1
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Parra B, Cockx B, Lutz VT, Brøndsted L, Smets BF, Dechesne A. Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids. Microbiol Spectr 2024; 12:e0253723. [PMID: 38063386 PMCID: PMC10782986 DOI: 10.1128/spectrum.02537-23] [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: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 12/23/2023] Open
Abstract
IMPORTANCE This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.
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Affiliation(s)
- Boris Parra
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Laboratorio de Investigación de Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Concepción, Chile
| | - Bastiaan Cockx
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veronika T. Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, København, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, København, Denmark
| | - Barth F. Smets
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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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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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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4
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Kang K, Ma Y, Sadakane K. Direct visualization of local activities of long DNA strands via image-time correlation. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:1139-1155. [PMID: 34499211 PMCID: PMC8566448 DOI: 10.1007/s00249-021-01570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/26/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
Bacteriophages with long DNA genomes are of interest due to their diverse mutations dependent on environmental factors. By lowering the ionic strength of a hydrophobic (PPh4Cl) antagonistic salt (at 1 mM), single long T4 DNA strand fluctuations were clearly observed, while condensed states of T4 DNA globules were formed above 5-10 mM salt. These long DNA strands were treated with fluorescently labeled probes, for which photo bleaching is often unavoidable over a short time of measurement. In addition, long (few tens of [Formula: see text]) length scales are required to have larger fields of view for better sampling, with shorter temporal resolutions. Thus, an optimization between length and time is crucial to obtain useful information. To facilitate the challenge of detecting large biomacromolecules, we here introduce an effective method of live image data analysis for direct visualization and quantification of local thermal fluctuations. The motions of various conformations for the motile long DNA strands were examined for the single- and multi-T4 DNA strands. We find that the unique correlation functions exhibit a relatively high-frequency oscillatory behavior superimposed on the overall slower decay of the correlation function with a splitting of amplitudes deriving from local activities of the long DNA strands. This work shows not only the usefulness of an image-time correlation for analyzing large biomacromolecules, but also provides insight into the effects of a hydrophobic antagonistic salt on active T4 bacteriophage long DNA strands, including thermal translocations in their electrostatic interactions.
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Affiliation(s)
- Kyongok Kang
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing, IBI-4, Forschungszentrum Jülich, Jülich, Germany
| | - Yue Ma
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394 Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394 Japan
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5
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Feast S, Fee C, Huber T, Clarke D. Printed monolith adsorption as an alternative to expanded bed adsorption for purifying M13 bacteriophage. J Chromatogr A 2021; 1652:462365. [PMID: 34246960 DOI: 10.1016/j.chroma.2021.462365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/14/2021] [Accepted: 06/19/2021] [Indexed: 11/18/2022]
Abstract
An ordered 3D printed chromatography stationary phase was used to purify M13 bacteriophage (M13) directly from crude cell culture. This new approach, which offers the same advantages as expanded bed adsorption (EBA) with regard to tolerating solids-laden feed streams but without the corresponding issues associated with fluidized bed stability that affect the latter, can be described as "printed monolith adsorption (PMA)". PMA columns (5, 10 and 15 cm length by 1 cm diameter) were made via a wax templating method from cross-linked cellulose hydrogel and functionalized with a quaternary amine ligand. The recovery of M13 was found to be strongly linked to load flow rate, with the highest recovery 89.7% ± 6% for 1.4 × 1011 pfu/mL of resin occurring at 76 cm/h with a 10 cm column length. A recovery of 87.7% ± 5% for 1.49 × 1011 pfu/mL of media was achieved with a 15 cm column length under conditions comparable to a reported EBA process. The PMA process was completed three times faster than EBA because PMA flow rates can readily be adjusted during operation, with high flow rates and low back pressure, which is unique to the ordered monolithic media geometry used. Equilibration, wash, and cleaning steps were carried out at high flow rates (611 cm/h), minimizing process time and were limited only by the volumetric flow rate capacity of the pumps used, rather than column back pressure (<0.1 MPa at 611 cm/hr). Initial capture of M13 appears to occur on the surface of the monolith solid phase (i.e. the mobile phase channel walls) and subsequently, at a slower rate, within the internal pores of the solid phase media. The difference in binding rate between these two sites is likely caused by slow pore diffusion of the large M13 particles into the pores, with similar slow diffusion out of the pores resulting in tailing of the elution peak. The results indicate that PMA is a promising technology for the efficient purification of viruses directly from crude cell culture.
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Affiliation(s)
- Sean Feast
- School of Product Design and the Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand.
| | - Conan Fee
- School of Product Design and the Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand.
| | - Tim Huber
- School of Product Design and the Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand.
| | - Daniel Clarke
- School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
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6
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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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7
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Kang K. Equilibrium phase diagram and thermal responses of charged DNA-virus rod-suspensions at low ionic strengths. Sci Rep 2021; 11:3472. [PMID: 33568703 PMCID: PMC7876043 DOI: 10.1038/s41598-021-82653-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
The collective behavior of DNA is important for exploring new types of bacteria in the means of detection, which is greatly interested in the understanding of interactions between DNAs in living systems. How they self-organize themselves is a physical common phenomenon for broad ranges of thermodynamic systems. In this work, the equilibrium phase diagrams of charged chiral rods (fd viruses) at low ionic strengths (below a few mM) are provided to demonstrate both replicas of (or self-organized) twist orders and replica symmetry breaking near high concentration glass-states. By varying the ionic strengths, it appears that a critical ionic strength is obtained below 1-2 mM salt, where the twist and freezing of nematic domains diverge. Also, the microscopic relaxation is revealed by the ionic strength-dependent effective Debye screening length. At a fixed low ionic strength, the local orientations of twist are shown by two different length scales of optical pitch, in the chiral-nematic N* phase and the helical domains [Formula: see text], for low and high concentration, respectively. RSB occurs in several cases of crossing phase boundary lines in the equilibrium phase diagram of DNA-rod concentration and ionic strength, including long-time kinetic arrests in the presence of twist orders. The different pathways of PATH I, II and III are due to many-body effects of randomized orientations for charged fd rods undergoing long-range electrostatic interactions in bulk elastic medium. In addition, the thermal stability are shown for chiral pitches of the N* phase and the abnormal cooling process of a specific heat in a structural glass. Here, the concentration-driven twist-effects of charged DNA rods are explored using various experimental methods involving image-time correlation, microscopic dynamics in small angle dynamic light scattering, optical activity in second harmonic generation, and differential scanning calorimetry for the glass state.
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Affiliation(s)
- Kyongok Kang
- Institute of Biological Information Processing, IBI-4, Biomacromolecular Systems and Processes, Forschungszentrum Jülich, Jülich, Germany.
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8
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Screening polymeric ionic liquids for chromatography-based purification of bacteriophage M13. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2020.117906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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9
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Phage Display for Imaging Agent Development. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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10
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Sozhamannan S, Hofmann ER. The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. Viruses 2020; 12:v12121393. [PMID: 33291831 PMCID: PMC7762055 DOI: 10.3390/v12121393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Accurate pathogen detection and diagnosis is paramount in clinical success of treating patients. There are two general paradigms in pathogen detection: molecular and immuno-based, and phage-based detection is a third emerging paradigm due to its sensitivity and selectivity. Molecular detection methods look for genetic material specific for a given pathogen in a sample usually by polymerase chain reaction (PCR). Immuno-methods look at the pathogen components (antigens) by antibodies raised against that pathogen specific antigens. There are different variations and products based on these two paradigms with advantages and disadvantages. The third paradigm at least for bacterial pathogen detection entails bacteriophages specific for a given bacterium. Sensitivity and specificity are the two key parameters in any pathogen detection system. By their very nature, bacteriophages afford the best sensitivity for bacterial detection. Bacteria and bacteriophages form the predator-prey pair in the evolutionary arms race and has coevolved over time to acquire the exquisite specificity of the pair, in some instances at the strain level. This specificity has been exploited for diagnostic purposes of various pathogens of concern in clinical and other settings. Many recent reviews focus on phage-based detection and sensor technologies. In this review, we focus on a very special group of pathogens that are of concern in biodefense because of their potential misuse in bioterrorism and their extremely virulent nature and as such fall under the Centers for Disease and Prevention (CDC) Category A pathogen list. We describe the currently available phage methods that are based on the usual modalities of detection from culture, to molecular and immuno- and fluorescent methods. We further highlight the gaps and the needs for more modern technologies and sensors drawing from technologies existing for detection and surveillance of other pathogens of clinical relevance.
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Affiliation(s)
- Shanmuga Sozhamannan
- National Security Science & Technology, Management Advisory Services, Logistics Management Institute, 7940 Jones Branch Drive, Tysons, VA 22102, USA;
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense (CBRND) Joint Project Lead (JPL) CBRND Enabling Biotechnologies (EB), 110 Thomas Johnson Drive, Suite 250, Frederick, MD 21702, USA
| | - Edward R. Hofmann
- EXCET, Inc., 6225 Brandon Ave #360, Springfield, VA 22150, USA
- US Army Combat Capabilities Development Command, Chemical Biological Center, 8908 Guard St, E3831, Edgewood, MD 21010, USA
- Correspondence:
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11
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CRP-binding bacteriophage as a new element of layer-by-layer assembly carbon nanofiber modified electrodes. Bioelectrochemistry 2020; 136:107629. [PMID: 32818758 DOI: 10.1016/j.bioelechem.2020.107629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/02/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Recently, bacteriophage particles have started to be applied as a new biomaterial for developing sensing platforms. They can be used as both a recognition element or/and as building blocks, template/scaffold. In this paper, we studied a bacteriophage selected through phage-display technology. The chosen bacteriophage acted as a building block for creating a carbon nanofiber-based electrode and as a new receptor/binding element that recognizes C-reactive protein (CRP) - one of the markers of inflammatory processes in the human body. The binding efficiency of the selected phage towards CRP is two orders of magnitude higher than in the wild type. We demonstrate that the phage-based sensor is selective against other proteins. Finally, we show that layer-by-layer methods are suitable for deposition of negatively charged phages (wild or CRP-binding) with positively charged carbon nanofibers for electrode surface modification. A three-layered electrode was successfully used for molecular recognition of CRP, and the molecular interactions were studied using electrochemical, biological, and optical methods, including microscopic and spectroscopic analyses.
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12
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Xu H, Cao B, Li Y, Mao C. Phage nanofibers in nanomedicine: Biopanning for early diagnosis, targeted therapy, and proteomics analysis. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 12:e1623. [PMID: 32147974 DOI: 10.1002/wnan.1623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/02/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
Display of a peptide or protein of interest on the filamentous phage (also known as bacteriophage), a biological nanofiber, has opened a new route for disease diagnosis and therapy as well as proteomics. Earlier phage display was widely used in protein-protein or antigen-antibody studies. In recent years, its application in nanomedicine is becoming increasingly popular and encouraging. We aim to review the current status in this research direction. For better understanding, we start with a brief introduction of basic biology and structure of the filamentous phage. We present the principle of phage display and library construction method on the basis of the filamentous phage. We summarize the use of the phage displayed peptide library for selecting peptides with high affinity against cells or tissues. We then review the recent applications of the selected cell or tissue targeting peptides in developing new targeting probes and therapeutics to advance the early diagnosis and targeted therapy of different diseases in nanomedicine. We also discuss the integration of antibody phage display and modern proteomics in discovering new biomarkers or target proteins for disease diagnosis and therapy. Finally, we propose an outlook for further advancing the potential impact of phage display on future nanomedicine. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Hong Xu
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Binrui Cao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Yan Li
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
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13
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Martin AD, Wojciechowski JP, Du EY, Rawal A, Stefen H, Au CG, Hou L, Cranfield CG, Fath T, Ittner LM, Thordarson P. Decoupling the effects of hydrophilic and hydrophobic moieties at the neuron-nanofibre interface. Chem Sci 2019; 11:1375-1382. [PMID: 34123262 PMCID: PMC8148083 DOI: 10.1039/c9sc05686f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Peptide-based nanofibres are a versatile class of tunable materials with applications in optoelectronics, sensing and tissue engineering. However, the understanding of the nanofibre surface at the molecular level is limited. Here, a series of homologous dilysine–diphenylalnine tetrapeptides were synthesised and shown to self-assemble into water-soluble nanofibres. Despite the peptide nanofibres displaying similar morphologies, as evaluated through atomic force microscopy and neutron scattering, significant differences were observed in their ability to support sensitive primary neurons. Contact angle and labelling experiments revealed that differential presentation of lysine moieties at the fibre surface did not affect neuronal viability; however the mobility of phenylalanine residues at the nanofibre surface, elucidated through solid- and gel-state NMR studies and confirmed through tethered bilayer lipid membrane experiments, was found to be the determining factor in governing the suitability of a given peptide as a scaffold for primary neurons. This work offers new insights into characterising and controlling the nanofibre surface at the molecular level. The mobility of hydrophobic moieties at a peptide nanofibre surface determines its suitability as a scaffold for sensitive primary cells.![]()
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Affiliation(s)
- Adam D Martin
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University Sydney NSW 2109 Australia
| | | | - Eric Y Du
- School of Chemistry, The Australian Centre for Nanomedicine, The ARC Centre of Excellence in Convergent Bio-Nano Science & Technology, University of New South Wales Sydney NSW 2052 Australia
| | - Aditya Rawal
- NMR Facility, Mark Wainwright Analytical Centre, The University of New South Wales Sydney 2052 New South Wales Australia
| | - Holly Stefen
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Carol G Au
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Liming Hou
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney Ultimo NSW 2007 Australia
| | - Thomas Fath
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Lars M Ittner
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Pall Thordarson
- School of Chemistry, The Australian Centre for Nanomedicine, The ARC Centre of Excellence in Convergent Bio-Nano Science & Technology, University of New South Wales Sydney NSW 2052 Australia
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14
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Putra BR, Szot-Karpińska K, Kudła P, Yin H, Boswell JA, Squires AM, Da Silva MA, Edler KJ, Fletcher PJ, Parker SC, Marken F. Bacteriophage M13 Aggregation on a Microhole Poly(ethylene terephthalate) Substrate Produces an Anionic Current Rectifier: Sensitivity toward Anionic versus Cationic Guests. ACS APPLIED BIO MATERIALS 2019; 3:512-521. [DOI: 10.1021/acsabm.9b00952] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Budi Riza Putra
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, West Java, Indonesia
| | - Katarzyna Szot-Karpińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Patryk Kudła
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Han Yin
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Jacob A. Boswell
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Adam M. Squires
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | | | - Karen J. Edler
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Philip J. Fletcher
- Material & Chemical Characterisation Facility MC2, University of Bath, Bath BA2 7AY, U.K
| | - Stephen C. Parker
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Frank Marken
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
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15
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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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16
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Tronolone JJ, Orrill M, Song W, Kim HS, Lee BY, LeBlanc S. Electric Field Assisted Self-Assembly of Viruses into Colored Thin Films. NANOMATERIALS 2019; 9:nano9091310. [PMID: 31540252 PMCID: PMC6781059 DOI: 10.3390/nano9091310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
Filamentous viruses called M13 bacteriophages are promising materials for devices with thin film coatings because phages are functionalizable, and they can self-assemble into smectic helicoidal nanofilament structures. However, the existing “pulling” approach to align the nanofilaments is slow and limits potential commercialization of this technology. This study uses an applied electric field to rapidly align the nanostructures in a fixed droplet. The electric field reduces pinning of the three-phase contact line, allowing it to recede at a constant rate. Atomic force microscopy reveals that the resulting aligned structures resemble those produced via the pulling method. The field-assisted alignment results in concentric color bands quantified with image analysis of red, green, and blue line profiles. The alignment technique shown here could reduce self-assembly time from hours to minutes and lend itself to scalable manufacturing techniques such as inkjet printing.
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Affiliation(s)
- James J Tronolone
- Department of Biomedical Engineering, The George Washington University, Washington, DC 20052, USA.
| | - Michael Orrill
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052, USA.
| | - Wonbin Song
- Department of Mechanical Engineering, Korea University, Seoul 02841, Korea.
| | - Hyun Soo Kim
- Department of Mechanical Engineering, Korea University, Seoul 02841, Korea.
| | - Byung Yang Lee
- Department of Mechanical Engineering, Korea University, Seoul 02841, Korea.
| | - Saniya LeBlanc
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052, USA.
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17
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Combinatorial Avidity Selection of Mosaic Landscape Phages Targeted at Breast Cancer Cells-An Alternative Mechanism of Directed Molecular Evolution. Viruses 2019; 11:v11090785. [PMID: 31454976 PMCID: PMC6784196 DOI: 10.3390/v11090785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 02/08/2023] Open
Abstract
Low performance of actively targeted nanomedicines required revision of the traditional drug targeting paradigm and stimulated the development of novel phage-programmed, self-navigating drug delivery vehicles. In the proposed smart vehicles, targeting peptides, selected from phage libraries using traditional principles of affinity selection, are substituted for phage proteins discovered through combinatorial avidity selection. Here, we substantiate the potential of combinatorial avidity selection using landscape phage in the discovery of Short Linear Motifs (SLiMs) and their partner domains. We proved an algorithm for analysis of phage populations evolved through multistage screening of landscape phage libraries against the MDA-MB-231 breast cancer cell line. The suggested combinatorial avidity selection model proposes a multistage accumulation of Elementary Binding Units (EBU), or Core Motifs (CorMs), in landscape phage fusion peptides, serving as evolutionary initiators for formation of SLiMs. Combinatorial selection has the potential to harness directed molecular evolution to create novel smart materials with diverse novel, emergent properties.
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18
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19
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Wang Y, Gao S, Lv J, Lin Y, Zhou L, Han L. Phage Display Technology and its Applications in Cancer Immunotherapy. Anticancer Agents Med Chem 2019; 19:229-235. [PMID: 30370861 DOI: 10.2174/1871520618666181029140814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 06/01/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Background:Phage display is an effective technology for generation and selection targeting protein for a variety of purpose, which is based on a direct linkage between the displayed protein and the DNA sequence encoding it and utilized in selecting peptides, improving peptides affinity and indicating protein-protein interactions. Phage particles displaying peptide have the potential to apply in the identification of cell-specific targeting molecules, identification of cancer cell surface biomarkers, identification anti-cancer peptide, and the design of peptide-based anticancer therapy.Method/Results:Literature searches, reviews and assessments about Phage were performed in this review from PubMed and Medline databases.Conclusion:The phage display technology is an inexpensive method for expressing exogenous peptides, generating unique peptides that bind any given target and investigating protein-protein interactions. Due to the powerful ability to insert exogenous gene and display exogenous peptides on the surface, phages may represent a powerful peptide delivery system that can be utilized to develop rapid, efficient, safe and inexpensive cancer therapy methods.
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Affiliation(s)
- Yicun Wang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, China
| | - Shuohui Gao
- Third Hospital of Jilin University, Changchun, China
| | - Jiayin Lv
- Third Hospital of Jilin University, Changchun, China
| | - Yang Lin
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, China
| | - Li Zhou
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, China
| | - Liying Han
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, China
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20
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Ru X, Li L, Wang C. Identification of Phage Viral Proteins With Hybrid Sequence Features. Front Microbiol 2019; 10:507. [PMID: 30972038 PMCID: PMC6443926 DOI: 10.3389/fmicb.2019.00507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/27/2019] [Indexed: 02/01/2023] Open
Abstract
The uniqueness of bacteriophages plays an important role in bioinformatics research. In real applications, the function of the bacteriophage virion proteins is the main area of interest. Therefore, it is very important to classify bacteriophage virion proteins and non-phage virion proteins accurately. Extracting comprehensive and effective sequence features from proteins plays a vital role in protein classification. In order to more fully represent protein information, this paper is more comprehensive and effective by combining the features extracted by the feature information representation algorithm based on sequence information (CCPA) and the feature representation algorithm based on sequence and structure information. After extracting features, the Max-Relevance-Max-Distance (MRMD) algorithm is used to select the optimal feature set with the strongest correlation between class labels and low redundancy between features. Given the randomness of the samples selected by the random forest classification algorithm and the randomness features for producing each node variable, a random forest method is employed to perform 10-fold cross-validation on the bacteriophage protein classification. The accuracy of this model is as high as 93.5% in the classification of phage proteins in this study. This study also found that, among the eight physicochemical properties considered, the charge property has the greatest impact on the classification of bacteriophage proteins These results indicate that the model discussed in this paper is an important tool in bacteriophage protein research.
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Affiliation(s)
- Xiaoqing Ru
- School of Information and Electrical Engineering, Hebei University of Engineering, Handan, China
| | - Lihong Li
- School of Information and Electrical Engineering, Hebei University of Engineering, Handan, China
| | - Chunyu Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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21
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Abstract
The filamentous bacteriophage IKe is one of many nonenveloped bacterial viruses that encapsulate a circular single-stranded viral genome in the phage capsid shell. The shell of IKe is comprised of about 3,100 copies of the IKe major coat protein. Atomic-resolution structures of filamentous phages are scarce, and the structure of the single-stranded DNA is a matter of debate. Our cryo-electron microscopy structure of the filamentous bacteriophage IKe at a resolution of 3.4 Å provides atomic details on the structure of the major coat protein, the symmetry of the capsid shell, and the key interactions driving its assembly. We propose a model for the conformation of the circular single-stranded DNA core and the interactions between the capsid shell and inner DNA core. The filamentous bacteriophage IKe infects Escherichia coli cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major coat protein [protein 8 (p8)] consists of 47 residues that fold into a ∼68-Å-long helix. An atomic model of the coat protein was built. Five p8 helices in a horizontal layer form a pentamer, and symmetrically neighboring p8 layers form a right-handed helical cylinder having a rise per pentamer of 16.77 Å and a twist of 38.52°. The inner surface of the capsid cylinder is positively charged and has direct interactions with the encapsulated circular single-stranded DNA genome, which has an electron density consistent with an unusual left-handed helix structure. Similar to capsid structures of other filamentous viruses, strong capsid packing in the IKe particle is maintained by hydrophobic residues. Despite having a different length and large sequence differences from other filamentous phages, π–π interactions were found between Tyr9 of one p8 and Trp29 of a neighboring p8 in IKe that are similar to interactions observed in phage M13, suggesting that, despite sequence divergence, overall structural features are maintained.
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22
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Kilper S, Jahnke T, Aulich M, Burghard Z, Rothenstein D, Bill J. Genetically Induced In Situ-Poling for Piezo-Active Biohybrid Nanowires. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805597. [PMID: 30548703 DOI: 10.1002/adma.201805597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/08/2018] [Indexed: 06/09/2023]
Abstract
Polycrystalline piezo-active materials only exhibit a high macroscopic piezoresponse if they consist of particles with oriented crystal directions and aligned intrinsic dipole moments. For ferroelectric materials, the postsynthesis alignment of the dipoles is generally achieved by electric poling procedures. However, there are numerous technically interesting non-ferroelectric piezo-active materials like zinc oxide (ZnO). These materials demand the alignment of their intrinsic dipoles during the fabrication process. Therefore, in situ-poling techniques have to be developed. This study utilizes genetically modified M13 phage templates for the generation of force fields, which directly control the ZnO dipole poling. By genetic modification of M13 phage template, the piezoelectric response of the ZnO/M13 phage hybrid nanowire is doubled compared to the hybrid nanowire based on unmodified M13 wild type (wt) phage templates. Thus, the formation of piezo-active domains consisting of oriented ZnO nanocrystals is directly induced by the genetic modification. By the combination of the fiber-like structure of individual M13 phages with the bioenhanced electromechanical properties of ZnO, hybrid nanowires with a length of ≈1.1 µm and a thickness of ≈63.5 nm are fabricated with a high piezoelectric coefficient of up to d33 = 7.8 pm V-1 for genetically modified M13 phage templates.
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Affiliation(s)
- Stefan Kilper
- Institute for Materials Science (IMW), University Stuttgart, Heisenbergstraße 3, 70569, Stuttgart, Germany
| | - Timotheus Jahnke
- Institute for Materials Science (IMW), University Stuttgart, Heisenbergstraße 3, 70569, Stuttgart, Germany
| | - Marc Aulich
- Institute for Materials Science (IMW), University Stuttgart, Heisenbergstraße 3, 70569, Stuttgart, Germany
| | - Zaklina Burghard
- Institute for Materials Science (IMW), University Stuttgart, Heisenbergstraße 3, 70569, Stuttgart, Germany
| | - Dirk Rothenstein
- Institute for Materials Science (IMW), University Stuttgart, Heisenbergstraße 3, 70569, Stuttgart, Germany
| | - Joachim Bill
- Institute for Materials Science (IMW), University Stuttgart, Heisenbergstraße 3, 70569, Stuttgart, Germany
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23
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Liu S, Zheng C, Ye Z, Blanc B, Zhi X, Shi L, Zhang Z. Filamentous Viruses Grafted with Thermoresponsive Block Polymers: Liquid Crystal Behaviors of a Rodlike Colloidal Model with “True” Attractive Interactions. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shuaiyu Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 300071 Tianjin, China
| | - Chunxiong Zheng
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 300071 Tianjin, China
| | - Zihan Ye
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 300071 Tianjin, China
| | - Baptiste Blanc
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Xueli Zhi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 300071 Tianjin, China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 300071 Tianjin, China
| | - Zhenkun Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, 300071 Tianjin, China
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24
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Ngo-Duc TT, Plank JM, Chen G, Harrison RES, Morikis D, Liu H, Haberer ED. M13 bacteriophage spheroids as scaffolds for directed synthesis of spiky gold nanostructures. NANOSCALE 2018; 10:13055-13063. [PMID: 29952390 DOI: 10.1039/c8nr03229g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The spherical form (s-form) of a genetically-modified gold-binding M13 bacteriophage was investigated as a scaffold for gold synthesis. Repeated mixing of the phage with chloroform caused a 15-fold contraction from a nearly one micron long filament to an approximately 60 nm diameter spheroid. The geometry of the viral template and the helicity of its major coat protein were monitored throughout the transformation process using electron microscopy and circular dichroism spectroscopy, respectively. The transformed virus, which retained both its gold-binding and mineralization properties, was used to assemble gold colloid clusters and synthesize gold nanostructures. Spheroid-templated gold synthesis products differed in morphology from filament-templated ones. Spike-like structures protruded from the spherical template while isotropic particles developed on the filamentous template. Using inductively coupled plasma-mass spectroscopy (ICP-MS), gold ion adsorption was found to be comparatively high for the gold-binding M13 spheroid, and likely contributed to the dissimilar gold morphology. Template contraction was believed to modify the density, as well as the avidity of gold-binding peptides on the scaffold surface. The use of the s-form of the M13 bacteriophage significantly expands the templating capabilities of this viral platform and introduces the potential for further morphological control of a variety of inorganic material systems.
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Affiliation(s)
- Tam-Triet Ngo-Duc
- Materials Science and Engineering Program, University of California, Riverside, USA.
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26
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Landscape Phage: Evolution from Phage Display to Nanobiotechnology. Viruses 2018; 10:v10060311. [PMID: 29880747 PMCID: PMC6024655 DOI: 10.3390/v10060311] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023] Open
Abstract
The development of phage engineering technology has led to the construction of a novel type of phage display library-a collection of nanofiber materials with diverse molecular landscapes accommodated on the surface of phage particles. These new nanomaterials, called the "landscape phage", serve as a huge resource of diagnostic/detection probes and versatile construction materials for the preparation of phage-functionalized biosensors and phage-targeted nanomedicines. Landscape-phage-derived probes interact with biological threat agents and generate detectable signals as a part of robust and inexpensive molecular recognition interfaces introduced in mobile detection devices. The use of landscape-phage-based interfaces may greatly improve the sensitivity, selectivity, robustness, and longevity of these devices. In another area of bioengineering, landscape-phage technology has facilitated the development and testing of targeted nanomedicines. The development of high-throughput phage selection methods resulted in the discovery of a variety of cancer cell-associated phages and phage proteins demonstrating natural proficiency to self-assemble into various drug- and gene-targeting nanovehicles. The application of this new "phage-programmed-nanomedicines" concept led to the development of a number of cancer cell-targeting nanomedicine platforms, which demonstrated anticancer efficacy in both in vitro and in vivo experiments. This review was prepared to attract the attention of chemical scientists and bioengineers seeking to develop functionalized nanomaterials and use them in different areas of bioscience, medicine, and engineering.
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27
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Electro-acoustic sensor for the real-time identification of the bacteriophages. Talanta 2018; 178:743-750. [DOI: 10.1016/j.talanta.2017.10.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 11/20/2022]
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28
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M13 bacteriophage purification using poly(ionic liquids) as alternative separation matrices. J Chromatogr A 2018; 1532:246-250. [DOI: 10.1016/j.chroma.2017.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/17/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023]
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29
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Gibaud T. Filamentous phages as building blocks for reconfigurable and hierarchical self-assembly. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:493003. [PMID: 29099393 DOI: 10.1088/1361-648x/aa97f9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties of diameter, length, rigidity, charge and chirality. Engineering these viruses leads to a library of colloidal rods, which can be used as building blocks for reconfigurable and hierarchical self-assembly. Their condensation in an aqueous solution with additive polymers, which act as depletants to induce attraction between the rods, leads to a myriad of fluid-like micronic structures ranging from isotropic/nematic droplets, colloid membranes, achiral membrane seeds, twisted ribbons, π-wall, pores, colloidal skyrmions, Möbius anchors, scallop membranes to membrane rafts. These structures, and the way that they shape-shift, not only shed light on the role of entropy, chiral frustration and topology in soft matter, but also mimic many structures encountered in different fields of science. On the one hand, filamentous phages being an experimental realization of colloidal hard rods, their condensation mediated by depletion interactions constitutes a blueprint for the self-assembly of rod-like particles and provides a fundamental foundation for bio- or material-oriented applications. On the other hand, the chiral properties of the viruses restrict the generalities of some results but vastly broaden the self-assembly possibilities.
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Affiliation(s)
- Thomas Gibaud
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France
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30
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Fibre diffraction studies of biological macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:43-87. [DOI: 10.1016/j.pbiomolbio.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 12/27/2022]
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31
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Guliy OI, Zaitsev BD, Borodina IA, Shikhabudinov AM, Teplykh AA. Analysis of interaction of bacterial cells and bacteriophages in conducting suspensions with an acoustic sensor. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817040068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Affiliation(s)
- Yicun Wang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, China
| | - Li Wang
- Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, 5268 Renmin Street, Changchun, 130042, China.
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33
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Abstract
Molecular imaging allows for the visualization of changes at the cellular level in diseases such as cancer. A successful molecular imaging agent must rely on disease-selective targets and ligands that specifically interact with those targets. Unfortunately, the translation of novel target-specific ligands into the clinic has been frustratingly slow with limitations including the complex design and screening approaches for ligand identification, as well as their subsequent optimization into useful imaging agents. This review focuses on combinatorial library approaches towards addressing these two challenges, with particular focus on phage display and one-bead one-compound (OBOC) libraries. Both of these peptide-based techniques have proven successful in identifying new ligands for cancer-specific targets and some of the success stories will be highlighted. New developments in screening methodology and sequencing technology have pushed the bounds of phage display and OBOC even further, allowing for even faster and more robust discovery of novel ligands. The combination of multiple high-throughput technologies will not only allow for more accurate identification, but also faster affinity maturation, while overall streamlining the process of translating novel ligands into clinical imaging agents.
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34
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Guliy OI, Zaitsev BD, Borodina IA, Teplykh AA, Ignatov OV. An acoustic method for the analysis of bacterial cells. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916040138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Guliy OI, Zaitsev BD, Shikhabudinov AM, Teplykh AA, Borodina IA, Pavliy SA, Larionova OS, Fomin AS, Staroverov SA, Dykman LA, Ignatov OV. Immunodetection of bacteriophages by a piezoelectric resonator with lateral electric field. APPL BIOCHEM MICRO+ 2016. [DOI: 10.1134/s0003683816040062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Dogic Z. Filamentous Phages As a Model System in Soft Matter Physics. Front Microbiol 2016; 7:1013. [PMID: 27446051 PMCID: PMC4927585 DOI: 10.3389/fmicb.2016.01013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/14/2016] [Indexed: 02/04/2023] Open
Abstract
Filamentous phages have unique physical properties, such as uniform particle lengths, that are not found in other model systems of rod-like colloidal particles. Consequently, suspensions of such phages provided powerful model systems that have advanced our understanding of soft matter physics in general and liquid crystals in particular. We described some of these advances. In particular we briefly summarize how suspensions of filamentous phages have provided valuable insight into the field of colloidal liquid crystals. We also describe recent experiments on filamentous phages that have elucidated a robust pathway for assembly of 2D membrane-like materials. Finally, we outline unique structural properties of filamentous phages that have so far remained largely unexplored yet have the potential to further advance soft matter physics and material science.
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Affiliation(s)
- Zvonimir Dogic
- Department of Physics, Brandeis University Waltham, MA, USA
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37
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Pei X, Zan T, Li H, Chen Y, Shi L, Zhang Z. Pure Anisotropic Hydrogel with an Inherent Chiral Internal Structure Based on the Chiral Nematic Liquid Crystal Phase of Rodlike Viruses. ACS Macro Lett 2015; 4:1215-1219. [PMID: 35614839 DOI: 10.1021/acsmacrolett.5b00677] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imparting ordered structures into otherwise amorphous hydrogels is expected to endow these popular materials with novel multiple-stimuli responsiveness that promises many applications. The current contribution reports a method to fabricate pure polymeric hydrogels with an inherent chiral internal structure by templating on the chiral nematic liquid crystal phase of a rodlike virus. A method was developed to form macroscopically homogeneous chiral templates by confinement induced self-assembly in the presence of monomers, cross-linkers and initiators. Polymerization induced gelation was performed without perturbing the elegant 3D chiral organization of the rodlike virus bearing double bonds. Furthermore, a suitable method was found to remove the organic virus template while keeping the desired polymeric replica intact, resulting in a pure polymeric hydrogel with a unique internal chiral feature that originates from the 3D chiral ordering of the cylindrical pores left by the virus. Multiple-stimuli responsiveness has been demonstrated and can be quantified by the change of the pitch of the chiral feature. The chiral structure endows the otherwise featureless hydrogel with a unique material property that might be used as a readout signal for sensing and acts as the basis for responsive, biomimetic nanostructured materials.
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Affiliation(s)
- Xiaodong Pei
- Key
Laboratory of Functional Polymer Materials of Ministry of Education,
Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tingting Zan
- School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hengming Li
- Key
Laboratory of Functional Polymer Materials of Ministry of Education,
Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yingjun Chen
- Key
Laboratory of Functional Polymer Materials of Ministry of Education,
Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Linqi Shi
- Key
Laboratory of Functional Polymer Materials of Ministry of Education,
Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhenkun Zhang
- Key
Laboratory of Functional Polymer Materials of Ministry of Education,
Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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38
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Pan P, Wang Y, Zhu Y, Gao X, Ju Z, Qiu P, Wang L, Mao C. Nontoxic virus nanofibers improve the detection sensitivity for the anti-p53 antibody, a biomarker in cancer patients. NANO RESEARCH 2015; 8:3562-3570. [PMID: 27818740 PMCID: PMC5091656 DOI: 10.1007/s12274-015-0856-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The presence of anti-p53 antibody in serum is a biomarker for cancer. However, its high sensitivity detection is still an issue in cancer diagnosis. To tackle this challenge, we used fd phage, a human-safe bacteria-specific virus nanofiber that can be mass-produced by infecting host bacteria in an error-free manner, and genetically engineered it to display a peptide capable of recognizing and capturing anti-p53 antibody on its side wall. We employed the resultant phage nanofibers as a capture probe to develop a modified version of the enzyme-linked immunosorbent assay (ELISA) method, termed phage-ELISA. We compared it to the traditional ELISA method for the detection of anti-p53 antibody, p53-ELISA, which uses recombinant wild-type p53 protein to capture anti-p53 antibody. We applied phage-ELISA to detect anti-p53 antibody in an experimental group of 316 patients with various types of malignant tumors. We found that a detection rate of 17.7% (56 positive cases) was achieved by phage-ELISA, which was comparable to the detection rate of 20.6% for p53-ELISA (65 positive cases). However, when both phage and p53 were combined to form antibody-capturing probes for phage/p53-ELISA, a detection rate of 30.4% (96 positive cases) was achieved. Our work showed that owing to the combined capture of the anti-p53 antibody by both phage nanofibers and p53, the phage/p53-ELISA achieved the highest diagnostic accuracy and detection efficiency for the anti-p53 antibody in patients with various types of cancers. Our work suggests that a combination of nanofibers and antigens, both of which capture antibody, could lead to increased detection sensitivity, which is useful for applications in the life sciences, clinical medicine, and environmental sciences.
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Affiliation(s)
- Pengtao Pan
- Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
| | - Yicun Wang
- Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
| | - Ye Zhu
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Xiang Gao
- Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
| | - Zhigang Ju
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Penghe Qiu
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Li Wang
- Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, USA
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39
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Guliy OI, Zaitsev BD, Kuznetsova IE, Shikhabudinov AM, Dykman LA, Staroverov SA, Karavaeva OA, Pavliy SA, Ignatov OV. Determination of the spectrum of lytic activity of bacteriophages by the method of acoustic analysis. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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40
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Zhang L, Zhang C, Gao R, Yang R. An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics. Int J Mol Sci 2015; 16:21734-58. [PMID: 26370987 PMCID: PMC4613277 DOI: 10.3390/ijms160921734] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/16/2015] [Accepted: 08/25/2015] [Indexed: 11/16/2022] Open
Abstract
Bacteriophage virion proteins and non-virion proteins have distinct functions in biological processes, such as specificity determination for host bacteria, bacteriophage replication and transcription. Accurate identification of bacteriophage virion proteins from bacteriophage protein sequences is significant to understand the complex virulence mechanism in host bacteria and the influence of bacteriophages on the development of antibacterial drugs. In this study, an ensemble method for bacteriophage virion protein prediction from bacteriophage protein sequences is put forward with hybrid feature spaces incorporating CTD (composition, transition and distribution), bi-profile Bayes, PseAAC (pseudo-amino acid composition) and PSSM (position-specific scoring matrix). When performing on the training dataset 10-fold cross-validation, the presented method achieves a satisfactory prediction result with a sensitivity of 0.870, a specificity of 0.830, an accuracy of 0.850 and Matthew's correlation coefficient (MCC) of 0.701, respectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous studies with a sensitivity of 0.853, a specificity of 0.815, an accuracy of 0.831 and MCC of 0.662 on the independent testing dataset. These results suggest that the proposed method can be a potential candidate for bacteriophage virion protein prediction, which may provide a useful tool to find novel antibacterial drugs and to understand the relationship between bacteriophage and host bacteria. For the convenience of the vast majority of experimental Int. J. Mol. Sci. 2015, 16,21735 scientists, a user-friendly and publicly-accessible web-server for the proposed ensemble method is established.
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Affiliation(s)
- Lina Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Chengjin Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Runtao Yang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
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41
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Liu S, Zan T, Chen S, Pei X, Li H, Zhang Z. Thermoresponsive Chiral to Nonchiral Ordering Transformation in the Nematic Liquid-Crystal Phase of Rodlike Viruses: Turning the Survival Strategy of a Virus into Valuable Material Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6995-7005. [PMID: 26053642 DOI: 10.1021/acs.langmuir.5b01476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The current work investigates the thermoresponsive in situ chiral to nonchiral ordering transformation of a rodlike virus in the naturally assembled state-the chiral nematic liquid crystal (CLC) phase. We take this as an elegant example of reconfigurable self-assembly, through which it is possible to realize in situ transformation from one assembled state to another without disrupting the preformed assembly in general or going through a secondary assembling procedure of the disassembled building blocks. The detailed investigation presented here reveals many unique characteristics of the thermoresponsive 3D chiral ordering of rodlike viruses induced by heat stress. The chiral to nonchiral ordering transformation is highly reversible in the temperature range of up to 60 °C and can be repeated many times. There exists a critical temperature around 40 °C which is independent of the ionic strength and virus concentration. Such reconfigurable ordering in the CLC phase stems from the intrinsic structure change of constituent coat proteins without disrupting the structural integrity of the virus, as revealed by three analytical techniques targeting levels ranging from the molecular, secondary conformation of the constituent proteins to the whole single virus, respectively. Such structural flexibility, also termed polymorphism, is relative to the survival strategies of a biological organism such as the virus and can be transformed into very precious material properties. The potential of the virus-based CLC phase as the chiral matrix to regulate chiro-optical properties of gold nanorods is also presented.
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Affiliation(s)
- Shuaiyu Liu
- †Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tingting Zan
- †Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- ‡School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Si Chen
- †Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiaodong Pei
- †Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Henmin Li
- †Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhenkun Zhang
- †Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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Abramov G, Morag O, Goldbourt A. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:80-90. [PMID: 25797007 DOI: 10.1016/j.jmr.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 06/04/2023]
Abstract
Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.
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Morag O, Sgourakis NG, Baker D, Goldbourt A. The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope. Proc Natl Acad Sci U S A 2015; 112:971-6. [PMID: 25587134 PMCID: PMC4313819 DOI: 10.1073/pnas.1415393112] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6-16.7 Å and a tilt of 36.1-36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.
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Affiliation(s)
- Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel; and
| | | | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel; and
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46
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Casey JP, Barbero RJ, Heldman N, Belcher AM. Versatile de novo enzyme activity in capsid proteins from an engineered M13 bacteriophage library. J Am Chem Soc 2014; 136:16508-14. [PMID: 25343220 DOI: 10.1021/ja506346f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biocatalysis has grown rapidly in recent decades as a solution to the evolving demands of industrial chemical processes. Mounting environmental pressures and shifting supply chains underscore the need for novel chemical activities, while rapid biotechnological progress has greatly increased the utility of enzymatic methods. Enzymes, though capable of high catalytic efficiency and remarkable reaction selectivity, still suffer from relative instability, high costs of scaling, and functional inflexibility. Herein, we developed a biochemical platform for engineering de novo semisynthetic enzymes, functionally modular and widely stable, based on the M13 bacteriophage. The hydrolytic bacteriophage described in this paper catalyzes a range of carboxylic esters, is active from 25 to 80 °C, and demonstrates greater efficiency in DMSO than in water. The platform complements biocatalysts with characteristics of heterogeneous catalysis, yielding high-surface area, thermostable biochemical structures readily adaptable to reactions in myriad solvents. As the viral structure ensures semisynthetic enzymes remain linked to the genetic sequences responsible for catalysis, future work will tailor the biocatalysts to high-demand synthetic processes by evolving new activities, utilizing high-throughput screening technology and harnessing M13's multifunctionality.
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Affiliation(s)
- John P Casey
- Biological Engineering, ‡Materials Science and Engineering, and §Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, 76-561, Cambridge, Massachusetts 02139, United States
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47
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Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
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Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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48
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Morag O, Abramov G, Goldbourt A. Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell. J Am Chem Soc 2014; 136:2292-301. [PMID: 24447194 DOI: 10.1021/ja412178n] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.
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Affiliation(s)
- Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Ramat Aviv 69978, Tel Aviv, Israel
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49
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Abstract
Phage display is a powerful tool to isolate specific binders from a large and diverse combinatorial library. Here we provide a step-by-step protocol in how to set up a successful phage panning experiment in order to isolate useful antibodies. The protocol includes testing antigens for their suitability in the phage panning procedure and optimizing the panning conditions and alternative screening methods to minimize nonspecific binding. We describe example phage panning experiments starting from the library transformation to the phage clone screening.
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Affiliation(s)
- Patrick Koenig
- Antibody Engineering Department, Genentech Inc., South San Francisco, CA, USA
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50
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Cao J, Liu S, Xiong J, Chen Y, Zhang Z. Stimuli responsive chiral liquid crystal phases of phenylboronic acid functionalized rodlike viruses and their interaction with biologically important diols. Chem Commun (Camb) 2014; 50:10402-5. [DOI: 10.1039/c4cc04639k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
M13 viruses decorated with phenylboronic acid moieties form pH-responsive chiral LC phases that are regulated by binding with biological diols.
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Affiliation(s)
- Jun Cao
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Shuaiyu Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Jie Xiong
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Yingjun Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Zhenkun Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
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