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Li D, Pucci F, Rooman M. Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks. Int J Mol Sci 2024; 25:5434. [PMID: 38791470 PMCID: PMC11121317 DOI: 10.3390/ijms25105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However, there are currently no reliable methods for predicting the antibodies that recognize a specific antigen region (or epitope) and, conversely, epitopes that recognize the binding region of a given antibody (or paratope). To fill this gap, we developed ImaPEp, a machine learning-based tool for predicting the binding probability of paratope-epitope pairs, where the epitope and paratope patches were simplified into interacting two-dimensional patches, which were colored according to the values of selected features, and pixelated. The specific recognition of an epitope image by a paratope image was achieved by using a convolutional neural network-based model, which was trained on a set of two-dimensional paratope-epitope images derived from experimental structures of antibody-antigen complexes. Our method achieves good performances in terms of cross-validation with a balanced accuracy of 0.8. Finally, we showcase examples of application of ImaPep, including extensive screening of large libraries to identify paratope candidates that bind to a selected epitope, and rescoring and refining antibody-antigen docking poses.
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Affiliation(s)
- Dong Li
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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2
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Gallo E. Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances. Mol Biotechnol 2024:10.1007/s12033-024-01064-2. [PMID: 38308755 DOI: 10.1007/s12033-024-01064-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen recognition, paratope site engineering, and biochemical refinements. In a parallel realm, deep sequencing has brought about a paradigm shift in molecular biology. It facilitates the prompt and cost-effective high-throughput sequencing of DNA and RNA molecules, enabling the comprehensive big data analysis of Ab transcriptomes, including specific regions of interest. Significantly, the integration of artificial intelligence (AI), based on machine- and deep- learning approaches, has fundamentally transformed our capacity to discern patterns hidden within deep sequencing big data, including distinctive Ab features and protein folding free energy landscapes. Ultimately, current AI advances can generate approximations of the most stable Ab structural configurations, enabling the prediction of de novo synthetic Abs. As a result, this manuscript comprehensively examines the latest and relevant literature concerning the intersection of deep sequencing big data and AI methodologies for the design and development of synthetic Abs. Together, these advancements have accelerated the exploration of antibody repertoires, contributing to the refinement of synthetic Ab engineering and optimizations, and facilitating advancements in the lead identification process.
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Affiliation(s)
- Eugenio Gallo
- Avance Biologicals, Department of Medicinal Chemistry, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- RevivAb, Department of Protein Engineering, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
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3
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Esmaili M, Eldeeb M. Cellular toxicity of scrapie prions in prion diseases; a biochemical and molecular overview. Mol Biol Rep 2023; 50:1743-1752. [PMID: 36446981 DOI: 10.1007/s11033-022-07806-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) or prion diseases consist of a broad range of fatal neurological disorders affecting humans and animals. Contrary to Watson and Crick's 'central dogma', prion diseases are caused by a protein, devoid of DNA involvement. Herein, we briefly review various cellular and biological aspects of prions and prion pathogenesis focusing mainly on historical milestones, biosynthesis, degradation, structure-function of cellular and scrapie forms of prions .
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Affiliation(s)
- Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Mohamed Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt.
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4
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Igel A, Fornara B, Rezaei H, Béringue V. Prion assemblies: structural heterogeneity, mechanisms of formation, and role in species barrier. Cell Tissue Res 2022; 392:149-166. [PMID: 36399162 PMCID: PMC10113350 DOI: 10.1007/s00441-022-03700-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
AbstractPrions are proteinaceous pathogens responsible for a wide range of neurodegenerative diseases in animal and human. Prions are formed from misfolded, ß-sheet rich, and aggregated conformers (PrPSc) of the host-encoded prion protein (PrPC). Prion replication stems from the capacity of PrPSc to self-replicate by templating PrPC conversion and polymerization. The question then arises about the molecular mechanisms of prion replication, host invasion, and capacity to contaminate other species. Studying these mechanisms has gained in recent years further complexity with evidence that PrPSc is a pleiomorphic protein. There is indeed compelling evidence for PrPSc structural heterogeneity at different scales: (i) within prion susceptible host populations with the existence of different strains with specific biological features due to different PrPSc conformers, (ii) within a single infected host with the co-propagation of different strains, and (iii) within a single strain with evidence for co-propagation of PrPSc assemblies differing in their secondary to quaternary structure. This review summarizes current knowledge of prion assembly heterogeneity, potential mechanisms of formation during the replication process, and importance when crossing the species barrier.
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5
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Zeng F, Li Y, Xu Y, Yang J, Liu Z, Li X, Ren L. Strategies Targeting Soluble β-Amyloid Oligomers and their Application to Early Diagnosis of Alzheimer's Disease. Curr Alzheimer Res 2020; 16:1132-1142. [PMID: 31670622 DOI: 10.2174/1567205016666191031163504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alzheimer's Disease (AD) is the most common neurodegenerative disorder, and it is still incurable. Early diagnosis and intervention are crucial for delaying the onset and progression of the disease. Mounting evidence indicates that the neurotoxic effects might be attributed to Soluble β-Amyloid Oligomers (SAβO). The SAβO are believed to be neurotoxic peptides more predominant than Aβ plaques in the early stage, and their key role in AD is self-evident. Unfortunately, identification of SAβO proves to be difficult due to their heterogeneous and transient nature. In spite of many obstacles, multiple techniques have recently been developed to target SAβO effectively. This review focuses on the recent progress in the approaches towards SAβO detection in order to shed some light on the future development of SAβO assays. METHODS Literatures were obtained from the following libraries: Web of Science, PubMed, EPO, SIPO, USPTO. Articles were critically reviewed based on their titles, abstracts, and contents. RESULTS A total of 85 papers are referenced in the review. Results are divided into three categories based on the types of detection methods: small molecule fluorescence probes, oligomer-specific antibodies and electrochemical biosensors. Finally, the improvements and challenges of these approaches applied in the early diagnosis of AD were discussed. CONCLUSION This review article covers three kinds of strategies that could be translated into clinic practice and lead to earlier diagnosis and therapeutic interventions of AD.
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Affiliation(s)
- Fantian Zeng
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
| | - Yuyan Li
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
| | - Yungen Xu
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
| | - Jian Yang
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
| | - Zhengshi Liu
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaofang Li
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
| | - Longfei Ren
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 211198, China
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6
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Colini Baldeschi A, Vanni S, Zattoni M, Legname G. Novel regulators of PrP C expression as potential therapeutic targets in prion diseases. Expert Opin Ther Targets 2020; 24:759-776. [PMID: 32631090 DOI: 10.1080/14728222.2020.1782384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Prion diseases are rare and fatal neurodegenerative disorders. The key molecular event in these disorders is the misfolding of the physiological form of the cellular prion protein, PrPC, leading to the accumulation of a pathological isoform, PrPSc, with unique features. Both isoforms share the same primary sequence, lacking detectable differences in posttranslational modification, a major hurdle for their biochemical or biophysical independent characterization. The mechanism underlying the conversion of PrPC to PrPSc is not completely understood, so finding an effective therapy to cure prion disorders is extremely challenging. AREAS COVERED This review discusses the strategies for decreasing prion replication and throws a spotlight on the relevance of PrPC in the prion accumulation process. EXPERT OPINION PrPC is the key substrate for prion pathology; hence, the most promising therapeutic approach appears to be the targeting of PrPC to block the production of the infectious isoform. The use of RNA interference and antisense oligonucleotide technologies may offer opportunities for treatment because of their success in clinical trials for other neurodegenerative diseases.
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Affiliation(s)
- Arianna Colini Baldeschi
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA) , Trieste, Italy
| | - Silvia Vanni
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per Lo Studio E La Cura Dei Tumori (IRST) IRCCS , Meldola, Italy
| | - Marco Zattoni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA) , Trieste, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA) , Trieste, Italy
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Spagnolli G, Rigoli M, Orioli S, Sevillano AM, Faccioli P, Wille H, Biasini E, Requena JR. Full atomistic model of prion structure and conversion. PLoS Pathog 2019; 15:e1007864. [PMID: 31295325 PMCID: PMC6622554 DOI: 10.1371/journal.ppat.1007864] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/23/2019] [Indexed: 11/19/2022] Open
Abstract
Prions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids. The first prion identified, the scrapie isoform (PrPSc) of the cellular prion protein (PrPC), caused epidemic and epizootic episodes [1]. Most aggregates of other misfolding-prone proteins are amyloids, often arranged in a Parallel-In-Register-β-Sheet (PIRIBS) [2] or β-solenoid conformations [3]. Similar folding models have also been proposed for PrPSc, although none of these have been confirmed experimentally. Recent cryo-electron microscopy (cryo-EM) and X-ray fiber-diffraction studies provided evidence that PrPSc is structured as a 4-rung β-solenoid (4RβS) [4, 5]. Here, we combined different experimental data and computational techniques to build the first physically-plausible, atomic resolution model of mouse PrPSc, based on the 4RβS architecture. The stability of this new PrPSc model, as assessed by Molecular Dynamics (MD) simulations, was found to be comparable to that of the prion forming domain of Het-s, a naturally-occurring β-solenoid. Importantly, the 4RβS arrangement allowed the first simulation of the sequence of events underlying PrPC conversion into PrPSc. This study provides the most updated, experimentally-driven and physically-coherent model of PrPSc, together with an unprecedented reconstruction of the mechanism underlying the self-catalytic propagation of prions.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- * E-mail: (GS); (EB); (JRR)
| | - Marta Rigoli
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- Department of Physics, Povo, Trento TN, ITALY
| | - Simone Orioli
- Department of Physics, Povo, Trento TN, ITALY
- INFN-TIFPA, Povo (Trento), ITALY
| | - Alejandro M. Sevillano
- Department of Pathology–University of California—San Diego, San Diego, California, United States of America
| | - Pietro Faccioli
- Department of Physics, Povo, Trento TN, ITALY
- INFN-TIFPA, Povo (Trento), ITALY
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases–University of Alberta, Edmonton (AB), CANADA
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- * E-mail: (GS); (EB); (JRR)
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago, SPAIN
- * E-mail: (GS); (EB); (JRR)
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8
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Suzuki A, Yamasaki T, Hasebe R, Horiuchi M. Enhancement of binding avidity by bivalent binding enables PrPSc-specific detection by anti-PrP monoclonal antibody 132. PLoS One 2019; 14:e0217944. [PMID: 31170247 PMCID: PMC6553756 DOI: 10.1371/journal.pone.0217944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/21/2019] [Indexed: 12/05/2022] Open
Abstract
Anti-prion protein (PrP) monoclonal antibody 132, which recognizes mouse PrP amino acids 119–127, enables us to reliably detect abnormal isoform prion protein (PrPSc) in cells or frozen tissue sections by immunofluorescence assay, although treatment with guanidinium salts is a prerequisite. Despite the benefit of this mAb, the mechanism of PrPSc-specific detection remains unclear. Therefore, to address this mechanism, we analyzed the reactivities of mono- and bivalent mAb 132 to recombinant mouse PrP (rMoPrP) by enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR). In ELISA, binding of the monovalent form was significantly weaker than that of the bivalent form, indicating that bivalent binding confers a higher binding stability to mAb 132. Compared with other anti-PrP mAbs tested, the reactivity of bivalent mAb 132 was easily affected by a decrease in antigen concentration. The binding kinetics of mAb 132 assessed by SPR were consistent with the results of ELISA. The dissociation constant of the monovalent form was approximately 260 times higher than that of the bivalent form, suggesting that monovalent binding is less stable than bivalent binding. Furthermore, the amount of mAb 132 that bound to rMoPrP decreased if the antigen density was too low to allow bivalent binding. If two cellular PrP (PrPC) are close enough to allow bivalent binding, mAb 132 binds to PrPC. These results indicate that weak monovalent binding to monomeric PrPC diminishes PrPC signals to background level, whereas after exposure of the epitope, mAb 132 binds stably to oligomeric PrPSc in a bivalent manner.
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Affiliation(s)
- Akio Suzuki
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Takeshi Yamasaki
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Rie Hasebe
- Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Kita-ku, Sapporo, Japan
- Global Station for Zoonosis Control. Global Institute for Collaborative Research and Education, Hokkaido University, Kita-ku, Sapporo, Japan
- * E-mail:
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9
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Mengel D, Hong W, Corbett GT, Liu W, DeSousa A, Solforosi L, Fang C, Frosch MP, Collinge J, Harris DA, Walsh DM. PrP-grafted antibodies bind certain amyloid β-protein aggregates, but do not prevent toxicity. Brain Res 2019; 1710:125-135. [PMID: 30593771 PMCID: PMC6431553 DOI: 10.1016/j.brainres.2018.12.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/26/2018] [Accepted: 12/23/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND The prion protein (PrP) is known to bind certain soluble aggregates of the amyloid β-protein (Aβ), and two regions of PrP, one centered around residues 19-33, and the other around 87-112, are thought to be particularly important for this interaction. When either of these sequences are grafted into a human IgG the resulting antibodies react with disease-associated PrP conformers, whereas the parental b12 IgG does not. METHODS Human antibodies containing grafts of PrP 19-33 or 87-112 were prepared as before (Solforosi et al., 2007) and tested for their ability to recognize synthetic and Alzheimer's disease (AD) brain-derived Aβ. Since aqueous extracts of AD brain contain a complex mixture of active and inactive Aβ species, we also assessed whether PrP-grafted antibodies could protect against neuritotoxicity mediated by AD brain-derived Aβ. For these experiments, human iPSC-derived neurons were grown in 96-well plates at 5000 cells per well and on post-induction day 21, AD brain extracts were added +/- test antibodies. Neurons were imaged for 3 days using an IncuCyte live-cell imaging system, and neurite number and density quantified. RESULTS Grafted antibodies bound a significant portion of aggregated Aβ in aqueous AD extracts, but when these antibodies were co-incubated with neurons treated with brain extracts they did not reduce toxicity. By contrast, the PrP fragment N1 did protect against Aβ. CONCLUSIONS These results further demonstrate that not all Aβ oligomers are toxic and suggest that PrP derivatives may allow development of agents that differentially recognize toxic and innocuous Aβ aggregates.
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Affiliation(s)
- David Mengel
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wei Hong
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Grant T Corbett
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wen Liu
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra DeSousa
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura Solforosi
- Laboratory of Microbiology and Virology, University Vita-Salute San Raffaele, Milan, Italy
| | - Cheng Fang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Matthew P Frosch
- Massachusetts General Institute for Neurodegenerative Disease, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - John Collinge
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; MRC Prion Unit at UCL, UCL Institute of Prion Diseases and NHS National Prion Clinic, UCL Hospitals NHS Foundation Trust, London, United Kingdom
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Dominic M Walsh
- Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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10
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Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018; 47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.
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Affiliation(s)
- Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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11
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Sarell CJ, Quarterman E, Yip DCM, Terry C, Nicoll AJ, Wadsworth JDF, Farrow MA, Walsh DM, Collinge J. Soluble Aβ aggregates can inhibit prion propagation. Open Biol 2018; 7:rsob.170158. [PMID: 29142106 PMCID: PMC5717343 DOI: 10.1098/rsob.170158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022] Open
Abstract
Mammalian prions cause lethal neurodegenerative diseases such as Creutzfeldt–Jakob disease (CJD) and consist of multi-chain assemblies of misfolded cellular prion protein (PrPC). Ligands that bind to PrPC can inhibit prion propagation and neurotoxicity. Extensive prior work established that certain soluble assemblies of the Alzheimer's disease (AD)-associated amyloid β-protein (Aβ) can tightly bind to PrPC, and that this interaction may be relevant to their toxicity in AD. Here, we investigated whether such soluble Aβ assemblies might, conversely, have an inhibitory effect on prion propagation. Using cellular models of prion infection and propagation and distinct Aβ preparations, we found that the form of Aβ assemblies which most avidly bound to PrP in vitro also inhibited prion infection and propagation. By contrast, forms of Aβ which exhibit little or no binding to PrP were unable to attenuate prion propagation. These data suggest that soluble aggregates of Aβ can compete with prions for binding to PrPC and emphasize the bidirectional nature of the interplay between Aβ and PrPC in Alzheimer's and prion diseases. Such inhibitory effects of Aβ on prion propagation may contribute to the apparent fall-off in the incidence of sporadic CJD at advanced age where cerebral Aβ deposition is common.
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Affiliation(s)
- Claire J Sarell
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Emma Quarterman
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Daniel C-M Yip
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Cassandra Terry
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Andrew J Nicoll
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Jonathan D F Wadsworth
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Mark A Farrow
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Dominic M Walsh
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK .,Laboratory for Neurodegenerative Research, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
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12
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Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurological disorders caused by prions, which are composed of a misfolded protein (PrPSc) that self-propagates in the brain of infected individuals by converting the normal prion protein (PrPC) into the pathological isoform. Here, we report a novel experimental strategy for preventing prion disease based on producing a self-replicating, but innocuous PrPSc-like form, termed anti-prion, which can compete with the replication of pathogenic prions. Our results show that a prophylactic inoculation of prion-infected animals with an anti-prion delays the onset of the disease and in some animals completely prevents the development of clinical symptoms and brain damage. The data indicate that a single injection of the anti-prion eliminated ~99% of the infectivity associated to pathogenic prions. Furthermore, this treatment caused significant changes in the profile of regional PrPSc deposition in the brains of animals that were treated, but still succumbed to the disease. Our findings provide new insights for a mechanistic understanding of prion replication and support the concept that prion replication can be separated from toxicity, providing a novel target for therapeutic intervention.
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13
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Julian MC, Li L, Garde S, Wilen R, Tessier PM. Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability. Sci Rep 2017; 7:45259. [PMID: 28349921 PMCID: PMC5368667 DOI: 10.1038/srep45259] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/27/2017] [Indexed: 12/31/2022] Open
Abstract
The ability of antibodies to accumulate affinity-enhancing mutations in their complementarity-determining regions (CDRs) without compromising thermodynamic stability is critical to their natural function. However, it is unclear if affinity mutations in the hypervariable CDRs generally impact antibody stability and to what extent additional compensatory mutations are required to maintain stability during affinity maturation. Here we have experimentally and computationally evaluated the functional contributions of mutations acquired by a human variable (VH) domain that was evolved using strong selections for enhanced stability and affinity for the Alzheimer’s Aβ42 peptide. Interestingly, half of the key affinity mutations in the CDRs were destabilizing. Moreover, the destabilizing effects of these mutations were compensated for by a subset of the affinity mutations that were also stabilizing. Our findings demonstrate that the accumulation of both affinity and stability mutations is necessary to maintain thermodynamic stability during extensive mutagenesis and affinity maturation in vitro, which is similar to findings for natural antibodies that are subjected to somatic hypermutation in vivo. These findings for diverse antibodies and antibody fragments specific for unrelated antigens suggest that the formation of the antigen-binding site is generally a destabilizing process and that co-enrichment for compensatory mutations is critical for maintaining thermodynamic stability.
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Affiliation(s)
- Mark C Julian
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lijuan Li
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Shekhar Garde
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Rebecca Wilen
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Center for Biotechnology &Interdisciplinary Studies, Isermann Dept. of Chemical &Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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14
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Nam DH, Fang K, Rodriguez C, Lopez T, Ge X. Generation of inhibitory monoclonal antibodies targeting matrix metalloproteinase-14 by motif grafting and CDR optimization. Protein Eng Des Sel 2016; 30:113-118. [PMID: 27986919 DOI: 10.1093/protein/gzw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 12/16/2022] Open
Abstract
Matrix metalloproteinase-14 (MMP-14) plays important roles in cancer metastasis, and the failures of broad-spectrum MMP compound inhibitors in clinical trials suggested selectivity is critical. By grafting an MMP-14 specific inhibition motif into complementarity determining region (CDR)-H3 of antibody scaffolds and optimizing other CDRs and the sequences that flank CDR-H3, we isolated a Fab 1F8 showing a binding affinity of 8.3 nM with >1000-fold enhancement on inhibition potency compared to the peptide inhibitor. Yeast surface display and fluorescence-activated cell sorting results indicated that 1F8 was highly selective to MMP-14 and competed with TIMP-2 on binding to the catalytic domain of MMP-14. Converting a low-affinity peptide inhibitor into a high potency antibody, the described methods can be used to develop other inhibitory antibodies of therapeutic significance.
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Affiliation(s)
- Dong Hyun Nam
- Department of Chemical and Environmental Engineering, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
| | - Kuili Fang
- Department of Chemical and Environmental Engineering, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
| | - Carlos Rodriguez
- Department of Chemical and Environmental Engineering, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
| | - Tyler Lopez
- Department of Chemical and Environmental Engineering, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California, Riverside 900 University Ave, Riverside, CA 92521, USA
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15
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Saijo E, Hughson AG, Raymond GJ, Suzuki A, Horiuchi M, Caughey B. PrPSc-Specific Antibody Reveals C-Terminal Conformational Differences between Prion Strains. J Virol 2016; 90:4905-4913. [PMID: 26937029 PMCID: PMC4859706 DOI: 10.1128/jvi.00088-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/19/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Understanding the structure of PrP(Sc) and its strain variation has been one of the major challenges in prion disease biology. To study the strain-dependent conformations of PrP(Sc), we purified proteinase-resistant PrP(Sc) (PrP(RES)) from mouse brains with three different murine-adapted scrapie strains (Chandler, 22L, and Me7) and systematically tested the accessibility of epitopes of a wide range of anti-PrP and anti-PrP(Sc) specific antibodies by indirect enzyme-linked immunosorbent assay (ELISA). We found that epitopes of most anti-PrP antibodies were hidden in the folded structure of PrP(RES), even though these epitopes are revealed with guanidine denaturation. However, reactivities to a PrP(Sc)-specific conformational C-terminal antibody showed significant differences among the three different prion strains. Our results provide evidence for strain-dependent conformational variation near the C termini of molecules within PrP(Sc) multimers. IMPORTANCE It has long been apparent that prion strains can have different conformations near the N terminus of the PrP(Sc) protease-resistant core. Here, we show that a C-terminal conformational PrP(Sc)-specific antibody reacts differently to three murine-adapted scrapie strains. These results suggest, in turn, that conformational differences in the C terminus of PrP(Sc) also contribute to the phenotypic distinction between prion strains.
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Affiliation(s)
- Eri Saijo
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Andrew G Hughson
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Gregory J Raymond
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Akio Suzuki
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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16
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Mutated but Not Deleted Ovine PrP(C) N-Terminal Polybasic Region Strongly Interferes with Prion Propagation in Transgenic Mice. J Virol 2015; 90:1638-46. [PMID: 26608316 DOI: 10.1128/jvi.02805-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mammalian prions are proteinaceous infectious agents composed of misfolded assemblies of the host-encoded, cellular prion protein (PrP). Physiologically, the N-terminal polybasic region of residues 23 to 31 of PrP has been shown to be involved in its endocytic trafficking and interactions with glycosaminoglycans or putative ectodomains of membrane-associated proteins. Several recent reports also describe this PrP region as important for the toxicity of mutant prion proteins and the efficiency of prion propagation, both in vitro and in vivo. The question remains as to whether the latter observations made with mouse PrP and mouse prions would be relevant to other PrP species/prion strain combinations given the dramatic impact on prion susceptibility of minimal amino acid substitutions and structural variations in PrP. Here, we report that transgenic mouse lines expressing ovine PrP with a deletion of residues 23 to 26 (KKRP) or mutated in this N-terminal region (KQHPH instead of KKRPK) exhibited a variable, strain-dependent susceptibility to prion infection with regard to the proportion of affected mice and disease tempo relative to findings in their wild-type counterparts. Deletion has no major effect on 127S scrapie prion pathogenesis, whereas mutation increased by almost 3-fold the survival time of the mice. Deletion marginally affected the incubation time of scrapie LA19K and ovine bovine spongiform encephalopathy (BSE) prions, whereas mutation caused apparent resistance to disease. IMPORTANCE Recent reports suggested that the N-terminal polybasic region of the prion protein could be a therapeutic target to prevent prion propagation or toxic signaling associated with more common neurodegenerative diseases such as Alzheimer's disease. Mutating or deleting this region in ovine PrP completes the data previously obtained with the mouse protein by identifying the key amino acid residues involved.
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17
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Lee CC, Julian MC, Tiller KE, Meng F, DuConge SE, Akter R, Raleigh DP, Tessier PM. Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide. J Biol Chem 2015; 291:2858-73. [PMID: 26601942 DOI: 10.1074/jbc.m115.682336] [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: 08/05/2015] [Indexed: 12/25/2022] Open
Abstract
Antibodies with conformational specificity are important for detecting and interfering with polypeptide aggregation linked to several human disorders. We are developing a motif-grafting approach for designing lead antibody candidates specific for amyloid-forming polypeptides such as the Alzheimer peptide (Aβ). This approach involves grafting amyloidogenic peptide segments into the complementarity-determining regions (CDRs) of single-domain (VH) antibodies. Here we have investigated the impact of polar mutations inserted at the edges of a large hydrophobic Aβ42 peptide segment (Aβ residues 17-42) in CDR3 on the solubility and conformational specificity of the corresponding VH domains. We find that VH expression and solubility are strongly enhanced by introducing multiple negatively charged or asparagine residues at the edges of CDR3, whereas other polar mutations are less effective (glutamine and serine) or ineffective (threonine, lysine, and arginine). Moreover, Aβ VH domains with negatively charged CDR3 mutations show significant preference for recognizing Aβ fibrils relative to Aβ monomers, whereas the same VH domains with other polar CDR3 mutations recognize both Aβ conformers. We observe similar behavior for a VH domain grafted with a large hydrophobic peptide from islet amyloid polypeptide (residues 8-37) that contains negatively charged mutations at the edges of CDR3. These findings highlight the sensitivity of antibody binding and solubility to residues at the edges of CDRs, and provide guidelines for designing other grafted antibody fragments with hydrophobic binding loops.
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Affiliation(s)
- Christine C Lee
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Mark C Julian
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Kathryn E Tiller
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Fanling Meng
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Sarah E DuConge
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Rehana Akter
- the Department of Chemistry, Stony Brook University, Stony Brook, New York 11794
| | - Daniel P Raleigh
- the Department of Chemistry, Stony Brook University, Stony Brook, New York 11794
| | - Peter M Tessier
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
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18
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Shikiya RA, Eckland TE, Young AJ, Bartz JC. Prion formation, but not clearance, is supported by protein misfolding cyclic amplification. Prion 2015; 8:415-20. [PMID: 25482601 DOI: 10.4161/19336896.2014.983759] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prion diseases are fatal transmissible neurodegenerative disorders that affect animals including humans. The kinetics of prion infectivity and PrP(Sc) accumulation can differ between prion strains and within a single strain in different tissues. The net accumulation of PrP(Sc) in animals is controlled by the relationship between the rate of PrP(Sc) formation and clearance. Protein misfolding cyclic amplification (PMCA) is a powerful technique that faithfully recapitulates PrP(Sc) formation and prion infectivity in a cell-free system. PMCA has been used as a surrogate for animal bioassay and can model species barriers, host range, strain co-factors and strain interference. In this study we investigated if degradation of PrP(Sc) and/or prion infectivity occurs during PMCA. To accomplish this we performed PMCA under conditions that do not support PrP(Sc) formation and did not observe either a reduction in PrP(Sc) abundance or an extension of prion incubation period, compared to untreated control samples. These results indicate that prion clearance does not occur during PMCA. These data have significant implications for the interpretation of PMCA based experiments such as prion amplification rate, adaptation to new species and strain interference where production and clearance of prions can affect the outcome.
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Affiliation(s)
- Ronald A Shikiya
- a Department of Medical Microbiology and Immunology ; School of Medicine; Creighton University ; Omaha, NE USA
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19
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Iraci N, Stincardini C, Barreca ML, Biasini E. Decoding the function of the N-terminal tail of the cellular prion protein to inspire novel therapeutic avenues for neurodegenerative diseases. Virus Res 2015; 207:62-8. [DOI: 10.1016/j.virusres.2014.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/18/2014] [Accepted: 10/14/2014] [Indexed: 01/13/2023]
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20
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Abstract
The use of monoclonal antibodies as therapeutics requires optimizing several of their key attributes. These include binding affinity and specificity, folding stability, solubility, pharmacokinetics, effector functions, and compatibility with the attachment of additional antibody domains (bispecific antibodies) and cytotoxic drugs (antibody-drug conjugates). Addressing these and other challenges requires the use of systematic design methods that complement powerful immunization and in vitro screening methods. We review advances in designing the binding loops, scaffolds, domain interfaces, constant regions, post-translational and chemical modifications, and bispecific architectures of antibodies and fragments thereof to improve their bioactivity. We also highlight unmet challenges in antibody design that must be overcome to generate potent antibody therapeutics.
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Affiliation(s)
- Kathryn E Tiller
- Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180;
| | - Peter M Tessier
- Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180;
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21
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Moroncini G, Grieco A, Nacci G, Paolini C, Tonnini C, Pozniak KN, Cuccioloni M, Mozzicafreddo M, Svegliati S, Angeletti M, Kazlauskas A, Avvedimento EV, Funaro A, Gabrielli A. Epitope Specificity Determines Pathogenicity and Detectability of Anti-Platelet-Derived Growth Factor Receptor α Autoantibodies in Systemic Sclerosis. Arthritis Rheumatol 2015; 67:1891-903. [DOI: 10.1002/art.39125] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 03/17/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Gianluca Moroncini
- Università Politecnica delle Marche and Ospedali Riuniti Ancona; Ancona Italy
| | - Antonella Grieco
- Università Politecnica delle Marche and Ospedali Riuniti Ancona; Ancona Italy
| | | | - Chiara Paolini
- Università Politecnica delle Marche and Ospedali Riuniti Ancona; Ancona Italy
| | - Cecilia Tonnini
- Università Politecnica delle Marche and Ospedali Riuniti Ancona; Ancona Italy
| | | | | | | | - Silvia Svegliati
- Università Politecnica delle Marche and Ospedali Riuniti Ancona; Ancona Italy
| | | | - Andrius Kazlauskas
- Schepens Eye Research Institute and Harvard Medical School; Boston Massachusetts
| | | | | | - Armando Gabrielli
- Università Politecnica delle Marche and Ospedali Riuniti Ancona; Ancona Italy
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22
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Murakami K. Conformation-specific antibodies to target amyloid β oligomers and their application to immunotherapy for Alzheimer's disease. Biosci Biotechnol Biochem 2015; 78:1293-305. [PMID: 25130729 DOI: 10.1080/09168451.2014.940275] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amyloid β-protein (Aβ) oligomers, intermediates of Aβ aggregation, cause cognitive impairment and synaptotoxicity in the pathogenesis of Alzheimer's disease (AD). Immunotherapy using anti-Aβ antibody is one of the most promising approaches for AD treatment. However, most clinical trials using conventional sequence-specific antibodies have proceeded with difficulty. This is probably due to the unintended removal of the non-pathological monomer and fibrils of Aβ as well as the pathological oligomers by these antibodies that recognize Aβ sequence, which is not involved in synaptotoxicity. Several efforts have been made recently to develop conformation-specific antibodies that target the tertiary structure of Aβ oligomers. Here, we review the recent findings of Aβ oligomers and anti-Aβ antibodies including our own, and discuss their potential as therapeutic and diagnostic tools.
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Affiliation(s)
- Kazuma Murakami
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
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23
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Requena JR, Wille H. The structure of the infectious prion protein: experimental data and molecular models. Prion 2015; 8:60-6. [PMID: 24583975 PMCID: PMC7030906 DOI: 10.4161/pri.28368] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The structures of the infectious prion protein, PrP(Sc), and that of its proteolytically truncated variant, PrP 27-30, have evaded experimental determination due to their insolubility and propensity to aggregate. Molecular modeling has been used to fill this void and to predict their structures, but various modeling approaches have produced significantly different models. The disagreement between the different modeling solutions indicates the limitations of this method. Over the years, in absence of a three-dimensional (3D) structure, a variety of experimental techniques have been used to gain insights into the structure of this biologically, medically, and agriculturally important isoform. Here, we present an overview of experimental results that were published in recent years, and which provided new insights into the molecular architecture of PrP(Sc) and PrP 27-30. Furthermore, we evaluate all published models in light of these recent, experimental data, and come to the conclusion that none of the models can accommodate all of the experimental constraints. Moreover, this conclusion constitutes an open invitation for renewed efforts to model the structure of PrP(Sc).
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24
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Detection of the disease-associated form of the prion protein in biological samples. Bioanalysis 2015; 7:253-61. [PMID: 25587841 DOI: 10.4155/bio.14.301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are neurodegenerative diseases that occur in a variety of mammals. In TSEs, a chromosomally encoded protein (PrPC) undergoes a conformational change to the disease-associated form (PrPd). PrPd is capable of inducing a change in additional molecules of PrPC to the PrPd conformation. TSEs are inevitably fatal and cross-species transmission is known to occur, and there is potential for transmission via blood transfusion and organ transplantation in humans. Thus, there is interest in high-quality diagnostics for both humans and animals. This review summarizes methods of TSE detection currently in use in diagnostic settings and discusses recent advances in PrPd detection that afford substantial enhancements in sensitivity over currently approved methods for use in clinical settings.
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25
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Doolan KM, Colby DW. Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing. J Mol Biol 2014; 427:328-40. [PMID: 25451031 DOI: 10.1016/j.jmb.2014.10.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 11/24/2022]
Abstract
Prion diseases are caused by a structural rearrangement of the cellular prion protein, PrP(C), into a disease-associated conformation, PrP(Sc), which may be distinguished from one another using conformation-specific antibodies. We used mutational scanning by cell-surface display to screen 1341 PrP single point mutants for attenuated interaction with four anti-PrP antibodies, including several with conformational specificity. Single-molecule real-time gene sequencing was used to quantify enrichment of mutants, returning 26,000 high-quality full-length reads for each screened population on average. Relative enrichment of mutants correlated to the magnitude of the change in binding affinity. Mutations that diminished binding of the antibody ICSM18 represented the core of contact residues in the published crystal structure of its complex. A similarly located binding site was identified for D18, comprising discontinuous residues in helix 1 of PrP, brought into close proximity to one another only when the alpha helix is intact. The specificity of these antibodies for the normal form of PrP likely arises from loss of this conformational feature after conversion to the disease-associated form. Intriguingly, 6H4 binding was found to depend on interaction with the same residues, among others, suggesting that its ability to recognize both forms of PrP depends on a structural rearrangement of the antigen. The application of mutational scanning and deep sequencing provides residue-level resolution of positions in the protein-protein interaction interface that are critical for binding, as well as a quantitative measure of the impact of mutations on binding affinity.
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Affiliation(s)
- Kyle M Doolan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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26
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McCutcheon S, Langeveld JPM, Tan BC, Gill AC, de Wolf C, Martin S, Gonzalez L, Alibhai J, Blanco ARA, Campbell L, Hunter N, Houston EF. Prion protein-specific antibodies that detect multiple TSE agents with high sensitivity. PLoS One 2014; 9:e91143. [PMID: 24608105 PMCID: PMC3946747 DOI: 10.1371/journal.pone.0091143] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/07/2014] [Indexed: 01/09/2023] Open
Abstract
This paper describes the generation, characterisation and potential applications of a panel of novel anti-prion protein monoclonal antibodies (mAbs). The mAbs were generated by immunising PRNP null mice, using a variety of regimes, with a truncated form of recombinant ovine prion protein spanning residues 94-233. Epitopes of specific antibodies were mapped using solid-phase Pepscan analysis and clustered to four distinct regions within the PrP molecule. We have demonstrated the utility of these antibodies by use of Western blotting and immunohistochemistry in tissues from a range of different species affected by transmissible spongiform encephalopathy (TSE). In comparative tests against extensively-used and widely-published, commercially available antibodies, similar or improved results can be obtained using these new mAbs, specifically in terms of sensitivity of detection. Since many of these antibodies recognise native PrPC, they could also be applied to a broad range of immunoassays such as flow cytometry, DELFIA analysis or immunoprecipitation. We are using these reagents to increase our understanding of TSE pathogenesis and for use in potential diagnostic screening assays.
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Affiliation(s)
- Sandra McCutcheon
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
- * E-mail:
| | | | - Boon Chin Tan
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Andrew C. Gill
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Christopher de Wolf
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Stuart Martin
- Animal Health and Veterinary Laboratories Agency, Lasswade Laboratory, Edinburgh, Scotland, United Kingdom
| | - Lorenzo Gonzalez
- Animal Health and Veterinary Laboratories Agency, Lasswade Laboratory, Edinburgh, Scotland, United Kingdom
| | - James Alibhai
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - A. Richard Alejo Blanco
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Lauren Campbell
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - Nora Hunter
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
| | - E. Fiona Houston
- Neurobiology Division, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, Easter Bush, Edinburgh, Scotland, United Kingdom
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27
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Shirai T, Saito M, Kobayashi A, Asano M, Hizume M, Ikeda S, Teruya K, Morita M, Kitamoto T. Evaluating prion models based on comprehensive mutation data of mouse PrP. Structure 2014; 22:560-71. [PMID: 24560805 DOI: 10.1016/j.str.2013.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 12/21/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
Abstract
The structural details of the essential entity of prion disease, fibril prion protein (PrP(Sc)), are still elusive despite the large body of evidence supporting the prion hypothesis. Five major working models of PrP(Sc) structure, which are not compatible with each other, have been proposed. However, no systematic evaluation has been performed on those models. We devised a method that combined systematic point mutation with threading on knowledge-based amino acid potentials. A comprehensive mutation experiment was performed on mouse prion protein, and the PrP(Sc) conversion efficiency of each mutant was examined. The models were evaluated based on the mutation data by using the threading method. Although the data turned out to be rather more consistent with the models that assumed a conversion of the N-terminal region of core PrP into a β helix than with others, substantial modifications were also required to further improve the current model based on recent experimental results.
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Affiliation(s)
- Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Bioinformatics Research Division, Japan Science and Technology Agency, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666 Japan.
| | - Mihoko Saito
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan; Bioinformatics Research Division, Japan Science and Technology Agency, 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-8666 Japan
| | - Atsushi Kobayashi
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masahiro Asano
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masaki Hizume
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Shino Ikeda
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Kenta Teruya
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masanori Morita
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; Research and Development Division, Benesis Corporation, Kitahama, Chuo-Ku, Osaka 541-850, Japan
| | - Tetsuyuki Kitamoto
- Department of Neurological Science, Tohoku University Graduate School of Medicine Research, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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28
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Ludewigs H, Zuber C, Vana K, Nikles D, Zerr I, Weiss S. Therapeutic approaches for prion disorders. Expert Rev Anti Infect Ther 2014; 5:613-30. [PMID: 17678425 DOI: 10.1586/14787210.5.4.613] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Prion diseases are lethal for both humans and animals, and affected individuals die after several months following a rapid disease progression. Although researchers have attempted for decades to develop effective therapeutics for the therapy of human prion disorders, until now no efficient drug has been available on the market for transmissible spongiform encephalopathy (TSE) treatment or cure. Approximately 200 patients worldwide have died or suffer from variant Creutzfeldt-Jakob disease (CJD). Incidences for sporadic and familial CJD are approximately 1.5-2 per million per year and one per 10 million per year, respectively, in Europe. This review summarizes classical and modern trials for the development of effective anti-TSE drugs, introduces potential effective delivery systems, such as lentiviral and adeno-associated virus systems for antiprion components, including antibodies and siRNAs, and presents vaccination trials. Most of the antiprion drugs target prion protein PrP(c) and/or PrP(Sc). Alternative targets are receptors and coreceptors for PrP, that is, the 37/67-kDa laminin receptor and heparan sulfate proteoglycanes. We review clinical trials for the treatment of TSEs and describe hindrances and chances for a breakthrough in therapy of prion disorders.
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Affiliation(s)
- Heike Ludewigs
- Laboratorium für Molekulare Biologie, Genzentrum, Institut für Biochemie der LMU München, München, Germany.
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Zurawel AA, Walsh DJ, Fortier SM, Chidawanyika T, Sengupta S, Zilm K, Supattapone S. Prion nucleation site unmasked by transient interaction with phospholipid cofactor. Biochemistry 2014; 53:68-76. [PMID: 24328062 DOI: 10.1021/bi4014825] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infectious mammalian prions can be formed de novo from purified recombinant prion protein (PrP) substrate through a pathway that requires the sequential addition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) and RNA cofactor molecules. Recent studies show that the initial interaction between PrP and POPG causes widespread and persistent conformational changes to form an insoluble intermediate species, termed PrP(Int1). Here, we characterize the mechanism and functional consequences of the interaction between POPG and PrP. Negative-stain electron microscopy of PrP(Int1) revealed the presence of amorphous aggregates. Pull-down and photoaffinity label experiments indicate that POPG induces the formation of a PrP(C) polybasic-domain-binding neoepitope within PrP(Int1). The ongoing presence of POPG is not required to maintain PrP(Int1) structure, as indicated by the absence of stoichiometric levels of POPG in solid-state NMR measurements of PrP(Int1). Together, these results show that a transient interaction with POPG cofactor unmasks a PrP(C) binding site, leading to PrP(Int1) aggregation.
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Affiliation(s)
- Ashley A Zurawel
- Departments of Biochemistry and ‡Medicine, Geisel School of Medicine at Dartmouth , Hanover, New Hampshire 03755, United States
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Suenaga M, Hiramoto Y, Matsunaga Y. Vitamin D 2 interacts with Human PrP(c) (90-231) and breaks PrP(c) oligomerization in vitro. Prion 2013; 7:312-8. [PMID: 23857314 DOI: 10.4161/pri.25739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
PrP(sc), the pathogenic isoform of PrP(c), can convert PrP(c) into PrP(sc) through direct interactions. PrP(c) oligomerization is a required processing step before PrP(sc) formation, and soluble oligomers appear to be the toxic species in amyloid-related disorders. In the current study, direct interactions between vitamin D 2 and human recombinant PrP(c) (90-231) were observed by Biacore assay, and 3F4 antibody, specific for amino acid fragment 109-112 of PrP(c), inhibited this interaction. An ELISA study using3F4 antibody showed that PrP(c) (101-130), corresponding sequence to human PrP, was affected by vitamin D 2, supporting the results of Biacore studies and suggesting that the PrP(c) sequence around the 3F4 epitope was responsible for the interaction with vitamin D 2. Furthermore, the effects of vitamin D 2 on disruption of PrP(c) (90-231) oligomerization were elucidated by dot blot analysis and differential protease k susceptibilities. While many chemical compounds have been proposed as potential therapeutic agents for the treatment of scrapie, most of these are toxic. However, given the safety and blood brain barrier permeability of vitamin D 2, we propose that vitamin D 2 may be a suitable agent to target PrP(c) in the brain and therefore is a potential therapeutic candidate for prion disease.
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Affiliation(s)
- Midori Suenaga
- Department of Medical Pharmacology; Faculty of Pharmaceutical Sciences; Tokushima Bunri University; Yamashiro-cho, Tokushima, Japan
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Masujin K, Kaku-Ushiki Y, Miwa R, Okada H, Shimizu Y, Kasai K, Matsuura Y, Yokoyama T. The N-terminal sequence of prion protein consists an epitope specific to the abnormal isoform of prion protein (PrP(Sc)). PLoS One 2013; 8:e58013. [PMID: 23469131 PMCID: PMC3585212 DOI: 10.1371/journal.pone.0058013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
The conformation of abnormal prion protein (PrPSc) differs from that of cellular prion protein (PrPC), but the precise characteristics of PrPSc remain to be elucidated. To clarify the properties of native PrPSc, we attempted to generate novel PrPSc-specific monoclonal antibodies (mAbs) by immunizing PrP-deficient mice with intact PrPSc purified from bovine spongiform encephalopathy (BSE)-affected mice. The generated mAbs 6A12 and 8D5 selectivity precipitated PrPSc from the brains of prion-affected mice, sheep, and cattle, but did not precipitate PrPC from the brains of healthy animals. In histopathological analysis, mAbs 6A12 and 8D5 strongly reacted with prion-affected mouse brains but not with unaffected mouse brains without antigen retrieval. Epitope analysis revealed that mAbs 8D5 and 6A12 recognized the PrP subregions between amino acids 31–39 and 41–47, respectively. This indicates that a PrPSc-specific epitope exists in the N-terminal region of PrPSc, and mAbs 6A12 and 8D5 are powerful tools with which to detect native and intact PrPSc. We found that the ratio of proteinase K (PK)-sensitive PrPSc to PK-resistant PrPSc was constant throughout the disease time course.
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Affiliation(s)
- Kentaro Masujin
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | | | - Ritsuko Miwa
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Okada
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Yoshihisa Shimizu
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Kazuo Kasai
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Yuichi Matsuura
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Takashi Yokoyama
- Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
- * E-mail:
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The N-terminal, polybasic region of PrP(C) dictates the efficiency of prion propagation by binding to PrP(Sc). J Neurosci 2012; 32:8817-30. [PMID: 22745483 DOI: 10.1523/jneurosci.1103-12.2012] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Prion propagation involves a templating reaction in which the infectious form of the prion protein (PrP(Sc)) binds to the cellular form (PrP(C)), generating additional molecules of PrP(Sc). While several regions of the PrP(C) molecule have been suggested to play a role in PrP(Sc) formation based on in vitro studies, the contribution of these regions in vivo is unclear. Here, we report that mice expressing PrP deleted for a short, polybasic region at the N terminus (residues 23-31) display a dramatically reduced susceptibility to prion infection and accumulate greatly reduced levels of PrP(Sc). These results, in combination with biochemical data, demonstrate that residues 23-31 represent a critical site on PrP(C) that binds to PrP(Sc) and is essential for efficient prion propagation. It may be possible to specifically target this region for treatment of prion diseases as well as other neurodegenerative disorders due to β-sheet-rich oligomers that bind to PrP(C).
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Chang B, Petersen R, Wisniewski T, Rubenstein R. Influence of Mabs on PrP(Sc) formation using in vitro and cell-free systems. PLoS One 2012; 7:e41626. [PMID: 22848548 PMCID: PMC3407222 DOI: 10.1371/journal.pone.0041626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/22/2012] [Indexed: 11/19/2022] Open
Abstract
PrPSc is believed to serve as a template for the conversion of PrPC to the abnormal isoform. This process requires contact between the two proteins and implies that there may be critical contact sites that are important for conversion. We hypothesized that antibodies binding to either PrPcor PrPSc would hinder or prevent the formation of the PrPC–PrPSc complex and thus slow down or prevent the conversion process. Two systems were used to analyze the effect of different antibodies on PrPSc formation: (i) neuroblastoma cells persistently infected with the 22L mouse-adapted scrapie stain, and (ii) protein misfolding cyclic amplification (PMCA), which uses PrPSc as a template or seed, and a series of incubations and sonications, to convert PrPC to PrPSc. The two systems yielded similar results, in most cases, and demonstrate that PrP-specific monoclonal antibodies (Mabs) vary in their ability to inhibit the PrPC–PrPSc conversion process. Based on the numerous and varied Mabs analyzed, the inhibitory effect does not appear to be epitope specific, related to PrPC conformation, or to cell membrane localization, but is influenced by the targeted PrP region (amino vs carboxy).
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Affiliation(s)
- Binggong Chang
- Departments of Neurology and Physiology/Pharmacology, State University New York Downstate Medical Center, Brooklyn, New York, United States of America
| | - Robert Petersen
- Departments of Pathology, Neuroscience, and Neurology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas Wisniewski
- Departments of Neurology, Psychiatry and Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Richard Rubenstein
- Departments of Neurology and Physiology/Pharmacology, State University New York Downstate Medical Center, Brooklyn, New York, United States of America
- * E-mail:
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Mouse prion protein (PrP) segment 100 to 104 regulates conversion of PrP(C) to PrP(Sc) in prion-infected neuroblastoma cells. J Virol 2012; 86:5626-36. [PMID: 22398286 DOI: 10.1128/jvi.06606-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prion diseases are characterized by the replicative propagation of disease-associated forms of prion protein (PrP(Sc); PrP refers to prion protein). The propagation is believed to proceed via two steps; the initial binding of the normal form of PrP (PrP(C)) to PrP(Sc) and the subsequent conversion of PrP(C) to PrP(Sc). We have explored the two-step model in prion-infected mouse neuroblastoma (ScN2a) cells by focusing on the mouse PrP (MoPrP) segment 92-GGTHNQWNKPSKPKTN-107, which is within a region previously suggested to be part of the binding interface or shown to differ in its accessibility to anti-PrP antibodies between PrP(C) and PrP(Sc). Exchanging the MoPrP segment with the corresponding chicken PrP segment (106-GGSYHNQKPWKPPKTN-121) revealed the necessity of MoPrP residues 99 to 104 for the chimeras to achieve the PrP(Sc) state, while segment 95 to 98 was replaceable with the chicken sequence. An alanine substitution at position 100, 102, 103, or 104 of MoPrP gave rise to nonconvertible mutants that associated with MoPrP(Sc) and interfered with the conversion of endogenous MoPrP(C). The interference was not evoked by a chimera (designated MCM2) in which MoPrP segment 95 to 104 was changed to the chicken sequence, though MCM2 associated with MoPrP(Sc). Incubation of the cells with a synthetic peptide composed of MoPrP residues 93 to 107 or alanine-substituted cognates did not inhibit the conversion, whereas an anti-P8 antibody recognizing the above sequence in PrP(C) reduced the accumulation of PrP(Sc) after 10 days of incubation of the cells. These results suggest the segment 100 to 104 of MoPrP(C) plays a key role in conversion after binding to MoPrP(Sc).
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Novel assay with fluorescence-labelled PrP peptides for differentiating L-type atypical and classical BSEs, and scrapie. FEBS Lett 2012; 586:325-9. [DOI: 10.1016/j.febslet.2012.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 11/18/2022]
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Structure-based design of conformation- and sequence-specific antibodies against amyloid β. Proc Natl Acad Sci U S A 2011; 109:84-9. [PMID: 22171009 DOI: 10.1073/pnas.1111232108] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Conformation-specific antibodies that recognize aggregated proteins associated with several conformational disorders (e.g., Parkinson and prion diseases) are invaluable for diagnostic and therapeutic applications. However, no systematic strategy exists for generating conformation-specific antibodies that target linear sequence epitopes within misfolded proteins. Here we report a strategy for designing conformation- and sequence-specific antibodies against misfolded proteins that is inspired by the molecular interactions governing protein aggregation. We find that grafting small amyloidogenic peptides (6-10 residues) from the Aβ42 peptide associated with Alzheimer's disease into the complementarity determining regions of a domain (V(H)) antibody generates antibody variants that recognize Aβ soluble oligomers and amyloid fibrils with nanomolar affinity. We refer to these antibodies as gammabodies for grafted amyloid-motif antibodies. Gammabodies displaying the central amyloidogenic Aβ motif (18VFFA21) are reactive with Aβ fibrils, whereas those displaying the amyloidogenic C terminus (34LMVGGVVIA42) are reactive with Aβ fibrils and oligomers (and weakly reactive with Aβ monomers). Importantly, we find that the grafted motifs target the corresponding peptide segments within misfolded Aβ conformers. Aβ gammabodies fail to cross-react with other amyloidogenic proteins and scrambling their grafted sequences eliminates antibody reactivity. Finally, gammabodies that recognize Aβ soluble oligomers and fibrils also neutralize the toxicity of each Aβ conformer. We expect that our antibody design strategy is not limited to Aβ and can be used to readily generate gammabodies against other toxic misfolded proteins.
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Spongiform encephalopathy in transgenic mice expressing a point mutation in the β2-α2 loop of the prion protein. J Neurosci 2011; 31:13840-7. [PMID: 21957246 DOI: 10.1523/jneurosci.3504-11.2011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Transmissible spongiform encephalopathies are fatal neurodegenerative diseases attributed to misfolding of the cellular prion protein, PrP(C), into a β-sheet-rich, aggregated isoform, PrP(Sc). We previously found that expression of mouse PrP with the two amino acid substitutions S170N and N174T, which result in high structural order of the β2-α2 loop in the NMR structure at pH 4.5 and 20°C, caused transmissible de novo prion disease in transgenic mice. Here we report that expression of mouse PrP with the single-residue substitution D167S, which also results in a structurally well ordered β2-α2 loop at 20°C, elicits spontaneous PrP aggregation in vivo. Transgenic mice expressing PrP(D167S) developed a progressive encephalopathy characterized by abundant PrP plaque formation, spongiform change, and gliosis. These results add to the evidence that the β2-α2 loop has an important role in intermolecular interactions, including that it may be a key determinant of prion protein aggregation.
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Rigter A, Priem J, Langeveld JPM, Bossers A. Prion protein self-interaction in prion disease therapy approaches. Vet Q 2011; 31:115-28. [PMID: 22029882 DOI: 10.1080/01652176.2011.604976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) or prion diseases are unique disorders that are not caused by infectious micro-organisms (bacteria or fungi), viruses or parasites, but rather seem to be the result of an infectious protein. TSEs are comprised of fatal neurodegenerative disorders affecting both human and animals. Prion diseases cause sponge-like degeneration of neuronal tissue and include (among others) Creutzfeldt-Jacob disease in humans, bovine spongiform encephalopathy (BSE) in cattle and scrapie in sheep. TSEs are characterized by the formation and accumulation of transmissible (infectious) disease-associated protease-resistant prion protein (PrP(Sc)), mainly in tissues of the central nervous system. The exact molecular processes behind the conversion of PrP(C) into PrP(Sc) are not clearly understood. Correlations between prion protein polymorphisms and disease have been found, however in what way these polymorphisms influence the conversion processes remains an enigma; is stabilization or destabilization of the prion protein the basis for a higher conversion propensity? Apart from the disease-associated polymorphisms of the prion protein, the molecular processes underlying conversion are not understood. There are some notions as to which regions of the prion protein are involved in refolding of PrP(C) into PrP(Sc) and where the most drastic structural changes take place. Direct interactions between PrP(C) molecules and/or PrP(Sc) are likely at the basis of conversion, however which specific amino acid domains are involved and to what extent these domains contribute to conversion resistance/sensitivity of the prion protein or the species barrier is still unknown.
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Affiliation(s)
- Alan Rigter
- Department of Infection Biology, Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands.
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Westergard L, Turnbaugh JA, Harris DA. A naturally occurring C-terminal fragment of the prion protein (PrP) delays disease and acts as a dominant-negative inhibitor of PrPSc formation. J Biol Chem 2011; 286:44234-44242. [PMID: 22025612 DOI: 10.1074/jbc.m111.286195] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cellular prion protein (PrPC) undergoes constitutive proteolytic cleavage between residues 111/112 to yield a soluble N-terminal fragment (N1) and a membrane-anchored C-terminal fragment (C1). The C1 fragment represents the major proteolytic fragment of PrPC in brain and several cell types. To explore the role of C1 in prion disease, we generated Tg(C1) transgenic mice expressing this fragment (PrP(Δ23-111)) in the presence and absence of endogenous PrP. In contrast to several other N-terminally deleted forms of PrP, the C1 fragment does not cause a spontaneous neurological disease in the absence of endogenous PrP. Tg(C1) mice inoculated with scrapie prions remain healthy and do not accumulate protease-resistant PrP, demonstrating that C1 is not a substrate for conversion to PrPSc (the disease-associated isoform). Interestingly, Tg(C1) mice co-expressing C1 along with wild-type PrP (either endogenous or encoded by a second transgene) become ill after scrapie inoculation, but with a dramatically delayed time course compared with mice lacking C1. In addition, accumulation of PrPSc was markedly slowed in these animals. Similar effects were produced by a shorter C-terminal fragment of PrP(Δ23-134). These results demonstrate that C1 acts as dominant-negative inhibitor of PrPSc formation and accumulation of neurotoxic forms of PrP. Thus, C1, a naturally occurring fragment of PrPC, might play a modulatory role during the course of prion diseases. In addition, enhancing production of C1, or exogenously administering this fragment, represents a potential therapeutic strategy for the treatment of prion diseases.
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Affiliation(s)
- Laura Westergard
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jessie A Turnbaugh
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118.
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Dissociation of infectivity from seeding ability in prions with alternate docking mechanism. PLoS Pathog 2011; 7:e1002128. [PMID: 21779169 PMCID: PMC3136465 DOI: 10.1371/journal.ppat.1002128] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 05/04/2011] [Indexed: 11/21/2022] Open
Abstract
Previous studies identified two mammalian prion protein (PrP) polybasic domains that bind the disease-associated conformer PrPSc, suggesting that these domains of cellular prion protein (PrPC) serve as docking sites for PrPSc during prion propagation. To examine the role of polybasic domains in the context of full-length PrPC, we used prion proteins lacking one or both polybasic domains expressed from Chinese hamster ovary (CHO) cells as substrates in serial protein misfolding cyclic amplification (sPMCA) reactions. After ∼5 rounds of sPMCA, PrPSc molecules lacking the central polybasic domain (ΔC) were formed. Surprisingly, in contrast to wild-type prions, ΔC-PrPSc prions could bind to and induce quantitative conversion of all the polybasic domain mutant substrates into PrPSc molecules. Remarkably, ΔC-PrPSc and other polybasic domain PrPSc molecules displayed diminished or absent biological infectivity relative to wild-type PrPSc, despite their ability to seed sPMCA reactions of normal mouse brain homogenate. Thus, ΔC-PrPSc prions interact with PrPC molecules through a novel interaction mechanism, yielding an expanded substrate range and highly efficient PrPSc propagation. Furthermore, polybasic domain deficient PrPSc molecules provide the first example of dissociation between normal brain homogenate sPMCA seeding ability from biological prion infectivity. These results suggest that the propagation of PrPSc molecules may not depend on a single stereotypic mechanism, but that normal PrPC/PrPSc interaction through polybasic domains may be required to generate prion infectivity. Prions are unconventional infectious agents that cause fatal diseases in humans and other animals. Previous studies have suggested that prion infectivity depends upon the ability of a sample to change the shape of a normal brain protein called the prion protein (PrP) into a disease-associated shape. Other studies have identified a pair of positively charged domains within the structure of PrP that appear to be important for the interaction between the normal and disease-associated shapes of the prion protein. In this report, we show that the shape of normal PrP can change into the disease-associated form through a novel mechanism that does not involve positively charged domains. However, it appears that interaction through the positively charged domains is required to produce infectious prions efficiently. Our results show for the first time that the ability to change the shape of normal PrP into its disease-associated state is not the sole determinant of prion infectivity.
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Cruite JT, Abalos GC, Bellon A, Solforosi L. Histidines in the octapeptide repeat of PrPC react with PrPSc at an acidic pH. Biochemistry 2011; 50:1618-23. [PMID: 21268659 DOI: 10.1021/bi1017683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellular PrP is actively cycled between the cell surface and the endosomal pathway. The exact site and mechanism of conversion from PrP(C) to PrP(Sc) remain unknown. We have previously used recombinant antibodies containing grafts of PrP sequence to identify three regions of PrP(C) (aa23-27, 98-110, and 136-158) that react with PrP(Sc) at neutral pH. To determine if any regions of PrP(C) react with PrP(Sc) at an acidic pH similar to that of an endosomal compartment, we tested our panel of grafted antibodies for the ability to precipitate PrP(Sc) in a range of pH conditions. At pH near or lower than 6, PrP-grafted antibodies representing the octapeptide repeat react strongly with PrP(Sc) but not PrP(C). Modified grafts in which the histidines of the octarepeat were replaced with alanines did not react with PrP(Sc). PrP(Sc) precipitated by the octapeptide at pH 5.7 was able to seed conversion of normal PrP to PrP(Sc) in vitro. However, modified PrP containing histidine to alanine substitutions within the octapeptide repeats was still converted to PrP(Sc) in N2a cells. These results suggest that once PrP has entered the endosomal pathway, the acidic environment facilitates the binding of PrP(Sc) to the octarepeat of PrP(C) by the change in charge of the histidines within the octarepeat.
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Affiliation(s)
- Justin T Cruite
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, United States.
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Biological effects and use of PrPSc- and PrP-specific antibodies generated by immunization with purified full-length native mouse prions. J Virol 2011; 85:4538-46. [PMID: 21345946 DOI: 10.1128/jvi.02467-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The prion agent is the infectious particle causing spongiform encephalopathies in animals and humans and is thought to consist of an altered conformation (PrP(Sc)) of the normal and ubiquitous prion protein PrP(C). The interaction of the prion agent with the immune system, particularly the humoral immune response, has remained unresolved. Here we investigated the immunogenicity of full-length native and infectious prions, as well as the specific biological effects of the resulting monoclonal antibodies (MAbs) on the binding and clearance of prions in cell culture and in in vivo therapy. Immunization of prion knockout (Prnp(0/0)) mice with phosphotungstic acid-purified mouse prions resulted in PrP-specific monoclonal antibodies with binding specificities selective for PrP(Sc) or for both PrP(C) and PrP(Sc). PrP(Sc)-specific MAb W261, of the IgG1 isotype, reacted with prions from mice, sheep with scrapie, deer with chronic wasting disease (CWD), and humans with sporadic and variant Creutzfeldt-Jakob disease (CJD) in assays including a capture enzyme-linked immunosorbent assay (ELISA) system. This PrP(Sc)-specific antibody was unable to clear prions from mouse neuroblastoma cells (ScN2a) permanently infected with scrapie, whereas the high-affinity MAb W226, recognizing both isoforms, PrP(Sc) and PrP(C), did clear prions from ScN2a cells, as determined by a bioassay. However, an attempt to treat intraperitoneally prion infected mice with full-length W226 or with a recombinant variable-chain fragment (scFv) from W226 could only slightly delay the incubation time. We conclude that (i) native, full-length PrP(Sc) elicits a prion-specific antibody response in PrP knockout mice, (ii) a PrP(Sc)-specific antibody had no prion-clearing effect, and (iii) even a high-affinity MAb that clears prions in vitro (W226) may not necessarily protect against prion infection, contrary to previous reports using different antibodies.
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Abstract
Prion diseases are associated with the presence of PrP(Sc), a disease-associated misfolded conformer of the prion protein. We report that superparamagnetic nanoparticles bind PrP(Sc) molecules efficiently and specifically, permitting magnetic separation of prions from a sample mixture. Captured PrP(Sc) molecules retain the activity to seed protein misfolding cyclic amplification (PMCA) reactions, enabling the rapid concentration of dilute prions to improve detection. Furthermore, superparamagnetic nanoparticles clear contaminated solutions of PrP(Sc). Our findings suggest that coupling magnetic nanoparticle capture with PMCA could accelerate and improve prion detection. Magnetic nanoparticles may also be useful for developing a nontoxic prion decontamination method for biologically derived products.
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Mueller DA, Heinig L, Ramljak S, Krueger A, Schulte R, Wrede A, Stuke AW. Conditional expression of full-length humanized anti-prion protein antibodies in Chinese hamster ovary cells. Hybridoma (Larchmt) 2010; 29:463-72. [PMID: 21087094 DOI: 10.1089/hyb.2010.0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Because of their high antigen specificity and metabolic stability, genetically engineered human monoclonal antibodies are on the way to becoming one of the most promising medical diagnostics and therapeutics. In order to establish an in vitro system capable of producing such biosimilar antibodies, we used human constant chain sequences to design the novel human antibody expressing vector cassette pMAB-ABX. A bidirectional tetracycline (tet)-controllable promotor was used for harmonized expression of immunoglobulin type G (IgG) heavy and light chains. As an example we used anti-prion protein (anti-PrP) IgGs. Therefore, the variable heavy (V(H)) and light chain (V(L)) sequences of anti-PrP antibodies, previously generated in our laboratory by DNA immunization of prion protein knock-out mice, were isolated from murine hybridoma cell lines and inserted into pMAB-ABX vector. After transfection of Chinese hamster ovary (CHO) cells, a number of stable antibody producing cell clones were selected. One cell line (pMAB-ABX-13F10/3B5) stably expressing the recombinant humanized antibody (rechuAb) 13F10/3B5 was selected for detailed characterization by Western blot, immunofluorescence, and flow cytometric analyses. The full-length recombinant humanized IgG antibody showed a high level of expression in the cytoplasm. In conclusion, the new cell system described here is a suitable tool to produce functional intact full-length humanized IgG antibodies.
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Affiliation(s)
- Daniel A Mueller
- German Primate Centre (DPZ) GmbH, Department of Infection Biology, Goettingen, Germany
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45
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Prion protein self-interactions: A gateway to novel therapeutic strategies? Vaccine 2010; 28:7810-23. [DOI: 10.1016/j.vaccine.2010.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 08/31/2010] [Accepted: 09/03/2010] [Indexed: 11/19/2022]
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Biasini E, Seegulam ME, Patti BN, Solforosi L, Medrano AZ, Christensen HM, Senatore A, Chiesa R, Williamson RA, Harris DA. Non-infectious aggregates of the prion protein react with several PrPSc-directed antibodies. J Neurochem 2010; 105:2190-204. [PMID: 18298665 DOI: 10.1111/j.1471-4159.2008.05306.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The key event in the pathogenesis of prion diseases is the conformational conversion of the normal prion protein (PrP) (PrP(C)) into an infectious, aggregated isoform (PrP(Sc)) that has a high content of beta-sheet. Historically, a great deal of effort has been devoted to developing antibodies that specifically recognize PrP(Sc) but not PrP(C), as such antibodies would have enormous diagnostic and experimental value. A mouse monoclonal IgM antibody (designated 15B3) and three PrP motif-grafted monoclonal antibodies (referred to as IgG 19-33, 89-112, and 136-158) have been previously reported to react specifically with infectious PrP(Sc) but not PrP(C). In this study, we extend the characterization of these four antibodies by testing their ability to immunoprecipitate and immunostain infectious and non-infectious aggregates of wild-type, mutant, and recombinant PrP. We find that 15B3 as well as the motif-grafted antibodies recognize multiple types of aggregated PrP, both infectious and non-infectious, including forms found in brain, in transfected cells, and induced in vitro from purified recombinant protein. These antibodies are exquisitely selective for aggregated PrP, and do not react with soluble PrP even when present in vast excess. Our results suggest that 15B3 and the motif-grafted antibodies recognize structural features common to both infectious and non-infectious aggregates of PrP. Our study extends the utility of these antibodies for diagnostic and experimental purposes, and it provides new insight into the structural changes that accompany PrP oligomerization and prion propagation.
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Affiliation(s)
- Emiliano Biasini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
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Stanker LH, Serban AV, Cleveland E, Hnasko R, Lemus A, Safar J, DeArmond SJ, Prusiner SB. Conformation-dependent high-affinity monoclonal antibodies to prion proteins. THE JOURNAL OF IMMUNOLOGY 2010; 185:729-37. [PMID: 20530267 DOI: 10.4049/jimmunol.0902930] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Prion diseases are fatal, neurodegenerative illnesses caused by the accumulation of PrP(Sc), an aberrantly folded isoform of the normal, cellular prion protein. Detection of PrP(Sc) commonly relies on immunochemical methods, a strategy hampered by the lack of Abs specific for this disease-causing isoform. In this article, we report the generation of eight mAbs against prion protein (PrP) following immunization of Prnp-null mice with rPrP. The eight mAbs exhibited distinct differential binding to cellular prion protein and PrP(Sc) from different species as well as PrP-derived synthetic peptides. Five of the eight mAbs exhibited binding to discontinuous PrP epitopes, all of which were disrupted by the addition of 2-ME or DTT, which reduced the single disulfide bond found in PrP. One mAb F20-29 reacted only with human PrP, whereas the F4-31 mAb bound bovine PrP; the K(D) values for mAbs F4-31 and F20-29 were ~500 pM. Binding of all five conformation-dependent mAbs to PrP was inhibited by 2-ME in ELISA, Western blots, and histoblots. One conformation-dependent mAb F4-31 increased the sensitivity of an ELISA-based test by nearly 500-fold when it was used as the capture Ab. These new conformation-dependent mAbs were found to be particularly useful in histoblotting studies, in which the low backgrounds after treatment with 2-ME created unusually high signal-to-noise ratios.
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Affiliation(s)
- Larry H Stanker
- Foodborne Contaminants Research Unit, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710, USA
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Ostapchenko VG, Sawaya MR, Makarava N, Savtchenko R, Nilsson KPR, Eisenberg D, Baskakov IV. Two amyloid States of the prion protein display significantly different folding patterns. J Mol Biol 2010; 400:908-21. [PMID: 20553730 DOI: 10.1016/j.jmb.2010.05.051] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/27/2010] [Accepted: 05/21/2010] [Indexed: 12/16/2022]
Abstract
It has been well established that a single amino acid sequence can give rise to several conformationally distinct amyloid states. The extent to which amyloid structures formed within the same sequence are different, however, remains unclear. To address this question, we studied two amyloid states (referred to as R- and S-fibrils) produced in vitro from highly purified full-length recombinant prion protein. Several biophysical techniques including X-ray diffraction, CD, Fourier transform infrared spectroscopy (FTIR), hydrogen-deuterium exchange, proteinase K digestion, and binding of a conformation-sensitive fluorescence dye revealed that R- and S-fibrils have substantially different secondary, tertiary, and quaternary structures. While both states displayed a 4. 8-A meridional X-ray diffraction typical for amyloid cross-beta-spines, they showed markedly different equatorial profiles, suggesting different folding pattern of beta-strands. The experiments on hydrogen-deuterium exchange monitored by FTIR revealed that only small fractions of amide protons were protected in R- or S-fibrils, an argument for the dynamic nature of their cross-beta-structure. Despite this fact, both amyloid states were found to be very stable conformationally as judged from temperature-induced denaturation monitored by FTIR and the conformation-sensitive dye. Upon heating to 80 degrees C, only local unfolding was revealed, while individual state-specific cross-beta features were preserved. The current studies demonstrated that the two amyloid states formed by the same amino acid sequence exhibited significantly different folding patterns that presumably reflect two different architectures of cross-beta-structure. Both S- and R-fibrils, however, shared high conformational stability, arguing that the energy landscape for protein folding and aggregation can contain several deep free-energy minima.
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Affiliation(s)
- Valeriy G Ostapchenko
- Center for Biomedical Engineering and Technology, University of Maryland, Baltimore, MD 21201, USA
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Hattori T, Umetsu M, Nakanishi T, Togashi T, Yokoo N, Abe H, Ohara S, Adschiri T, Kumagai I. High affinity anti-inorganic material antibody generation by integrating graft and evolution technologies: potential of antibodies as biointerface molecules. J Biol Chem 2010; 285:7784-93. [PMID: 20044483 PMCID: PMC2844222 DOI: 10.1074/jbc.m109.020156] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 12/23/2009] [Indexed: 02/02/2023] Open
Abstract
Recent advances in molecular evolution technology enabled us to identify peptides and antibodies with affinity for inorganic materials. In the field of nanotechnology, the use of the functional peptides and antibodies should aid the construction of interface molecules designed to spontaneously link different nanomaterials; however, few material-binding antibodies, which have much higher affinity than short peptides, have been identified. Here, we generated high affinity antibodies from material-binding peptides by integrating peptide-grafting and phage-display techniques. A material-binding peptide sequence was first grafted into an appropriate loop of the complementarity determining region (CDR) of a camel-type single variable antibody fragment to create a low affinity material-binding antibody. Application of a combinatorial library approach to another CDR loop in the low affinity antibody then clearly and steadily promoted affinity for a specific material surface. Thermodynamic analysis demonstrated that the enthalpy synergistic effect from grafted and selected CDR loops drastically increased the affinity for material surface, indicating the potential of antibody scaffold for creating high affinity small interface units. We show the availability of the construction of antibodies by integrating graft and evolution technology for various inorganic materials and the potential of high affinity material-binding antibodies in biointerface applications.
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Affiliation(s)
- Takamitsu Hattori
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579
| | - Mitsuo Umetsu
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579
- the Center for Interdisciplinary Research, Tohoku University, Sendai 980-8578
| | - Takeshi Nakanishi
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579
| | - Takanari Togashi
- the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, and
| | - Nozomi Yokoo
- the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, and
| | - Hiroya Abe
- the Joining and Welding Research Institute, Osaka University, Osaka 567-0047, Japan
| | - Satoshi Ohara
- the Joining and Welding Research Institute, Osaka University, Osaka 567-0047, Japan
| | - Tadafumi Adschiri
- the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, and
| | - Izumi Kumagai
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579
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50
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Ushiki-Kaku Y, Endo R, Iwamaru Y, Shimizu Y, Imamura M, Masujin K, Yamamoto T, Hattori S, Itohara S, Irie S, Yokoyama T. Tracing conformational transition of abnormal prion proteins during interspecies transmission by using novel antibodies. J Biol Chem 2010; 285:11931-6. [PMID: 20177064 DOI: 10.1074/jbc.m109.058859] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conformational differences in abnormal prion proteins (PrP(Sc)) have been postulated to produce different prion phenotypes. During the interspecies transmission of prions, the conformation of PrP(Sc) may change with passage; however, little is known about the mechanism of PrP(Sc) transition. In this study, novel PrP(Sc)-specific monoclonal antibodies (mAbs) were developed that could detect the PrP(Sc) of mouse but not that of sheep. By using these mAbs, we attempted to examine PrP(Sc) accumulated in mice inoculated with sheep scrapie serially up to five passages. The presence of PrP(Sc) in the mice was confirmed at all passages; however, mAb-bound PrP(Sc) conformer was detected only from the third passage onward. The generated mAb enabled tracing of a particular conformer during adaptation in sheep-to-mice transmission of prion, suggesting that the conformational transition of PrP(Sc) was caused by propagation of this conformer. Such mAbs capable of discriminating conformational differences may allow us to address questions concerning PrP(Sc) conformation and strain diversity.
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Affiliation(s)
- Yuko Ushiki-Kaku
- Nippi Research Institute of Biomatrix, Toride, Ibaraki 302-0017, Japan
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