies of folded proteins fused to either the N or the C termini of the hubs, which modeling indicates form the external and internal surfaces of the particles, respectively. Up to 15% of the hubs can be functionalized without compromising the integrity of the pSAGEs. This corresponds to hundreds of copies giving mM local concentrations of protein in the particles. Moreover, and illustrating the modularity of the SAGE system, we show that multiple different proteins can be assembled simultaneously into the same particle. As the peptide-protein fusions are made via recombinant expression of synthetic genes, we envisage that pSAGE systems could be developed modularly to actively encapsulate or to present a wide variety of functional proteins, allowing them to be developed as nanoreactors through the immobilization of enzyme cascades or as vehicles for presenting whole antigenic proteins as synthetic vaccine platforms.
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Affiliation(s)
- James F Ross
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Angela Bridges
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Jordan M Fletcher
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Deborah Shoemark
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | | | - Harriet E V Bray
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Joseph L Beesley
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - William M Dawson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | | | | | | | - Colin M Edge
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Richard B Sessions
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - David Tew
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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34
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Matsuura K. Construction of Functional Biomaterials by Biomolecular Self-Assembly. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170133] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552
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35
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Small amphipathic peptides are responsible for the assembly of cruciferin nanoparticles. Sci Rep 2017; 7:7819. [PMID: 28798358 PMCID: PMC5552735 DOI: 10.1038/s41598-017-07908-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/04/2017] [Indexed: 12/30/2022] Open
Abstract
Amphipathic peptides are versatile building blocks for fabricating well-ordered nanostructures, which have gained much attention owing to their enormous design possibilities and bio-functionalities. However, using amphipathic peptides from natural proteins to create tunable nanostructures is challenging because of their heterogeneity and great tendency to form aggregates. Here we fabricated two well-defined nanoparticles from cruciferin amphipathic peptides by integrating top-down and bottom-up approach. Alkali hydrolysis (pH 12, 120 °C for 30 min) was introduced to break down intact cruciferin into peptides (top–down). The cruciferin peptides and their fractions were then assembled into nanoparticles (bottom–up) in the presence of calcium ions. The permeate fraction from 10 kDa cut-off membrane formed smaller nanoparticles (F1-NPs) (around 82 nm) than that of unfractionated cruciferin peptides (CRU-NPs, around 185 nm); the electrostatic and hydrophobic interactions were the main driving forces for particle formation. LC-MS/MS analysis characterised that the small amphipathic peptides (Xn1Zn2Xn3Zn4, n1–4 = 0~5), composed of alternating hydrophobic (X) and hydrophilic (Z) amino acid with a length of 5–15 and 5–20 residues for F1-NPs and CRU-NPs, respectively, were responsible for particle formation. Our study established the mechanism of particle formation of the cold gelation is through assembly of amphipathic peptides.
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36
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Bella A, Ray S, Ryadnov MG. Linear and orthogonal peptide templating of silicified protein fibres. Org Biomol Chem 2017; 15:5380-5385. [PMID: 28620669 DOI: 10.1039/c7ob01134b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biomineralisation is essential for biology. Specialist proteins use peptide motifs that catalyse mineral deposition into nano-to-microscale inorganic materials. Unlike in native proteins, the motifs incorporated into self-assembled fibres can persistently propagate on the microscopic scale enabling empirically defined silica nanostructures. Herein we show that the two main modes of motif templating - linear and orthogonal - in self-assembling, fibre-forming peptide sequences effectively silicify protein fibres. We show that the mere charge and morphology of protein fibres are not sufficient for silica deposition, but it is the synergy between fibrillogenesis and silica-specific motifs regularly spaced in fibres that ensures silica templating, regardless of the relative orientation of the motifs.
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Affiliation(s)
- Angelo Bella
- National Physical Laboratory, Teddington, Middlesex TW11 0LW, UK.
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37
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Nakamura Y, Yamada S, Nishikawa S, Matsuura K. DNA-modified artificial viral capsids self-assembled from DNA-conjugated β-annulus peptide. J Pept Sci 2017; 23:636-643. [PMID: 28133866 DOI: 10.1002/psc.2967] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 01/01/2023]
Abstract
β-Annulus peptides from tomato bushy stunt virus conjugated with DNAs (dA20 and dT20 ) at the C-terminal were synthesized. The DNA-modified β-annulus peptides self-assembled into artificial viral capsids with sizes of 45-160 nm. ζ-Potential measurements revealed that the DNAs were coated on the surface of artificial viral capsids. Fluorescence assays indicated that the DNAs on the artificial viral capsids were partially hybridized with the complementary DNAs. Moreover, the DNA-modified artificial viral capsids formed aggregates by adding complementary polynucleotides. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Yoko Nakamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Saki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Shoko Nishikawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
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38
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Noble JE, De Santis E, Ravi J, Lamarre B, Castelletto V, Mantell J, Ray S, Ryadnov MG. A De Novo Virus-Like Topology for Synthetic Virions. J Am Chem Soc 2016; 138:12202-10. [PMID: 27585246 DOI: 10.1021/jacs.6b05751] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A de novo topology of virus-like assembly is reported. The design is a trifaceted coiled-coil peptide helix, which self-assembles into ultrasmall, monodisperse, anionic virus-like shells that encapsulate and transfer both RNA and DNA into human cells. Unlike existing artificial systems, these shells share the same physical characteristics of viruses being anionic, nonaggregating, abundant, hollow, and uniform in size, while effectively mediating gene silencing and transgene expression. These are the smallest virus-like structures reported to date, both synthetic and native, with the ability to adapt and transfer small and large nucleic acids. The design thus offers a promising solution for engineering bespoke artificial viruses with desired functions.
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Affiliation(s)
- James E Noble
- National Physical Laboratory , Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Emiliana De Santis
- National Physical Laboratory , Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Jascindra Ravi
- National Physical Laboratory , Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Baptiste Lamarre
- National Physical Laboratory , Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Valeria Castelletto
- Department of Chemistry, University of Reading , Reading RG6 6AD, United Kingdom
| | - Judith Mantell
- Wolfson Bio-imaging Facility, Department of Biochemistry, University of Bristol , Bristol BS8 1TD, United Kingdom
| | - Santanu Ray
- SET, University of Brighton , Brighton BN2 4GJ, United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road, Teddington TW11 0LW, United Kingdom
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