1
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Korkmaz N, Himawan S, Usman M, Baik S, Kim M. Bacteriophage Engineering for Improved Copper Ion Binding. Macromol Biosci 2024; 24:e2300354. [PMID: 37985183 DOI: 10.1002/mabi.202300354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/13/2023] [Indexed: 11/22/2023]
Abstract
In this study, fd viruses are genetically modified to display seven cropped versions (H, HG, HGF, HGFA, HGFAN, HGFANV and HGFANVA) of the previously identified Cu(II) specific peptide (HGFANVA). Atomic force microscopy (AFM) imaging reveals the typical filamentous structures of recombinant phages with thicknesses of ≈2-5 nm in dry state. Scanning electron microscopy (SEM) imaging shows that HGFANVA viruses form larger elongated assemblies than H viruses that are deposited with a mineral layer after Cu(II) treatment. C and N peaks are detected for virus samples through Energy dispersive X-ray spectroscopy (EDX) analyses confirming the presence of phage organic material. Cu peak is only detected for engineered viruses after Cu(II) exposure. Enzyme-linked immunosorbent assay (ELISA) analyses show the selective Cu(II) binding of engineered phages. Agarose gel electrophoresis (AGE) and zeta potential analyses reveal negative surface charges of engineered viral constructs. Positively charged Cytopore beads are coated with bacteriophages and used for Cu(II) ion sorption studies. ICP-MS analyses clearly show the improved Cu(II) binding of engineered viruses with respect to wild-type fd phages. Such bottom-up constructed, genetically engineered virus-based biomaterials may be applied in bioremediation studies targeting metal species from environmental samples.
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Affiliation(s)
- Nuriye Korkmaz
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Sandiego Himawan
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
- Bioprogrammable Materials Group, INM - Leibniz Institute for New Materials, Campus D 2.2, D-66123, Saarbrücken, Germany
| | - Muhammed Usman
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Seungyun Baik
- Environmental Safety Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
| | - Minyoung Kim
- Biosensor Group, Korea Institute of Science and Technology Europe Forschungsgesellschaft mbH, Campus E 7.1, D-66123, Saarbrücken, Germany
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2
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Böhning J, Graham M, Letham SC, Davis LK, Schulze U, Stansfeld PJ, Corey RA, Pearce P, Tarafder AK, Bharat TAM. Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa. Nat Commun 2023; 14:8429. [PMID: 38114502 PMCID: PMC10730611 DOI: 10.1038/s41467-023-44160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Inoviruses are filamentous phages infecting numerous prokaryotic phyla. Inoviruses can self-assemble into mesoscale structures with liquid-crystalline order, termed tactoids, which protect bacterial cells in Pseudomonas aeruginosa biofilms from antibiotics. Here, we investigate the structural, biophysical, and protective properties of tactoids formed by the P. aeruginosa phage Pf4 and Escherichia coli phage fd. A cryo-EM structure of the capsid from fd revealed distinct biochemical properties compared to Pf4. Fd and Pf4 formed tactoids with different morphologies that arise from differing phage geometries and packing densities, which in turn gave rise to different tactoid emergent properties. Finally, we showed that tactoids formed by either phage protect rod-shaped bacteria from antibiotic treatment, and that direct association with a tactoid is required for protection, demonstrating the formation of a diffusion barrier by the tactoid. This study provides insights into how filamentous molecules protect bacteria from extraneous substances in biofilms and in host-associated infections.
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Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Miles Graham
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Suzanne C Letham
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Luke K Davis
- Department of Mathematics, University College London, London, WC1H 0AY, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Philip Pearce
- Department of Mathematics, University College London, London, WC1H 0AY, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Abul K Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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3
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Kim JT, Lee CH, Jung D, Choi S, Jeong SH, Lee D, Lee Y, Chung TD. Virus-templated redox nanowire network for enzyme electrode. Biosens Bioelectron 2023; 237:115518. [PMID: 37442029 DOI: 10.1016/j.bios.2023.115518] [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] [Received: 05/05/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Viruses have unique coat proteins that are genetically modifiable. Their surface can serve as a nano-template on which electroactive molecules are immobilized. In this study, we report filamentous bacteriophage as a backbone to which redox mediators are covalently and densely tethered, constructing redox nanowire, i.e. an electron conducting biomaterial. The highly ordered coat proteins of a filamentous bacteriophage provide flexible and biocompatible platform to constitute a biohybrid redox nanowire. Incorporating bacteriophage and redox molecules form an entangled assembly of nanowires enabling facile electron transfer. Electron transfer among the molecular mediators in the entangled assembly originates apparent electron diffusion of which the electron transfer rate is comparable to that observed in conventional redox polymers. Programming peptide terminals suggests further enhancement in electron mediation by increasing redox species mobility. In addition, the redox nanowire film functions as a favorable matrix for enzyme encapsulation. The stability of the enzymes entrapped in this unique matrix is substantially improved.
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Affiliation(s)
- Ji Tae Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang Heon Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongwook Jung
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sejong Choi
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Hee Jeong
- Program in Nano Science and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Suwon-Si, Gyeonggi-do, 16229, Republic of Korea
| | - Dahye Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yan Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taek Dong Chung
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea; Program in Nano Science and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Suwon-Si, Gyeonggi-do, 16229, Republic of Korea; Electrochemistry Laboratory, Advanced Institutes of Convergence Technology, Suwon-Si, Gyeonggi-do, 16229, Republic of Korea.
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4
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Jia Q, Xiang Y. Cryo-EM structure of a bacteriophage M13 mini variant. Nat Commun 2023; 14:5421. [PMID: 37669979 PMCID: PMC10480500 DOI: 10.1038/s41467-023-41151-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM structure of a ~500 Å long bacteriophage M13 mini variant. The distal ends of the mini phage are sealed by two cap-like complexes composed of the minor coat proteins. The top cap complex consists of pVII and pIX, both exhibiting a single helix structure. Arg33 of pVII and Glu29 of pIX, located on the inner surface of the cap, play a key role in recognizing the genome packaging signal. The bottom cap complex is formed by the hook-like structures of pIII and pVI, arranged in helix barrels. Most of the inner ssDNA genome adopts a double helix structure with a similar pitch to that of the A-form double-stranded DNA. These findings provide insights into the assembly of filamentous bacteriophages.
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Affiliation(s)
- Qi Jia
- Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P.R. China
| | - Ye Xiang
- Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, P.R. China.
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5
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Conners R, León-Quezada RI, McLaren M, Bennett NJ, Daum B, Rakonjac J, Gold VAM. Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly. Nat Commun 2023; 14:2724. [PMID: 37169795 PMCID: PMC10175506 DOI: 10.1038/s41467-023-37915-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.
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Affiliation(s)
- Rebecca Conners
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rayén Ignacia León-Quezada
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Nanophage Technologies, Palmerston North, New Zealand
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Nicholas J Bennett
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Jasna Rakonjac
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Nanophage Technologies, Palmerston North, New Zealand.
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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6
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Pantaleone S, Sodupe M, Ugliengo P, Rimola A. On the stability of peptide secondary structures on the TiO 2 (101) anatase surface: a computational insight. Phys Chem Chem Phys 2022; 25:392-401. [PMID: 36477070 DOI: 10.1039/d2cp04395e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The biological activity of proteins is partly due to their secondary structures and conformational states. Peptide chains are rather flexible so that finding ways inducing protein folding in a well-defined state is of great importance. Among the different constraint techniques, the interaction of proteins with inorganic surfaces is a fruitful strategy to stabilize selected folded states. Surface-induced peptide folding can have potential applications in different biomedicine areas, but it can also be of fundamental interest in prebiotic chemistry since the biological activity of a peptide can turn-on when folded in a given state. In this work, periodic quantum mechanical simulations (including implicit solvation effects) at the PBE-D2* level have been carried out to study the adsorption and the stability of the secondary structures (α-helix and β-sheet) of polypeptides with different chemical composition (i.e., polyglycine, polyalanine, polyglutamic acid, polylysine, and polyarginine) on the TiO2 (101) anatase surface. The computational cost is reduced by applying periodic boundary conditions to both the surface and the peptides, thus obtaining full periodic polypeptide/TiO2 surface systems. At variance with polyglycine, the interaction of the other polypeptides with the surface takes place with the lateral chain functionalities, leaving the secondary structures almost undistorted. Results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet, with the exception of the polyglutamic acid. According to the calculated adsorption energies, the affinity trend of the polypeptides with the (101) anatase surface is: polyarginine ≈ polylysine > polyglutamic acid > polyglycine ≈ polyalanine, both when adsorbed in gas phase and in presence of the implicit water solvent, which is very similar to the trend for the single amino acids. A set of implications related to the areas of surface-induced peptide folding, biomedicine and prebiotic chemistry are finally discussed.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain. .,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
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7
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M13 Bacteriophage-Based Bio-nano Systems for Bioapplication. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00069-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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8
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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9
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Kamstrup Sell D, Sloth AB, Bakhshinejad B, Kjaer A. A White Plaque, Associated with Genomic Deletion, Derived from M13KE-Based Peptide Library Is Enriched in a Target-Unrelated Manner during Phage Display Biopanning Due to Propagation Advantage. Int J Mol Sci 2022; 23:ijms23063308. [PMID: 35328728 PMCID: PMC8950111 DOI: 10.3390/ijms23063308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
The nonspecific enrichment of target-unrelated peptides during biopanning remains a major drawback for phage display technology. The commercial Ph.D.TM-7 phage display library is used extensively for peptide discovery. This library is based on the M13KE vector, which carries the lacZα sequence, leading to the formation of blue plaques on IPTG-X-gal agar plates. In the current study, we report the isolation of a fast-propagating white clone (displaying WSLGYTG peptide) identified through screening against a recombinant protein. Sanger sequencing demonstrated that white plaques are not contamination from environmental M13-like phages, but derive from the library itself. Whole genome sequencing revealed that the white color of the plaques results from a large 827-nucleotide genomic deletion. The phenotypic characterization of propagation capacity through plaque count- and NGS-based competitive propagation assay supported the higher propagation rate of Ph-WSLGYTG clone compared with the library. According to our data, white plaques are likely to arise endogenously in Ph.D. libraries due to mutations in the M13KE genome and should not always be viewed as exogenous contamination. Our findings also led to the conclusion that the deletion observed here might be an ancestral mutation already present in the naïve library, which causes target-unrelated nonspecific enrichment of white clone during biopanning due to propagation advantage.
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10
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Zanotti G, Grinzato A. Structure of filamentous viruses. Curr Opin Virol 2021; 51:25-33. [PMID: 34592708 DOI: 10.1016/j.coviro.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/21/2021] [Accepted: 09/12/2021] [Indexed: 12/17/2022]
Abstract
Despite filamentous viruses represent an important portion of the universe of viruses, their 3D structures available are quite limited, particularly if compared to the large number of structures of icosahedral viruses present in the Protein Data Bank. As a matter of fact, flexible filamentous viruses cannot be grown as single crystals and past structural studies have mostly been limited to X-ray fiber diffraction or to the determination of the structure of isolated viral proteins. Only very recently, several structures of filamentous viruses have become available, owing to the recent development of cryo-electron microscopy. This technique has given a strong impulse to the field and has allowed the building of reliable molecular models of entire viruses, in some cases at a nearly atomic resolution level. In this paper we briefly describe the architecture of filamentous viruses that infect bacteria, archaea, plants and humans. It is easy to foresee that more new structures of filamentous viruses will become available soon and they will allow a better understanding of the rules underlying the structural organization of these organisms so relevant for the life on our planet.
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Affiliation(s)
- Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua, 35131, Italy.
| | - Alessandro Grinzato
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua, 35131, Italy.
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11
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Abstract
Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.
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Affiliation(s)
| | - Julie M. Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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12
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Porat G, Lusky OS, Dayan N, Goldbourt A. Nonuniformly sampled exclusively- 13 C/ 15 N 4D solid-state NMR experiments: Assignment and characterization of IKe phage capsid. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:237-246. [PMID: 32603513 DOI: 10.1002/mrc.5072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
An important step in the process of protein research by NMR is the assignment of chemical shifts. In the coat protein of IKe bacteriophage, there are 53 residues making up a long helix resulting in relatively high spectral ambiguity. Assignment thus requires the collection of a set of three-dimensional (3D) experiments and the preparation of sparsely labeled samples. Increasing the dimensionality can facilitate fast and reliable assignment of IKe and of larger proteins. Recent progress in nonuniform sampling techniques made the application of multidimensional NMR solid-state experiments beyond 3D more practical. 4D 1 H-detected experiments have been demonstrated in high-fields and at spinning speeds of 60 kHz and higher but are not practical at spinning speeds of 10-20 kHz for fully protonated proteins. Here, we demonstrate the applicability of a nonuniformly sampled 4D 13 C/15 N-only correlation experiment performed at a moderate field of 14.1 T, which can incorporate sufficiently long acquisition periods in all dimensions. We show how a single CANCOCX experiment, supported by several 2D carbon-based correlation experiments, is utilized for the assignment of heteronuclei in the coat protein of the IKe bacteriophage. One sparsely labeled sample was used to validate sidechain assignment of several hydrophobic-residue sidechains. A comparison to solution NMR studies of isolated IKe coat proteins embedded in micelles points to key residues involved in structural rearrangement of the capsid upon assembly of the virus. The benefits of 4D to a quicker assignment are discussed, and the method may prove useful for studying proteins at relatively low fields.
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Affiliation(s)
- Gal Porat
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, 19716, USA
| | - Orr Simon Lusky
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Nir Dayan
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
- Schulich Faculty of Chemistry, Technion-Institute of Technology, Haifa, Israel
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
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13
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Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nat Commun 2021; 12:407. [PMID: 33462223 PMCID: PMC7814010 DOI: 10.1038/s41467-020-20689-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Charles Modlin
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Puneet Juneja
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA. .,The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.
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Akremi I, Holtappels D, Brabra W, Jlidi M, Hadj Ibrahim A, Ben Ali M, Fortuna K, Ahmed M, Meerbeek BV, Rhouma A, Lavigne R, Ben Ali M, Wagemans J. First Report of Filamentous Phages Isolated from Tunisian Orchards to Control Erwinia amylovora. Microorganisms 2020; 8:microorganisms8111762. [PMID: 33182526 PMCID: PMC7697814 DOI: 10.3390/microorganisms8111762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023] Open
Abstract
Newly discovered Erwinia amylovora phages PEar1, PEar2, PEar4 and PEar6 were isolated from three different orchards in North Tunisia to study their potential as biocontrol agents. Illumina sequencing revealed that the PEar viruses carry a single-strand DNA genome between 6608 and 6801 nucleotides and belong to the Inoviridae, making them the first described filamentous phages of E. amylovora. Interestingly, phage-infected cells show a decreased swimming and swarming motility and a cocktail of the four phages can significantly reduce infection of E. amylovora in a pear bioassay, potentially making them suitable candidates for phage biocontrol.
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Affiliation(s)
- Ismahen Akremi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Wided Brabra
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Mouna Jlidi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
| | - Adel Hadj Ibrahim
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
| | - Manel Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Kiandro Fortuna
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Mohammed Ahmed
- Biomaterials Research Group (BIOMAT), Department of Oral Sciences, KU Leuven, Kapucijnenvoer 7-Block A Box 7001, 3000 Leuven, Belgium; (M.A.); (B.V.M.)
- Department of Dental Biomaterials, Tanta University, Biomedical Campus, 32511 Tanta, Gharbia Governorate, Egypt
| | - Bart Van Meerbeek
- Biomaterials Research Group (BIOMAT), Department of Oral Sciences, KU Leuven, Kapucijnenvoer 7-Block A Box 7001, 3000 Leuven, Belgium; (M.A.); (B.V.M.)
| | - Ali Rhouma
- Laboratory of Integrated Olive Production, Olive Tree Institute, BP208 Marhajene City, Tunis 1082, Tunisia;
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Mamdouh Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
- Correspondence: ; Tel.: +32-1637-4622
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15
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Zheng W, Pena A, Low WW, Wong JLC, Frankel G, Egelman EH. Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae. Structure 2020; 28:1321-1328.e2. [PMID: 32916103 DOI: 10.1016/j.str.2020.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 01/19/2023]
Abstract
Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism in the spread of antibiotic resistance. Filamentous bacteriophages have been shown to exist in two different structural classes: those with a 5-fold rotational symmetry and those with a one-start helix with approximately 5 subunits per turn. Structures for the F and the F-like pED208 conjugation pilus have shown that they have 5-fold rotational symmetry. Here, we report the cryoelectron-microscopic structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae, encoded on the IncFIIK pKpQIL plasmid, at 3.9 Å resolution and show that it has a one-start helix. These results establish that conjugation pili can exist in at least two structural classes, consistent with other results showing that relatively small perturbations are needed to change the helical symmetry of polymers.
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Affiliation(s)
- Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Alejandro Pena
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Wen Wen Low
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Joshua L C Wong
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Gad Frankel
- Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
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16
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Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria. Proc Natl Acad Sci U S A 2020; 117:4724-4731. [PMID: 32071243 PMCID: PMC7060675 DOI: 10.1073/pnas.1917726117] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this study, we investigate how phage molecules secreted by pathogenic Pseudomonas aeruginosa bacteria drive antibiotic tolerance by forming phase-separated liquid crystalline compartments around bacterial cells. This study spans across spatial scales, combining atomic structure determination using electron cryomicroscopy with cellular electron cryotomography, optical microscopy, and biochemical reconstitution. We show that encapsulation of rod-shaped bacteria by spindle-shaped liquid crystalline droplets made of phage molecules is a process profoundly influenced by shape and size complementarity. The opportunistic pathogen Pseudomonas aeruginosa is a major cause of antibiotic-tolerant infections in humans. P. aeruginosa evades antibiotics in bacterial biofilms by up-regulating expression of a symbiotic filamentous inoviral prophage, Pf4. We investigated the mechanism of phage-mediated antibiotic tolerance using biochemical reconstitution combined with structural biology and high-resolution cellular imaging. We resolved electron cryomicroscopy atomic structures of Pf4 with and without its linear single-stranded DNA genome, and studied Pf4 assembly into liquid crystalline droplets using optical microscopy and electron cryotomography. By biochemically replicating conditions necessary for antibiotic protection, we found that phage liquid crystalline droplets form phase-separated occlusive compartments around rod-shaped bacteria leading to increased bacterial survival. Encapsulation by these compartments was observed even when inanimate colloidal rods were used to mimic rod-shaped bacteria, suggesting that shape and size complementarity profoundly influences the process. Filamentous inoviruses are pervasive across prokaryotes, and in particular, several Gram-negative bacterial pathogens including Neisseria meningitidis, Vibrio cholerae, and Salmonella enterica harbor these prophages. We propose that biophysical occlusion mediated by secreted filamentous molecules such as Pf4 may be a general strategy of bacterial survival in harsh environments.
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17
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Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol 2020; 18:125-138. [PMID: 32015529 DOI: 10.1038/s41579-019-0311-5] [Citation(s) in RCA: 358] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Abstract
Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Frank Oechslin
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
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18
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Recent Developments and Prospects of M13- Bacteriophage Based Piezoelectric Energy Harvesting Devices. NANOMATERIALS 2020; 10:nano10010093. [PMID: 31906516 PMCID: PMC7022932 DOI: 10.3390/nano10010093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/24/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023]
Abstract
Recently, biocompatible energy harvesting devices have received a great deal of attention for biomedical applications. Among various biomaterials, viruses are expected to be very promising biomaterials for the fabrication of functional devices due to their unique characteristics. While other natural biomaterials have limitations in mass-production, low piezoelectric properties, and surface modification, M13 bacteriophages (phages), which is one type of virus, are likely to overcome these issues with their mass-amplification, self-assembled structure, and genetic modification. Based on these advantages, many researchers have started to develop virus-based energy harvesting devices exhibiting superior properties to previous biomaterial-based devices. To enhance the power of these devices, researchers have tried to modify the surface properties of M13 phages, form biomimetic hierarchical structures, control the dipole alignments, and more. These methods for fabricating virus-based energy harvesting devices can form a powerful strategy to develop high-performance biocompatible energy devices for a wide range of practical applications in the future. In this review, we discuss all these issues in detail.
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19
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Goldbourt A. Structural characterization of bacteriophage viruses by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:192-210. [PMID: 31779880 DOI: 10.1016/j.pnmrs.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.
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Affiliation(s)
- Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
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20
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Raja IS, Kim C, Song SJ, Shin YC, Kang MS, Hyon SH, Oh JW, Han DW. Virus-Incorporated Biomimetic Nanocomposites for Tissue Regeneration. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E1014. [PMID: 31311134 PMCID: PMC6669830 DOI: 10.3390/nano9071014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Owing to the astonishing properties of non-harmful viruses, tissue regeneration using virus-based biomimetic materials has been an emerging trend recently. The selective peptide expression and enrichment of the desired peptide on the surface, monodispersion, self-assembly, and ease of genetic and chemical modification properties have allowed viruses to take a long stride in biomedical applications. Researchers have published many reviews so far describing unusual properties of virus-based nanoparticles, phage display, modification, and possible biomedical applications, including biosensors, bioimaging, tissue regeneration, and drug delivery, however the integration of the virus into different biomaterials for the application of tissue regeneration is not yet discussed in detail. This review will focus on various morphologies of virus-incorporated biomimetic nanocomposites in tissue regeneration and highlight the progress, challenges, and future directions in this area.
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Affiliation(s)
| | - Chuntae Kim
- Department of Nanofusion Technology, College of Nanoscience & Nanotechnology, Pusan National University, Busan 46241, Korea
| | - Su-Jin Song
- Department of Cogno-Mechatronics Engineering, College of Nanoscience & Nanotechnology, Pusan National University, Busan 46241, Korea
| | - Yong Cheol Shin
- Department of Medical Engineering, Yonsei University, College of Medicine, Seoul 03722, Korea
| | - Moon Sung Kang
- Department of Cogno-Mechatronics Engineering, College of Nanoscience & Nanotechnology, Pusan National University, Busan 46241, Korea
| | - Suong-Hyu Hyon
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-8580, Japan
| | - Jin-Woo Oh
- Department of Nanofusion Technology, College of Nanoscience & Nanotechnology, Pusan National University, Busan 46241, Korea.
| | - Dong-Wook Han
- Department of Cogno-Mechatronics Engineering, College of Nanoscience & Nanotechnology, Pusan National University, Busan 46241, Korea.
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