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Spiliotopoulos A, Maurer SK, Tsoumpeli MT, Bonfante JAF, Owen JP, Gough KC, Dreveny I. Next-Generation Phage Display to Identify Peptide Ligands of Deubiquitinases. Methods Mol Biol 2023; 2591:189-218. [PMID: 36350550 DOI: 10.1007/978-1-0716-2803-4_12] [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] [Indexed: 06/16/2023]
Abstract
Phage display (PD) is a powerful method and has been extensively used to generate monoclonal antibodies and identify epitopes, mimotopes, and protein interactions. More recently, the combination of next-generation sequencing (NGS) with PD (NGPD) has revolutionized the capabilities of the method by creating large data sets of sequences from affinity selection-based approaches (biopanning) otherwise challenging to obtain. NGPD can monitor motif enrichment, allow tracking of the selection process over consecutive rounds, and highlight unspecific binders. To tackle the wealth of data obtained, bioinformatics tools have been developed that allow for identifying specific binding sequences (binders) that can then be validated. Here, we provide a detailed account of the use of NGPD experiments to identify ubiquitin-specific protease peptide ligands.
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Affiliation(s)
- Anastasios Spiliotopoulos
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
- Vertex Pharmaceuticals, Abingdon, Oxfordshire, UK
| | - Sigrun K Maurer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Maria T Tsoumpeli
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Juan A F Bonfante
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Jonathan P Owen
- ADAS UK, School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Loughborough, Leicestershire, UK
| | - Kevin C Gough
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK.
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK.
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2
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Tsoumpeli MT, Varghese A, Owen JP, Maddison BC, Daly JM, Gough KC. Mapping Polyclonal Antibody Responses to Infection Using Next-Generation Phage Display. Methods Mol Biol 2023; 2702:467-487. [PMID: 37679636 DOI: 10.1007/978-1-0716-3381-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Peptide phage display has historically been used to epitope map monoclonal antibodies. More recently, by coupling this method with next-generation sequencing (so-called next-generation phage display, NGPD) to mass screen peptide binding events, the methodology has been successfully applied to map polyclonal antibody responses to infection. This leads to the identification of panels of mimotopes that represent the pathogen's epitopes. One potential advantage of using such an approach is that the mimotopes can represent not just linear epitopes but also conformational epitopes or those produced from post-translational modifications of proteins or from other non-protein macromolecules. The mapping of such complex immunological recognition of a pathogen can inform novel serological assay development and vaccine design. Here, we provide detailed methods for the application of NGPD to identify panels of mimotopes that are recognized specifically by antibodies from individuals with a particular infection.
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Affiliation(s)
- Maria T Tsoumpeli
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Anitha Varghese
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | | | | | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Kevin C Gough
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK.
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3
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Rojas G, Carmenate T, García-Pérez G, Pérez-Martínez D. Phagekines: Directed Evolution and Characterization of Functional Cytokines Displayed on Phages. Methods Mol Biol 2023; 2702:149-189. [PMID: 37679619 DOI: 10.1007/978-1-0716-3381-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The current chapter focuses on the use of filamentous phages to display and modify biologically active cytokines, with special emphasis on directed evolution of novel variants showing improved receptor binding. Cytokines are essential protein mediators involved in cell-to-cell communication. Their functional importance and the complexity of their interactions with multichain receptors make cytokine engineering a promising tool for the discovery and optimization of therapeutic molecules. Protocols used at the laboratory are illustrated through examples of manipulation of interleukin-2 and interleukin-6, two members of the family of alpha-helix-bundle cytokines playing pivotal roles in immunity and inflammation.
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4
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Domain-level epitope mapping of polyclonal antibodies against HER-1 and HER-2 receptors using phage display technology. Sci Rep 2022; 12:12268. [PMID: 35851313 PMCID: PMC9293994 DOI: 10.1038/s41598-022-16411-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
HER-1 and HER-2 are tumor-associated antigens overexpressed in several epithelial tumors, and successfully targeted by therapeutic approaches against cancer. Vaccination with their recombinant extracellular domains has had encouraging results in the pre-clinical setting. As complex humoral responses targeting multiple epitopes within each antigen are the ultimate goal of such active immunotherapy strategies, molecular dissection of the mixture of antibody specificities is required. The current work exploits phage display of antigenic versions of HER-1 and HER-2 domains to accomplish domain-level epitope mapping. Recognition of domains I, III and IV of both antigens by antibodies of immunized mice was shown, indicating diverse responses covering a broad range of antigenic regions. The combination of phage display and site-directed mutagenesis allowed mutational screening of antigen surface, showing polyclonal antibodies' recognition of mutated receptor escape variants known to arise in patients under the selective pressure of the anti-HER-1 antibody cetuximab. Phage-displayed HER domains have thus the potential to contribute to fine specificity characterization of humoral responses during future development of anti-cancer vaccines.
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5
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Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology. Antibodies (Basel) 2022; 11:antib11030048. [PMID: 35892708 PMCID: PMC9326607 DOI: 10.3390/antib11030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Combinatorial biology methods such as phage and yeast display, suitable for the generation and screening of huge numbers of protein fragments and mutated variants, have been useful when dissecting the molecular details of the interactions between antibodies and their target antigens (mainly those of protein nature). The relevance of these studies goes far beyond the mere description of binding interfaces, as the information obtained has implications for the understanding of the chemistry of antibody–antigen binding reactions and the biological effects of antibodies. Further modification of the interactions through combinatorial methods to manipulate the key properties of antibodies (affinity and fine specificity) can result in the emergence of novel research tools and optimized therapeutics.
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6
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A Simple Whole-Plasmid PCR Method to Construct High-Diversity Synthetic Phage Display Libraries. Mol Biotechnol 2022; 64:791-803. [PMID: 35107752 PMCID: PMC9217769 DOI: 10.1007/s12033-021-00442-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 12/17/2021] [Indexed: 11/03/2022]
Abstract
Phage display technology utilises peptide and antibody libraries with very high diversities to select ligands with specific binding properties. The production of such libraries can be labour intensive and technically challenging and whilst there are commercial sources of libraries, the exploitation of the resulting binders is constrained by ownership of the libraries. Here, a peptide library of ~ 1 × 109 variants for display on gene VIII was produced alongside three VHH antibody libraries with similar diversity, where 12mer, 16mer or 21mer CDR3s were introduced into the highly stable cAbBCII10 scaffold displayed on gene III. The cloning strategy used a simple whole-plasmid PCR method and type IIS restriction enzyme assembly that facilitate the seamless insertion of diversity into any suitable phage coat protein or antibody scaffold. This method reproducibly produced 1 × 109 variants from just 10 transformations and the four libraries had relatively low bias with 82 to 86% of all sequences present as single copies. The functionality of both peptide and antibody libraries were demonstrated by selection of ligands with specific binding properties by biopanning. The peptide library was used to epitope map a monoclonal antibody. The VHH libraries were pooled and used to select an antibody to recombinant human collagen type 1.
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7
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Incidence of Phage Capsid Organization on the Resistance to High Energy Proton Beams. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12030988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The helical geometry of virus capsid allows simple self-assembly of identical protein subunits with a low request of free energy and a similar spiral path to virus nucleic acid. Consequently, small variations in protein subunits can affect the stability of the entire phage particle. Previously, we observed that rearrangement in the capsid structure of M13 engineered phages affected the resistance to UV-C exposure, while that to H2O2 was mainly ascribable to the amino acids’ sequence of the foreign peptide. Based on these findings, in this work, the resistance to accelerated proton beam exposure (5.0 MeV energy) of the same phage clones was determined at different absorbed doses and dose rates. Then, the number of viral particles able to infect and replicate in the natural host, Escherichia coli F+, was evaluated. By comparing the results with the M13 wild-type vector (pC89), we observed that 12III1 phage clones, with the foreign peptide containing amino acids favorable to carbonylation, exhibited the highest reduction in phage titer associated with a radiation damage (RD) of 35 × 10−3/Gy at 50 dose Gy. On the other hand, P9b phage clones, containing amino acids unfavorable to carbonylation, showed the lowest reduction with an RD of 4.83 × 10−3/Gy at 500 dose Gy. These findings could improve the understanding of the molecular mechanisms underlying the radiation resistance of viruses
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8
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Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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9
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Chikaev AN, Chikaev AN, Rudometov AP, Merkulyeva YA, Karpenko LI. Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies. Vavilovskii Zhurnal Genet Selektsii 2021; 25:562-572. [PMID: 34595378 PMCID: PMC8453360 DOI: 10.18699/vj21.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/14/2021] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
Combinatorial biology methods offer a good solution for targeting interactions of specif ic molecules
by a high-throughput screening and are widely used for drug development, diagnostics, identif ication of novel
monoclonal antibodies, search for linear peptide mimetics of discontinuous epitopes for the development of
immunogens or vaccine components. Among all currently available techniques, phage display remains one of
the most popular approaches. Despite being a fairly old method, phage display is still widely used for studying
protein-protein, peptide-protein and DNA-protein interactions due to its relative simplicity and versatility. Phage
display allows highly representative libraries of peptides, proteins or their fragments to be created. Each phage
particle in a library displays peptides or proteins fused to its coat protein and simultaneously carries the DNA
sequence encoding the displayed peptide/protein in its genome. The biopanning procedure allows isolation of
specif ic clones for almost any target, and due to the physical link between the genotype and the phenotype of
recombinant phage particles it is possible to determine the structure of selected molecules. Phage display technology
continues to play an important role in HIV research. A major obstacle to the development of an effective
HIV vaccine is an extensive genetic and antigenic variability of the virus. According to recent data, in order to provide
protection against HIV infection, the so-called broadly neutralizing antibodies that are cross-reactive against
multiple viral strains of HIV must be induced, which makes the identif ication of such antibodies a key area of HIV
vaccinology. In this review, we discuss the use of phage display as a tool for identif ication of HIV-specif ic antibodies
with broad neutralizing activity. We provide an outline of phage display technology, brief ly describe the
design of antibody phage libraries and the affinity selection procedure, and discuss the biology of HIV-1-specif ic
broadly neutralizing antibodies. Finally, we summarize the studies aimed at identif ication of broadly neutralizing
antibodies using various types of phage libraries.
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Affiliation(s)
| | - A N Chikaev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A P Rudometov
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - Yu A Merkulyeva
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
| | - L I Karpenko
- State Research Center of Virology and Biotechnology "Vector", Rospotrebnadzor, Koltsovo, Novosibirsk region, Russia
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10
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Plano LMD, Franco D, Rizzo MG, Zammuto V, Gugliandolo C, Silipigni L, Torrisi L, Guglielmino SPP. Role of Phage Capsid in the Resistance to UV-C Radiations. Int J Mol Sci 2021; 22:3408. [PMID: 33810266 PMCID: PMC8037334 DOI: 10.3390/ijms22073408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
The conformational variation of the viral capsid structure plays an essential role both for the environmental resistance and acid nuclear release during cellular infection. The aim of this study was to evaluate how capsid rearrangement in engineered phages of M13 protects viral DNA and peptide bonds from damage induced by UV-C radiation. From in silico 3D modelling analysis, two M13 engineered phage clones, namely P9b and 12III1, were chosen for (i) chemical features of amino acids sequences, (ii) rearrangements in the secondary structure of their pVIII proteins and (iii) in turn the interactions involved in phage capsid. Then, their resistance to UV-C radiation and hydrogen peroxide (H2O2) was compared to M13 wild-type vector (pC89) without peptide insert. Results showed that both the phage clones acquired an advantage against direct radiation damage, due to a reorganization of interactions in the capsid for an increase of H-bond and steric interactions. However, only P9b had an increase in resistance against H2O2. These results could help to understand the molecular mechanisms involved in the stability of new virus variants, also providing quick and necessary information to develop effective protocols in the virus inactivation for human activities, such as safety foods and animal-derived materials.
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Affiliation(s)
- Laura Maria De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (L.M.D.P.); (M.G.R.); (V.Z.); (C.G.); (S.P.P.G.)
| | - Domenico Franco
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (L.M.D.P.); (M.G.R.); (V.Z.); (C.G.); (S.P.P.G.)
| | - Maria Giovanna Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (L.M.D.P.); (M.G.R.); (V.Z.); (C.G.); (S.P.P.G.)
| | - Vincenzo Zammuto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (L.M.D.P.); (M.G.R.); (V.Z.); (C.G.); (S.P.P.G.)
| | - Concetta Gugliandolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (L.M.D.P.); (M.G.R.); (V.Z.); (C.G.); (S.P.P.G.)
| | - Letteria Silipigni
- Department of Mathematical and Computational Sciences, Physical Sciences and Earth Sciences, University of Messina, 98166 Messina, Italy; (L.S.); (L.T.)
| | - Lorenzo Torrisi
- Department of Mathematical and Computational Sciences, Physical Sciences and Earth Sciences, University of Messina, 98166 Messina, Italy; (L.S.); (L.T.)
| | - Salvatore P. P. Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (L.M.D.P.); (M.G.R.); (V.Z.); (C.G.); (S.P.P.G.)
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11
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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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12
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Ricca E, Baccigalupi L, Isticato R. Spore-adsorption: Mechanism and applications of a non-recombinant display system. Biotechnol Adv 2020; 47:107693. [PMID: 33387640 DOI: 10.1016/j.biotechadv.2020.107693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
Abstract
Surface display systems have been developed to express target molecules on almost all types of biological entities from viruses to mammalian cells and on a variety of synthetic particles. Various approaches have been developed to achieve the display of many different target molecules, aiming at several technological and biomedical applications. Screening of libraries, delivery of drugs or antigens, bio-catalysis, sensing of pollutants and bioremediation are commonly considered as fields of potential application for surface display systems. In this review, the non-recombinant approach to display antigens and enzymes on the surface of bacterial spores is discussed. Examples of molecules displayed on the spore surface and their potential applications are summarized and a mechanism of display is proposed.
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Affiliation(s)
- Ezio Ricca
- Department of Biology, Federico II University of Naples, Italy.
| | - Loredana Baccigalupi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Italy
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13
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De Plano LM, Carnazza S, Franco D, Rizzo MG, Conoci S, Petralia S, Nicoletti A, Zappia M, Campolo M, Esposito E, Cuzzocrea S, Guglielmino SPP. Innovative IgG Biomarkers Based on Phage Display Microbial Amyloid Mimotope for State and Stage Diagnosis in Alzheimer's Disease. ACS Chem Neurosci 2020; 11:1013-1026. [PMID: 32176482 PMCID: PMC7997372 DOI: 10.1021/acschemneuro.9b00549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
![]()
An
innovative approach to identify new conformational antigens
of Aβ1–42 recognized by IgG autoantibodies
as biomarkers of state and stage in Alzheimer’s disease (AD)
patients is described. In particular, through the use of bioinformatics
modeling, conformational similarities between several Aβ1–42 forms and other amyloid-like proteins with F1 capsular
antigen (Caf1) of Yersinia pestis were first found.
pVIII M13 phage display libraries were then screened against YPF19,
anti-Caf1 monoclonal antibody, and IgGs of AD patients, in alternate
biopanning cycles of a so-called “double binding” selection.
From the selected phage clones, one, termed 12III1, was found to be
able to prevent in vitro Aβ1–42-induced cytotoxicity in SH-SY5Y cells, as well as to promote disaggregation
of preformed fibrils, to a greater extent with respect to wild-type
phage (pC89). IgG levels detected by 12III1 provided a significant
level of discrimination between diseased and nondemented subjects,
as well as a good correlation with the state progression of the disease.
These results give significant impact in AD state and stage diagnosis,
paving the way for the development not only for an innovative blood
diagnostic assay for AD precise diagnosis, progressive clinical assessment,
and screening but also for new effective treatments.
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Affiliation(s)
- Laura M. De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Santina Carnazza
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Domenico Franco
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Maria Giovanna Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Sabrina Conoci
- STmicroelectronics, Stradale Primosole, 50, 95121 Catania, Italy
- Distretto Tecnologico Micro e Nano Sistemi Sicilia, Strada VII-Zona Industriale, 95121 Catania, Italy
| | | | - Alessandra Nicoletti
- Neurology Clinic, Department “G.F. Ingrassia”, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123 Catania, Italy
| | - Mario Zappia
- Neurology Clinic, Department “G.F. Ingrassia”, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123 Catania, Italy
| | - Michela Campolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Salvatore P. P. Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
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14
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Baghallab I, Reyes-Ruiz JM, Abulnaja K, Huwait E, Glabe C. Epitomic Characterization of the Specificity of the Anti-Amyloid Aβ Monoclonal Antibodies 6E10 and 4G8. J Alzheimers Dis 2019; 66:1235-1244. [PMID: 30412489 PMCID: PMC6294585 DOI: 10.3233/jad-180582] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The monoclonal antibodies 6E10 and 4G8 are among the first anti-amyloid monoclonal antibodies against Aβ and the most widely used antibodies in Alzheimer's disease research. Although the epitopes for 6E10 and 4G8 have been reported to correspond to residues 1-16 and 17-24, a more recent high-resolution mapping approach indicates that 6E10 maps to residues 4-10 while 4G8 maps to residues 18-23. To characterize the binding specificity of both antibodies in greater detail, we used immunoselection of random sequences from phage display library followed by deep sequencing and analysis of resulting patterns from thousands of immunoselected sequences. We found that the minimum sequence required for 6E10 binding is R-x-D with over half (53%) of the immunoselected sequences conforming to this pattern. The vast majority of these sequences contain an H at position x (R-H-D), corresponding to residues 5-7 of the Aβ target sequences, but Y is also permitted at this position in a minority of sequences. For 4G8 we found that the most frequent pattern is F-x-A contained in approximately 30% of the sequences, followed by F-A, L-x(3)-A, L-x-F, and F-F each accounting for approximately 18% of the sequences. The F-x-A motif also occurs in islet amyloid poly peptide which may explain why 4G8 also recognizes amyloid fibrils of this peptide. Immunoselection of random sequences and deep sequencing may also be a facile and efficient means of determining residues critical for antibody binding and validating the specificity of monoclonal antibodies and polyclonal antisera.
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Affiliation(s)
- Ibtisam Baghallab
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Khalid Abulnaja
- Department of Biochemistry, Faculty of Science, Bioactive Natural Products Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Etimad Huwait
- Department of Biochemistry, Faculty of Science; Vitamin D Pharmacogenomics Research Group and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Charles Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
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15
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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16
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Bao Q, Li X, Han G, Zhu Y, Mao C, Yang M. Phage-based vaccines. Adv Drug Deliv Rev 2019; 145:40-56. [PMID: 30594492 DOI: 10.1016/j.addr.2018.12.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 10/01/2018] [Accepted: 12/17/2018] [Indexed: 02/08/2023]
Abstract
Bacteriophages, or more colloquially as phages, are viruses that possess the ability to infect and replicate with bacterial cells. They are assembled from two major types of biomolecules, the nucleic acids and the proteins, with the latter forming a capsid and the former being encapsulated. In the eukaryotic hosts, phages are inert particulate antigens and cannot trigger pathogenesis. In recent years, many studies have been explored about using phages as nanomedicine platforms for developing vaccines due to their unique biological characteristics. The whole phage particles can be used for vaccine design in the form of phage-displayed vaccines or phage DNA vaccines. Phage-displayed vaccines are the phages with peptide or protein antigens genetically displayed on their surfaces as well as those with antigens chemically conjugated or biologically bound on their surfaces. The phages can then deliver the immunogenic peptides or proteins to the target cells or tissues. Phage DNA vaccines are the eukaryotic promoter-driven vaccine genes inserted in the phage genomes, which are carried by phages to the target cells to generate antigens. The antigens, either as the immunogenic peptides or proteins displayed on the phages, or as the products expressed from the vaccine genes, can serve as vaccines to elicit immune responses for disease prevention and treatment. Both phage-displayed vaccines and phage DNA vaccines promise a brilliant future for developing vaccines. This review presents the recent advancements in the field of phage-based vaccines and their applications in both the prevention and treatment of various diseases. It also discusses the challenges and perspectives in moving this field forwards.
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17
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Phage Display Libraries: From Binders to Targeted Drug Delivery and Human Therapeutics. Mol Biotechnol 2019; 61:286-303. [DOI: 10.1007/s12033-019-00156-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Spiliotopoulos A, Blokpoel Ferreras L, Densham RM, Caulton SG, Maddison BC, Morris JR, Dixon JE, Gough KC, Dreveny I. Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11. J Biol Chem 2019; 294:424-436. [PMID: 30373771 PMCID: PMC6333900 DOI: 10.1074/jbc.ra118.004469] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/11/2018] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) reverse ubiquitination and regulate virtually all cellular processes. Defined noncatalytic domains in USP4 and USP15 are known to interact with E3 ligases and substrate recruitment factors. No such interactions have been reported for these domains in the paralog USP11, a key regulator of DNA double-strand break repair by homologous recombination. We hypothesized that USP11 domains adjacent to its protease domain harbor unique peptide-binding sites. Here, using a next-generation phage display (NGPD) strategy, combining phage display library screening with next-generation sequencing, we discovered unique USP11-interacting peptide motifs. Isothermal titration calorimetry disclosed that the highest affinity peptides (KD of ∼10 μm) exhibit exclusive selectivity for USP11 over USP4 and USP15 in vitro Furthermore, a crystal structure of a USP11-peptide complex revealed a previously unknown binding site in USP11's noncatalytic ubiquitin-like (UBL) region. This site interacted with a helical motif and is absent in USP4 and USP15. Reporter assays using USP11-WT versus a binding pocket-deficient double mutant disclosed that this binding site modulates USP11's function in homologous recombination-mediated DNA repair. The highest affinity USP11 peptide binder fused to a cellular delivery sequence induced significant nuclear localization and cell cycle arrest in S phase, affecting the viability of different mammalian cell lines. The USP11 peptide ligands and the paralog-specific functional site in USP11 identified here provide a framework for the development of new biochemical tools and therapeutic agents. We propose that an NGPD-based strategy for identifying interacting peptides may be applied also to other cellular targets.
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Affiliation(s)
- Anastasios Spiliotopoulos
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
- the School of Veterinary Medicine and Science, Sutton Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD
| | - Lia Blokpoel Ferreras
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Ruth M Densham
- the Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham B15 2TT, and
| | - Simon G Caulton
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Ben C Maddison
- ADAS, School of Veterinary Medicine and Science, Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Joanna R Morris
- the Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham B15 2TT, and
| | - James E Dixon
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Kevin C Gough
- the School of Veterinary Medicine and Science, Sutton Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD,
| | - Ingrid Dreveny
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD,
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Cyclic Peptides: Promising Scaffolds for Biopharmaceuticals. Genes (Basel) 2018; 9:genes9110557. [PMID: 30453533 PMCID: PMC6267108 DOI: 10.3390/genes9110557] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 12/31/2022] Open
Abstract
To date, small molecules and macromolecules, including antibodies, have been the most pursued substances in drug screening and development efforts. Despite numerous favorable features as a drug, these molecules still have limitations and are not complementary in many regards. Recently, peptide-based chemical structures that lie between these two categories in terms of both structural and functional properties have gained increasing attention as potential alternatives. In particular, peptides in a circular form provide a promising scaffold for the development of a novel drug class owing to their adjustable and expandable ability to bind a wide range of target molecules. In this review, we discuss recent progress in methodologies for peptide cyclization and screening and use of bioactive cyclic peptides in various applications.
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20
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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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Lo Passo C, Zippilli L, Angiolillo A, Costa I, Pernice I, Galbo R, Felici F, Beernink PT. Molecular characterization of two sub-family specific monoclonal antibodies to meningococcal Factor H binding protein. Heliyon 2018; 4:e00591. [PMID: 29644339 PMCID: PMC5889710 DOI: 10.1016/j.heliyon.2018.e00591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/07/2018] [Accepted: 03/27/2018] [Indexed: 11/29/2022] Open
Abstract
Factor H binding protein (FHbp) is a component of two licensed vaccines for prevention of sepsis and meningitis caused by serogroup B meningococci. FHbp binds human Factor H (FH), which contributes to evasion of host immunity and FHbp sequence variants can be classified into two sub-families. Antibodies against FHbp elicit complement-mediated killing and can inhibit recruitment of FH to the bacterial surface. We report epitope mapping studies of two murine IgG mAbs, designated JAR 31 and JAR 36, isolated from a mouse immunized with FHbp in sub-family A, which is present in ∼30-40% of invasive isolates. In the present study, we tested the reactivity of mAbs JAR 31 and JAR 36 with seven natural FHbp sequence variants from different phylogenic groups. We screened bacteriophage-displayed peptide libraries to identify amino acid residues contributing to the JAR 36 epitope. Based on the reactivities of mAbs JAR 31 and JAR 36 with the seven FHbp variants, and the frequent occurrences of aspartate (D) and lysine (K) residues in the JAR 36-bound phage peptides, we selected six residues in the carboxyl-terminal region of FHbp for replacement with alanine (A). The D201A and K203A substitutions respectively eliminated and decreased binding of mAbs JAR 31 and JAR 36 to FHbp. These substitutions did not affect binding of the control mAb JAR 33 or of human FH. JAR 31 or JAR 36 mediated cooperative complement-mediated bactericidal activity with other anti-FHbp mAbs. The identification of two amino acid residues involved in the epitopes recognized by these anti-FHbp mAbs may contribute to a more complete understanding of the spatial requirements for cooperative anti-FHbp mAb bactericidal activity.
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Affiliation(s)
- C Lo Passo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
| | - L Zippilli
- Department of Biosciences and Territory, University of Molise, Pesche (CB), Italy
| | - A Angiolillo
- Department of Medicine and Health Sciences, University of Molise, Campobasso, Italy
| | - I Costa
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
| | - I Pernice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
| | - R Galbo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
| | - F Felici
- Department of Biosciences and Territory, University of Molise, Pesche (CB), Italy
| | - P T Beernink
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA.,Department of Pediatrics, School of Medicine, University of California, San Francisco, USA
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22
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Rojas G, Carmenate T. Phagekines: Screening Binding Properties and Biological Activity of Functional Cytokines Displayed on Phages. Methods Mol Biol 2018; 1701:535-560. [PMID: 29116526 DOI: 10.1007/978-1-4939-7447-4_30] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The current chapter focuses on the use of filamentous phages to display, modify, and characterize cytokines, which are proteins belonging to a versatile group of essential mediators involved in cell-cell communication. Cytokines exhibit a considerable diversity, both in functions and in structural features underlying their biological effects. A broad variety of cytokines have been successfully displayed on phages, allowing the high-throughput study of their binding properties and biological activities and the discovery of novel therapeutics through directed evolution. The technical singularities and some potential applications of cytokine phage display are illustrated here with the case of Interleukin-2, a prototypic member of the four-alpha-helix bundle cytokine family playing a pivotal role in the immune response and having a long history of therapeutic use.
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Affiliation(s)
- Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, La Habana, CP, 11300, Cuba.
| | - Tania Carmenate
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, La Habana, CP, 11300, Cuba
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23
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Isaac RS, Sanulli S, Tibble R, Hornsby M, Ravalin M, Craik CS, Gross JD, Narlikar GJ. Biochemical Basis for Distinct Roles of the Heterochromatin Proteins Swi6 and Chp2. J Mol Biol 2017; 429:3666-3677. [PMID: 28942089 DOI: 10.1016/j.jmb.2017.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/23/2017] [Accepted: 09/15/2017] [Indexed: 11/29/2022]
Abstract
Heterochromatin protein 1 (HP1) family proteins are conserved chromatin binding proteins involved in gene silencing, chromosome packaging, and chromosome segregation. These proteins recognize histone H3 lysine 9 methylated tails via their chromodomain and recruit additional ligand proteins with diverse activities through their dimerization domain, the chromoshadow domain. Species that have HP1 proteins possess multiple paralogs that perform non-overlapping roles in vivo. How different HP1 proteins, which are highly conserved, perform different functions is not well understood. Here, we use the two Schizosaccharomyces pombe HP1 paralogs, Swi6 and Chp2, as model systems to compare and contrast their biophysical properties. We find that Swi6 and Chp2 have similar dimerization and oligomerization equilibria, and that Swi6 binds slightly (~3-fold) more strongly to nucleosomes than Chp2. Furthermore, while Swi6 binding to the H3K9me3 mark is regulated by a previously described auto-inhibition mechanism, the binding of Chp2 to the H3K9me3 mark is not analogously regulated. In the context of chromoshadow domain interactions, we show using a newly identified peptide sequence from the Clr3 histone deacetylase and a previously identified sequence from the protein Shugoshin that the Swi6 chromoshadow domain binds both ligands more strongly than the Chp2. Overall, our findings uncover quantitative differences in how Swi6 and Chp2 interact with nucleosomal and non-nucleosomal ligands and qualitative differences in how their assembly on nucleosomes is regulated. These findings provide a biochemical framework to explain the varied functions of Chp2 and Swi6 in vivo.
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Affiliation(s)
- R Stefan Isaac
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158 United States; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - Serena Sanulli
- Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158 United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - Ryan Tibble
- Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158 United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - Michael Hornsby
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - John D Gross
- Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158 United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158 United States
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158 United States.
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Specific and selective probes for Staphylococcus aureus from phage-displayed random peptide libraries. Colloids Surf B Biointerfaces 2017; 157:473-480. [DOI: 10.1016/j.colsurfb.2017.05.081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/12/2017] [Accepted: 05/29/2017] [Indexed: 12/16/2022]
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Mapping B-cell responses to Salmonella enterica serovars Typhimurium and Enteritidis in chickens for the discrimination of infected from vaccinated animals. Sci Rep 2016; 6:31186. [PMID: 27510219 PMCID: PMC4980624 DOI: 10.1038/srep31186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/13/2016] [Indexed: 12/17/2022] Open
Abstract
Serological surveillance and vaccination are important strategies for controlling infectious diseases of food production animals. However, the compatibility of these strategies is limited by a lack of assays capable of differentiating infected from vaccinated animals (DIVA tests) for established killed or attenuated vaccines. Here, we used next generation phage-display (NGPD) and a 2-proportion Z score analysis to identify peptides that were preferentially bound by IgY from chickens infected with Salmonella Typhimurium or S. Enteritidis compared to IgY from vaccinates, for both an attenuated and an inactivated commercial vaccine. Peptides that were highly enriched against IgY from at least 4 out of 10 infected chickens were selected: 18 and 12 peptides for the killed and attenuated vaccines, respectively. The ten most discriminatory peptides for each vaccine were identified in an ELISA using a training set of IgY samples. These peptides were then used in multi-peptide assays that, when analysing a wider set of samples from infected and vaccinated animals, diagnosed infection with 100% sensitivity and specificity. The data describes a method for the development of DIVA assays for conventional attenuated and killed vaccines.
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Epitope Mapping of a Monoclonal Antibody Directed against Neisserial Heparin Binding Antigen Using Next Generation Sequencing of Antigen-Specific Libraries. PLoS One 2016; 11:e0160702. [PMID: 27508302 PMCID: PMC4980009 DOI: 10.1371/journal.pone.0160702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/22/2016] [Indexed: 01/07/2023] Open
Abstract
We explore here the potential of a newly described technology, which is named PROFILER and is based on next generation sequencing of gene-specific lambda phage-displayed libraries, to rapidly and accurately map monoclonal antibody (mAb) epitopes. For this purpose, we used a novel mAb (designated 31E10/E7) directed against Neisserial Heparin-Binding Antigen (NHBA), a component of the anti-group B meningococcus Bexsero® vaccine. An NHBA phage-displayed library was affinity-selected with mAb 31E10/E7, followed by massive sequencing of the inserts present in antibody-selected phage pools. Insert analysis identified an amino acid stretch (D91-A128) in the N-terminal domain, which was shared by all of the mAb-enriched fragments. Moreover, a recombinant fragment encompassing this sequence could recapitulate the immunoreactivity of the entire NHBA molecule against mAb 31E10/E7. These results were confirmed using a panel of overlapping recombinant fragments derived from the NHBA vaccine variant and a set of chemically synthetized peptides covering the 10 most frequent antigenic variants. Furthermore, hydrogen-deuterium exchange mass-spectrometry analysis of the NHBA-mAb 31E10/E7 complex was also compatible with mapping of the epitope to the D91-A128 region. Collectively, these results indicate that the PROFILER technology can reliably identify epitope-containing antigenic fragments and requires considerably less work, time and reagents than other epitope mapping methods.
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28
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Mapping polyclonal antibody responses to bacterial infection using next generation phage display. Sci Rep 2016; 6:24232. [PMID: 27072017 PMCID: PMC4829855 DOI: 10.1038/srep24232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
Mapping polyclonal antibody responses to infectious diseases to identify individual epitopes has the potential to underpin the development of novel serological assays and vaccines. Here, phage-peptide library panning coupled with screening using next generation sequencing was used to map antibody responses to bacterial infections. In the first instance, pigs experimentally infected with Salmonella enterica serovar Typhimurium was investigated. IgG samples from twelve infected pigs were probed in parallel and phage binding compared to that with equivalent IgG from pre-infected animals. Seventy-seven peptide mimotopes were enriched specifically against sera from multiple infected animals. Twenty-seven of these peptides were tested in ELISA and twenty-two were highly discriminatory for sera taken from pigs post-infection (P < 0.05) indicating that these peptides are mimicking epitopes from the bacteria. In order to further test this methodology, it was applied to differentiate antibody responses in poultry to infections with distinct serovars of Salmonella enterica. Twenty-seven peptides were identified as being enriched specifically against IgY from multiple animals infected with S. Enteritidis compared to those infected with S. Hadar. Nine of fifteen peptides tested in ELISA were highly discriminatory for IgY following S. Enteritidis infection (p < 0.05) compared to infections with S. Hadar or S. Typhimurium.
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Cariccio VL, Domina M, Benfatto S, Venza M, Venza I, Faleri A, Bruttini M, Bartolini E, Giuliani MM, Santini L, Brunelli B, Norais N, Borgogni E, Midiri A, Galbo R, Romeo L, Biondo C, Masignani V, Teti G, Felici F, Beninati C. Phage display revisited: Epitope mapping of a monoclonal antibody directed against Neisseria meningitidis adhesin A using the PROFILER technology. MAbs 2016; 8:741-50. [PMID: 26963435 DOI: 10.1080/19420862.2016.1158371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
There is a strong need for rapid and reliable epitope mapping methods that can keep pace with the isolation of increasingly larger numbers of mAbs. We describe here the identification of a conformational epitope using Phage-based Representation OF ImmunoLigand Epitope Repertoire (PROFILER), a recently developed high-throughput method based on deep sequencing of antigen-specific lambda phage-displayed libraries. A novel bactericidal monoclonal antibody (mAb 9F11) raised against Neisseria meningitidis adhesin A (NadA), an important component of the Bexsero(®) anti-meningococcal vaccine, was used to evaluate the technique in comparison with other epitope mapping methods. The PROFILER technology readily identified NadA fragments that were capable of fully recapitulating the reactivity of the entire antigen against mAb 9F11. Further analysis of these fragments using mutagenesis and hydrogen-deuterium exchange mass-spectrometry allowed us to identify the binding site of mAb 9F11 (A250-D274) and an adjoining sequence (V275-H312) that was also required for the full functional reconstitution of the epitope. These data suggest that, by virtue of its ability to detect a great variety of immunoreactive antigen fragments in phage-displayed libraries, the PROFILER technology can rapidly and reliably identify epitope-containing regions and provide, in addition, useful clues for the functional characterization of conformational mAb epitopes.
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Affiliation(s)
| | | | - Salvatore Benfatto
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Mario Venza
- c Department Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Isabella Venza
- c Department Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | | | - Marco Bruttini
- d GSK Vaccines , Siena , Italy.,e Department of Life Sciences , University of Siena , Siena , Italy
| | | | | | | | | | | | | | - Angelina Midiri
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Roberta Galbo
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Letizia Romeo
- b Department of Human Pathology , University of Messina , Messina , Italy
| | - Carmelo Biondo
- b Department of Human Pathology , University of Messina , Messina , Italy
| | | | - Giuseppe Teti
- c Department Clinical and Experimental Medicine , University of Messina , Messina , Italy.,f Charybdis Vaccines Srl , Messina , Italy
| | - Franco Felici
- g Department of Biosciences and Territory , University of Molise , Pesche , Isernia , Italy
| | - Concetta Beninati
- a Scylla Biotech Srl , Messina , Italy.,b Department of Human Pathology , University of Messina , Messina , Italy
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Rojas G, Tundidor Y, Infante YC. High throughput functional epitope mapping: revisiting phage display platform to scan target antigen surface. MAbs 2015; 6:1368-76. [PMID: 25484050 DOI: 10.4161/mabs.36144] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antibody engineering must be accompanied by mapping strategies focused on identifying the epitope recognized by each antibody to define its unique functional identity. High throughput fine specificity determination remains technically challenging. We review recent experiences aimed at revisiting the oldest and most extended display technology to develop a robust epitope mapping platform, based on the ability to manipulate target-derived molecules (ranging from the whole native antigen to antigen domains and smaller fragments) on filamentous phages. Single, multiple and combinatorial mutagenesis allowed comprehensive scanning of phage-displayed antigen surface that resulted in the identification of clusters of residues contributing to epitope formation. Functional pictures of the epitope(s) were thus delineated in the natural context. Successful mapping of antibodies against interleukin-2, epidermal growth factor and its receptor, and vascular endothelial growth factor showed the versatility of these procedures, which combine the accuracy of site-directed mutagenesis with the high throughput potential of phage display.
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Key Words
- Abs, antibodies
- Ag, antigen
- EGF
- EGF receptor
- EGF, epidermal growth factor
- EGFR, EGF receptor
- ELISA, enzyme-linked immunosorbent assay
- IL-2
- IL-2, interleukin-2
- PCR, polymerase chain reaction
- VEGF
- VEGF, vascular endothelial growth factor
- aa, amino acid
- epitope mapping
- library
- mAb, monoclonal Ab
- phage display
- site-directed mutagenesis
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Affiliation(s)
- Gertrudis Rojas
- a Systems Biology Department ; Center of Molecular Immunology ; La Habana , Cuba
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31
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Ullman C, Mathonet P, Oleksy A, Diamandakis A, Tomei L, Demartis A, Nardi C, Sambucini S, Missineo A, Alt K, Hagemeyer CE, Harris M, Hedt A, Weis R, Gehlsen KR. High Affinity Binders to EphA2 Isolated from Abdurin Scaffold Libraries; Characterization, Binding and Tumor Targeting. PLoS One 2015; 10:e0135278. [PMID: 26313909 PMCID: PMC4552014 DOI: 10.1371/journal.pone.0135278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/21/2015] [Indexed: 01/15/2023] Open
Abstract
Abdurins are a novel antibody-like scaffold derived from the engineering of a single isolated CH2 domain of human IgG. Previous studies established the prolonged serum half-life of Abdurins, the result of a retained FcRn binding motif. Here we present data on the construction of large, diverse, phage-display and cell-free DNA display libraries and the isolation of high affinity binders to the cancer target, membrane-bound ephrin receptor tyrosine kinase class A2 (EphA2). Antigen binding regions were created by designing combinatorial libraries into the structural loops and Abdurins were selected using phage display methods. Initial binders were reformatted into new maturation libraries and low nanomolar binders were isolated using cell-free DNA display, CIS display. Further characterization confirmed binding of the Abdurins to both human and murine EphA2 proteins and exclusively to cell lines that expressed EphA2, followed by rapid internalization. Two different EphA2 binders were labeled with 64Cu, using a bifunctional MeCOSar chelator, and administered to mice bearing tumors from transplanted human prostate cancer cells, followed by PET/CT imaging. The anti-EphA2 Abdurins localized in the tumors as early as 4 hours after injection and continued to accumulate up to 48 hours when the imaging was completed. These data demonstrate the ability to isolate high affinity binders from the engineered Abdurin scaffold, which retain a long serum half-life, and specifically target tumors in a xenograft model.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Karen Alt
- Vascular Biotechnology, Baker IDI, Melbourne, Australia
| | | | - Matt Harris
- Clarity Pharmaceuticals, Ltd. Sydney, Australia
| | - Amos Hedt
- Clarity Pharmaceuticals, Ltd. Sydney, Australia
| | | | - Kurt R. Gehlsen
- Research Corporation Technologies, Inc. Tucson, Arizona, United States of America
- * E-mail:
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Phage-AgNPs complex as SERS probe for U937 cell identification. Biosens Bioelectron 2015; 74:398-405. [PMID: 26164011 DOI: 10.1016/j.bios.2015.05.073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/24/2015] [Accepted: 05/26/2015] [Indexed: 12/21/2022]
Abstract
The early diagnosis of malignancy is the most critical factor for patient survival and the treatment of cancer. In particular, leukemic cells are highly heterogeneous, and there is a need to develop new rapid and accurate detection systems for early diagnosis and monitoring of minimal residual disease. This study reports the utilization of molecular networks consisting of entire bacteriophage structure, displaying specific peptides, directly assembled with silver nanoparticles as a new Surface Enhanced Raman Spectroscopy (SERS) probe for U937 cells identification in vitro. A 9-mer pVIII M13 phage display library is screened against U937 to identify peptides that selectively recognize these cells. Then, phage clone is assembled with silver nanoparticles and the resulting network is used to obtain a SERS signal on cell-type specific molecular targets. The proposed strategy could be a very sensitive tool for the design of biosensors for highly specific and selective identification of hematological cancer cells and for detection of minimal residual disease in a significant proportion of human blood malignancy.
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Henning LM, Bhatia S, Bertazzon M, Marczynke M, Seitz O, Volkmer R, Haag R, Freund C. Exploring monovalent and multivalent peptides for the inhibition of FBP21-tWW. Beilstein J Org Chem 2015; 11:701-706. [PMID: 26124874 PMCID: PMC4464085 DOI: 10.3762/bjoc.11.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/29/2015] [Indexed: 12/03/2022] Open
Abstract
The coupling of peptides to polyglycerol carriers represents an important route towards the multivalent display of protein ligands. In particular, the inhibition of low affinity intracellular protein–protein interactions can be addressed by this design. We have applied this strategy to develop binding partners for FBP21, a protein which is important for the splicing of pre-mRNA in the nucleus of eukaryotic cells. Firstly, by using phage display the optimized sequence WPPPPRVPR was derived which binds with KDs of 80 μM and 150 µM to the individual WW domains and with a KD of 150 μM to the tandem-WW1–WW2 construct. Secondly, this sequence was coupled to a hyperbranched polyglycerol (hPG) that allowed for the multivalent display on the surface of the dendritic polymer. This novel multifunctional hPG-peptide conjugate displayed a KD of 17.6 µM which demonstrates that the new carrier provides a venue for the future inhibition of proline-rich sequence recognition by FBP21 during assembly of the spliceosome.
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Affiliation(s)
- Lisa Maria Henning
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Thielallee 63, Freie Universität Berlin, 14195 Berlin, Germany
| | - Sumati Bhatia
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Miriam Bertazzon
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Thielallee 63, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michaela Marczynke
- Institute for Chemistry, Humboldt-Universität Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Oliver Seitz
- Institute for Chemistry, Humboldt-Universität Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Rudolf Volkmer
- Leibniz Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str.10, 13125 Berlin, Germany.,Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rainer Haag
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Thielallee 63, Freie Universität Berlin, 14195 Berlin, Germany
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Abstract
ABSTRACT
A variety of bioactive peptides and proteins have been successfully displayed on the surface of recombinant spores of
Bacillus subtilis
and other sporeformers. In most cases, spore display has been achieved by stably anchoring the foreign molecules to endogenous surface proteins or parts of them. Recombinant spores have been proposed for a large number of potential applications ranging from oral vaccine vehicles to bioremediation tools, and including biocatalysts, probiotics for animal or human use, as well as the generation and screening of mutagenesis libraries. In addition, a nonrecombinant approach has been recently developed to adsorb antigens and enzymes on the spore surface. This nonrecombinant approach appears particularly well suited for applications involving the delivery of active molecules to human or animal mucosal surfaces. Both the recombinant and nonrecombinant spore display systems have a number of advantages over cell- or phage-based systems. The stability, safety of spores of several bacterial species, and amenability to laboratory manipulations, together with the lack of some constraints limiting the use of other systems, make the spore a highly efficient platform to display heterologous proteins.
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Polonelli L, Beninati C, Teti G, Felici F, Ciociola T, Giovati L, Sperindè M, Passo CL, Pernice I, Domina M, Arigò M, Papasergi S, Mancuso G, Conti S, Magliani W. Yeast killer toxin-like candidacidal Ab6 antibodies elicited through the manipulation of the idiotypic cascade. PLoS One 2014; 9:e105727. [PMID: 25162681 PMCID: PMC4146504 DOI: 10.1371/journal.pone.0105727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/23/2014] [Indexed: 12/11/2022] Open
Abstract
A mouse anti-anti-anti-idiotypic (Id) IgM monoclonal antibody (mAb K20, Ab4), functionally mimicking a Wyckerhamomyces anomalus (Pichia anomala) killer toxin (KT) characterized by fungicidal activity against yeasts presenting specific cell wall receptors (KTR) mainly constituted by β-1,3-glucan, was produced from animals presenting anti-KT Abs (Ab3) following immunization with a rat IgM anti-Id KT-like mAb (mAb K10, Ab2). MAb K10 was produced by immunization with a KT-neutralizing mAb (mAb KT4, Ab1) bearing the internal image of KTR. MAb K20, likewise mAb K10, proved to be fungicidal in vitro against KT-sensitive Candida albicans cells, an activity neutralized by mAb KT4, and was capable of binding to β-1,3-glucan. MAb K20 and mAb K10 competed with each other and with KT for binding to C. albicans KTR. MAb K20 was used to identify peptide mimics of KTR by the selection of phage clones from random peptide phage display libraries. Using this strategy, four peptides (TK 1-4) were selected and used as immunogen in mice in the form of either keyhole limpet hemocyanin (KLH) conjugates or peptide-encoding minigenes. Peptide and DNA immunization could induce serum Abs characterized by candidacidal activity, which was inhibited by laminarin, a soluble β-1,3-glucan, but not by pustulan, a β-1,6-glucan. These findings show that the idiotypic cascade can not only overcome the barrier of animal species but also the nature of immunogens and the type of technology adopted.
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Affiliation(s)
- Luciano Polonelli
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Concetta Beninati
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Giuseppe Teti
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Franco Felici
- Dipartimento di Bioscienze e Territorio (DiBT), Università degli Studi del Molise, Contrada Fonte Lappone, Pesche (IS), Italy
| | - Tecla Ciociola
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Laura Giovati
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Martina Sperindè
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Carla Lo Passo
- Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi di Messina, Messina, Italy
| | - Ida Pernice
- Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi di Messina, Messina, Italy
| | - Maria Domina
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Milena Arigò
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Salvatore Papasergi
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Giuseppe Mancuso
- Metchnikoff Laboratory, Dipartimento di Scienze Pediatriche, Ginecologiche, Microbiologiche e Biomediche, Università degli Studi di Messina, Messina, Italy
| | - Stefania Conti
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
| | - Walter Magliani
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Unità di Microbiologia e Virologia, Università degli Studi di Parma, Parma, Italy
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Infante YC, Pupo A, Rojas G. A combinatorial mutagenesis approach for functional epitope mapping on phage-displayed target antigen: application to antibodies against epidermal growth factor. MAbs 2014; 6:637-48. [PMID: 24589624 DOI: 10.4161/mabs.28395] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although multiple different procedures to characterize the epitopes recognized by antibodies have been developed, site-directed mutagenesis remains the method of choice to define the energetic contribution of antigen residues to binding. These studies are useful to identify critical residues and to delineate functional maps of the epitopes. However, they tend to underestimate the roles of residues that are not critical for binding on their own, but contribute to the formation of the target epitope in an additive, or even cooperative, way. Mapping antigenic determinants with a diffuse energetic landscape, which establish multiple individually weak interactions with the antibody paratope, resulting in high affinity and specificity recognition of the epitope as a whole, is thus technically challenging. The current work was aimed at developing a combinatorial strategy to overcome the limitations of site-directed mutagenesis, relying on comprehensive randomization of discrete antigenic regions within phage-displayed antigen libraries. Two model antibodies recognizing epidermal growth factor were used to validate the mapping platform. Abrogation of antibody recognition due to the introduction of simultaneous replacements was able to show the involvement of particular amino acid clusters in epitope formation. The abundance of some of the original residues (or functionally equivalent amino acids sharing their physicochemical properties) among the set of mutated antigen variants selected on a given antibody highlighted their contributions and allowed delineation of a detailed functional map of the corresponding epitope. The use of the combinatorial approach could be expanded to map the interactions between other antigens/antibodies.
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Affiliation(s)
| | - Amaury Pupo
- Systems Biology Department; Center of Molecular Immunology; La Habana, Cuba
| | - Gertrudis Rojas
- Systems Biology Department; Center of Molecular Immunology; La Habana, Cuba
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Rojas G, Cabrera Infante Y, Pupo A, Carmenate T. Fine epitope specificity of antibodies against interleukin-2 explains their paradoxical immunomodulatory effects. MAbs 2013; 6:273-85. [PMID: 24253188 DOI: 10.4161/mabs.27224] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The functional dichotomy of antibodies against interleukin-2 (IL-2) is thought to depend upon recognition of different cytokine epitopes. Beyond functional studies, the only molecular evidence obtained so far located the epitopes recognized by the immunoenhancing antibodies S4B6 and JES6-5H4 within the predicted interface of IL-2 with the α receptor subunit, explaining the preferential stimulation of effector cells displaying only β and γ receptor chains. A consistent functional map of the epitope bound by the immunoregulatory antibody JES6-1A12 has now been delineated by screening the interactions of phage-displayed antigen variants (with single and multiple mutations) and antigen mimotopes. The target determinant resides in a region between the predicted interfaces with α and β/γ receptor subunits, supporting the dual inhibitory role of the antibody on both interactions. Binding by JES6-1A12 would thus convert complexed IL-2 into a very weak agonist, reinforcing the advantage of T regulatory cells (displaying the high affinity αβγ heterotrimeric receptor) to capture the cytokine by competition and expand over effector cells, ultimately resulting in the observed strong tolerogenic effect of this antibody. Detailed knowledge of the epitopes recognized by anti-IL-2 antibodies with either immunoenhancing or immunoregulatory properties completes the molecular scenario underlying their use to boost or inhibit immune responses in multiple experimental systems. The expanded functional mapping platform now available could be exploited to study other interactions involving related molecular pairs with the final goal of optimizing cytokine and anti-cytokine therapies.
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Affiliation(s)
- Gertrudis Rojas
- Systems Biology Department; Center of Molecular Immunology; La Habana, Cuba
| | | | - Amaury Pupo
- Systems Biology Department; Center of Molecular Immunology; La Habana, Cuba
| | - Tania Carmenate
- Systems Biology Department; Center of Molecular Immunology; La Habana, Cuba
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Oligopeptide m13 phage display in pathogen research. Viruses 2013; 5:2531-45. [PMID: 24136040 PMCID: PMC3814601 DOI: 10.3390/v5102531] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 12/19/2022] Open
Abstract
Phage display has become an established, widely used method for selection of peptides, antibodies or alternative scaffolds. The use of phage display for the selection of antigens from genomic or cDNA libraries of pathogens which is an alternative to the classical way of identifying immunogenic proteins is not well-known. In recent years several new applications for oligopeptide phage display in disease related fields have been developed which has led to the identification of various new antigens. These novel identified immunogenic proteins provide new insights into host pathogen interactions and can be used for the development of new diagnostic tests and vaccines. In this review we focus on the M13 oligopeptide phage display system for pathogen research but will also give examples for lambda phage display and for applications in other disease related fields. In addition, a detailed technical work flow for the identification of immunogenic oligopeptides using the pHORF system is given. The described identification of immunogenic proteins of pathogens using oligopeptide phage display can be linked to antibody phage display resulting in a vaccine pipeline.
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40
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Qi H, Lu H, Qiu HJ, Petrenko V, Liu A. Phagemid Vectors for Phage Display: Properties, Characteristics and Construction. J Mol Biol 2012; 417:129-43. [PMID: 22310045 DOI: 10.1016/j.jmb.2012.01.038] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/20/2012] [Accepted: 01/24/2012] [Indexed: 11/20/2022]
Affiliation(s)
- Huan Qi
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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41
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Aavula SM, Nimmagadda SV, Biradhar N, Sula S, Chandran D, Lingala R, Villuppanoor SA. Generation and Characterization of an scFv Directed against Site II of Rabies Glycoprotein. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2011; 2011:652147. [PMID: 22007309 PMCID: PMC3189463 DOI: 10.4061/2011/652147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/04/2011] [Accepted: 08/10/2011] [Indexed: 12/11/2022]
Abstract
Recombinant antibody phage display technology is a vital tool that facilitates identification of specific binding molecules to a target enabling the rapid generation and selection of high affinity, fully human, or mouse antibody product candidates essentially directed towards disease target appropriate for antibody therapy. In this study, a recombinant single-chain Fv antibody fragment (scFv) A11 was isolated from immune spleen cells obtained from mice immunized with inactivated rabies virus (Pasteur strain) using standard methodology and was characterized for its specificity towards the rabies virus glycoprotein. Epitope mapping using peptide libraries and truncated glycoprotein polypeptides suggested that A11 bound to the antigenic site II of rabies glycoprotein against which a majority of rabies virus neutralizing antibodies are directed. The use of the above technology could, therefore, allow development of scFvs with different specificities against the rabies glycoprotein as an alternative to the more cumbersome protocols used for the development of monoclonal antibodies.
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Affiliation(s)
- Shukra M Aavula
- Research and Development Center, Indian Immunologicals Limited, Rakshapuram, Gachibowli, Hyderabad 500032, India
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Searching for antigen epitope specificities in the monoclonal IgG molecules of patients with multiple myeloma. The description of a monoclonal antibody with a dynein-specific antigen epitope character. Ann Hematol 2011; 90:1227-8. [DOI: 10.1007/s00277-010-1148-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 12/20/2010] [Indexed: 11/27/2022]
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Carducci M, Perfetto L, Briganti L, Paoluzi S, Costa S, Zerweck J, Schutkowski M, Castagnoli L, Cesareni G. The protein interaction network mediated by human SH3 domains. Biotechnol Adv 2011; 30:4-15. [PMID: 21740962 DOI: 10.1016/j.biotechadv.2011.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/31/2011] [Accepted: 06/13/2011] [Indexed: 10/18/2022]
Abstract
Families of conserved protein domains, specialized in mediating interactions with short linear peptide motifs, are responsible for the formation of a variety of dynamic complexes in the cell. An important subclass of these motifs are characterized by a high proline content and play a pivotal role in biological processes requiring the coordinated assembly of multi-protein complexes. This is achieved via interaction of proteins containing modules such as Src Homology-3 (SH3) or WW domains and specific proline rich patterns. Here we make available via a publicly accessible database a synopsis of our current understanding of the interaction landscape of the human SH3 protein family. This is achieved by integrating an information extraction strategy with a new experimental approach. In a first approach we have used a text mining strategy to capture a large number of manuscripts reporting interactions between SH3 domains and target peptides. Relevant information was annotated in the MINT database. In a second experimental approach we have used a variant of the WISE (Whole Interactome Scanning Experiment) strategy to probe a large number of naturally occurring and chemically-synthesized peptides arrayed at high density on a glass surface. By this method we have tested 60 human SH3 domains for their ability to bind a collection of 9192 poly-proline containing peptides immobilized on a glass chip. To evaluate the quality of the resulting interaction dataset, we retested some of the interactions on a smaller scale and performed a series of pull down experiments on native proteins. Peptide chips, pull down assays, SPOT synthesis and phage display experiments have allowed us to further characterize the specificity and promiscuity of proline-rich binding domains and to map their interaction network. Both the information captured from the literature and the interactions inferred from the peptide chip experiments were collected and stored in the PepspotDB (http://mint.bio.uniroma2.it/PepspotDB/).
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Affiliation(s)
- Martina Carducci
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.
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Specificity of mimotope-induced anti-high molecular weight-melanoma associated antigen (HMW-MAA) antibodies does not ensure biological activity. PLoS One 2011; 6:e19383. [PMID: 21573118 PMCID: PMC3089623 DOI: 10.1371/journal.pone.0019383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 03/28/2011] [Indexed: 01/26/2023] Open
Abstract
Vaccines based on peptide mimics (mimotopes) of conformational tumor antigen epitopes have been investigated for a variety of human tumors including breast cancer, tumors expressing the carcinoembryonic antigen, B cell lymphoma, neuroblastoma, and melanoma. In our previous work, we designed a vaccine based on a mimotope of the high molecular weight-melanoma associated antigen (HMW-MAA) that elicited HMW-MAA-specific antibodies (Abs) with anti-tumor activity in vitro and in vivo. In this study, we aimed to identify mimotopes of additional distinct HMW-MAA epitopes, since they could be used to construct a polymimotope melanoma vaccine. For this purpose, random peptide phage libraries were screened with the anti-HMW-MAA monoclonal antibodies (mAbs) VT80.12 and VF1-TP43 yielding one peptide ligand for each mAb. Both peptides inhibited the binding of the corresponding mAb to the HMW-MAA. Furthermore, when coupled to the carrier protein keyhole limpet hemocyanin (KLH), both HMW-MAA mimotopes elicited peptide-specific Abs in rabbits or BALB/c mice, but only the mimotope isolated with the mAb VT80.12 elicited HMW-MAA-specific Abs and only in mice. However, the latter Abs had no detectable effect on HMW-MAA expressing human melanoma cells in vitro. These results describe limitations related to the phage display technique and emphasize the need to characterize the functional properties of the mAb utilized to isolate mimotopes of the corresponding epitopes.
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45
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Georgieva Y, Konthur Z. Design and screening of M13 phage display cDNA libraries. Molecules 2011; 16:1667-81. [PMID: 21330956 PMCID: PMC6259656 DOI: 10.3390/molecules16021667] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/14/2011] [Accepted: 02/15/2011] [Indexed: 12/17/2022] Open
Abstract
The last decade has seen a steady increase in screening of cDNA expression product libraries displayed on the surface of filamentous bacteriophage. At the same time, the range of applications extended from the identification of novel allergens over disease markers to protein-protein interaction studies. However, the generation and selection of cDNA phage display libraries is subjected to intrinsic biological limitations due to their complex nature and heterogeneity, as well as technical difficulties regarding protein presentation on the phage surface. Here, we review the latest developments in this field, discuss a number of strategies and improvements anticipated to overcome these challenges making cDNA and open reading frame (ORF) libraries more readily accessible for phage display. Furthermore, future trends combining phage display with next generation sequencing (NGS) will be presented.
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Affiliation(s)
- Yuliya Georgieva
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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Borja MS, Piotukh K, Freund C, Gross JD. Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition. RNA (NEW YORK, N.Y.) 2011; 17:278-90. [PMID: 21148770 PMCID: PMC3022277 DOI: 10.1261/rna.2382011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/08/2010] [Indexed: 05/20/2023]
Abstract
Cap hydrolysis is a critical step in several eukaryotic mRNA decay pathways and is carried out by the evolutionarily conserved decapping complex containing Dcp2 at the catalytic core. In yeast, Dcp1 is an essential activator of decapping and coactivators such as Edc1 and Edc2 are thought to enhance activity, though their mechanism remains elusive. Using kinetic analysis we show that a crucial function of Dcp1 is to couple the binding of coactivators of decapping to activation of Dcp2. Edc1 and Edc2 bind Dcp1 via its EVH1 proline recognition site and stimulate decapping by 1000-fold, affecting both the K(M) for mRNA and rate of the catalytic step. The C-terminus of Edc1 is necessary and sufficient to enhance the catalytic step, while the remainder of the protein likely increases mRNA binding to the decapping complex. Lesions in the Dcp1 EVH1 domain or the Edc1 proline-rich sequence are sufficient to block stimulation. These results identify a new role of Dcp1, which is to link the binding of coactivators to substrate recognition and activation of Dcp2.
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Affiliation(s)
- Mark S Borja
- Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94158, USA
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47
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Isolation of a novel neutralizing antibody fragment against human vascular endothelial growth factor from a phage-displayed human antibody repertoire using an epitope disturbing strategy. J Biotechnol 2011; 151:166-74. [DOI: 10.1016/j.jbiotec.2010.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/22/2010] [Accepted: 12/03/2010] [Indexed: 11/21/2022]
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48
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Woo MK, Heo CK, Hwang HM, Ko JH, Yoo HS, Cho EW. Optimization of phage-immobilized ELISA for autoantibody profiling in human sera. Biotechnol Lett 2010; 33:655-61. [DOI: 10.1007/s10529-010-0483-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 11/17/2010] [Indexed: 11/30/2022]
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Abstract
Phage display has been extensively used to study protein-protein interactions, receptor- and antibody-binding sites, and immune responses, to modify protein properties, and to select antibodies against a wide range of different antigens. In the format most often used, a polypeptide is displayed on the surface of a filamentous phage by genetic fusion to one of the coat proteins, creating a chimeric coat protein, and coupling phenotype (the protein) to genotype (the gene within). As the gene encoding the chimeric coat protein is packaged within the phage, selection of the phage on the basis of the binding properties of the polypeptide displayed on the surface simultaneously results in the isolation of the gene encoding the polypeptide. This unit describes the background to the technique, and illustrates how it has been applied to a number of different problems, each of which has its neurobiological counterparts. Although this overview concentrates on the use of filamentous phage, which is the most popular platform, other systems are also described.
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50
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Velappan N, Fisher HE, Pesavento E, Chasteen L, D’Angelo S, Kiss C, Longmire M, Pavlik P, Bradbury ARM. A comprehensive analysis of filamentous phage display vectors for cytoplasmic proteins: an analysis with different fluorescent proteins. Nucleic Acids Res 2010; 38:e22. [PMID: 19955231 PMCID: PMC2831335 DOI: 10.1093/nar/gkp809] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 09/14/2009] [Indexed: 01/11/2023] Open
Abstract
Filamentous phage display has been extensively used to select proteins with binding properties of specific interest. Although many different display platforms using filamentous phage have been described, no comprehensive comparison of their abilities to display similar proteins has been conducted. This is particularly important for the display of cytoplasmic proteins, which are often poorly displayed with standard filamentous phage vectors. In this article, we have analyzed the ability of filamentous phage to display a stable form of green fluorescent protein and modified variants in nine different display vectors, a number of which have been previously proposed as being suitable for cytoplasmic protein display. Correct folding and display were assessed by phagemid particle fluorescence, and with anti-GFP antibodies. The poor correlation between phagemid particle fluorescence and recognition of GFP by antibodies, indicates that proteins may fold correctly without being accessible for display. The best vector used a twin arginine transporter leader to transport the displayed protein to the periplasm, and a coil-coil arrangement to link the displayed protein to g3p. This vector was able to display less robust forms of GFP, including ones with inserted epitopes, as well as fluorescent proteins of the Azami green series. It was also functional in mock selection experiments.
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