1
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Menzies SK, Arinto-Garcia R, Amorim FG, Cardoso IA, Abada C, Crasset T, Durbesson F, Edge RJ, El-Kazzi P, Hall S, Redureau D, Stenner R, Boldrini-França J, Sun H, Roldão A, Alves PM, Harrison RA, Vincentelli R, Berger I, Quinton L, Casewell NR, Schaffitzel C. ADDovenom: Thermostable Protein-Based ADDomer Nanoparticles as New Therapeutics for Snakebite Envenoming. Toxins (Basel) 2023; 15:673. [PMID: 38133177 PMCID: PMC10747859 DOI: 10.3390/toxins15120673] [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: 10/16/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Snakebite envenoming can be a life-threatening medical emergency that requires prompt medical intervention to neutralise the effects of venom toxins. Each year up to 138,000 people die from snakebites and threefold more victims suffer life-altering disabilities. The current treatment of snakebite relies solely on antivenom-polyclonal antibodies isolated from the plasma of hyperimmunised animals-which is associated with numerous deficiencies. The ADDovenom project seeks to deliver a novel snakebite therapy, through the use of an innovative protein-based scaffold as a next-generation antivenom. The ADDomer is a megadalton-sized, thermostable synthetic nanoparticle derived from the adenovirus penton base protein; it has 60 high-avidity binding sites to neutralise venom toxins. Here, we outline our experimental strategies to achieve this goal using state-of-the-art protein engineering, expression technology and mass spectrometry, as well as in vitro and in vivo venom neutralisation assays. We anticipate that the approaches described here will produce antivenom with unparalleled efficacy, safety and affordability.
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Affiliation(s)
- Stefanie K. Menzies
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Raquel Arinto-Garcia
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Fernanda Gobbi Amorim
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Iara Aimê Cardoso
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Camille Abada
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Thomas Crasset
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Rebecca J. Edge
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Priscila El-Kazzi
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Sophie Hall
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Damien Redureau
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Richard Stenner
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Johara Boldrini-França
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Huan Sun
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - António Roldão
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Paula M. Alves
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Robert A. Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Imre Berger
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
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2
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Romano JD, Li H, Napolitano T, Realubit R, Karan C, Holford M, Tatonetti NP. Discovering Venom-Derived Drug Candidates Using Differential Gene Expression. Toxins (Basel) 2023; 15:451. [PMID: 37505720 PMCID: PMC10467105 DOI: 10.3390/toxins15070451] [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: 05/15/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023] Open
Abstract
Venoms are a diverse and complex group of natural toxins that have been adapted to treat many types of human disease, but rigorous computational approaches for discovering new therapeutic activities are scarce. We have designed and validated a new platform-named VenomSeq-to systematically identify putative associations between venoms and drugs/diseases via high-throughput transcriptomics and perturbational differential gene expression analysis. In this study, we describe the architecture of VenomSeq and its evaluation using the crude venoms from 25 diverse animal species and 9 purified teretoxin peptides. By integrating comparisons to public repositories of differential expression, associations between regulatory networks and disease, and existing knowledge of venom activity, we provide a number of new therapeutic hypotheses linking venoms to human diseases supported by multiple layers of preliminary evidence.
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Affiliation(s)
- Joseph D. Romano
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hai Li
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; (H.L.); (R.R.); (C.K.)
- Columbia Genome Center, Columbia University, New York, NY 10032, USA
| | - Tanya Napolitano
- Department of Chemistry, CUNY Hunter College, New York, NY 10032, USA (M.H.)
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Ronald Realubit
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; (H.L.); (R.R.); (C.K.)
- Columbia Genome Center, Columbia University, New York, NY 10032, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; (H.L.); (R.R.); (C.K.)
- Columbia Genome Center, Columbia University, New York, NY 10032, USA
| | - Mandë Holford
- Department of Chemistry, CUNY Hunter College, New York, NY 10032, USA (M.H.)
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, New York, NY 10016, USA
- The PhD Program in Chemistry, Graduate Center of the City University of New York, New York, NY 10016, USA
- The PhD Program in Biology, Graduate Center of the City University of New York, New York, NY 10016, USA
- Department of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10032, USA
| | - Nicholas P. Tatonetti
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90069, USA
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3
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Cardoso FC, Walker AA, King GF, Gomez MV. Holistic profiling of the venom from the Brazilian wandering spider Phoneutria nigriventer by combining high-throughput ion channel screens with venomics. Front Mol Biosci 2023; 10:1069764. [PMID: 36865382 PMCID: PMC9972223 DOI: 10.3389/fmolb.2023.1069764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction: Spider venoms are a unique source of bioactive peptides, many of which display remarkable biological stability and neuroactivity. Phoneutria nigriventer, often referred to as the Brazilian wandering spider, banana spider or "armed" spider, is endemic to South America and amongst the most dangerous venomous spiders in the world. There are 4,000 envenomation accidents with P. nigriventer each year in Brazil, which can lead to symptoms including priapism, hypertension, blurred vision, sweating, and vomiting. In addition to its clinical relevance, P. nigriventer venom contains peptides that provide therapeutic effects in a range of disease models. Methods: In this study, we explored the neuroactivity and molecular diversity of P. nigriventer venom using fractionation-guided high-throughput cellular assays coupled to proteomics and multi-pharmacology activity to broaden the knowledge about this venom and its therapeutic potential and provide a proof-of-concept for an investigative pipeline to study spider-venom derived neuroactive peptides. We coupled proteomics with ion channel assays using a neuroblastoma cell line to identify venom compounds that modulate the activity of voltage-gated sodium and calcium channels, as well as the nicotinic acetylcholine receptor. Results: Our data revealed that P. nigriventer venom is highly complex compared to other neurotoxin-rich venoms and contains potent modulators of voltage-gated ion channels which were classified into four families of neuroactive peptides based on their activity and structures. In addition to the reported P. nigriventer neuroactive peptides, we identified at least 27 novel cysteine-rich venom peptides for which their activity and molecular target remains to be determined. Discussion: Our findings provide a platform for studying the bioactivity of known and novel neuroactive components in the venom of P. nigriventer and other spiders and suggest that our discovery pipeline can be used to identify ion channel-targeting venom peptides with potential as pharmacological tools and to drug leads.
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Affiliation(s)
- F. C. Cardoso
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia,Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia,*Correspondence: F. C. Cardoso,
| | - A. A. Walker
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia,Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia
| | - G. F. King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia,Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Australia
| | - M. V. Gomez
- Department of Neurotransmitters, Institute of Education and Research, Santa Casa, Belo Horizonte, Brazil
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4
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Romo E, Torres M, Martin-Solano S. Current situation of snakebites envenomation in the Neotropics: Biotechnology, a versatile tool in the production of antivenoms. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.04.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Snakebite envenomation is a neglected tropical disease that affects millions of people around the world with a great impact on health and the economy. Unfortunately, public health programs do not include this kind of disease as a priority in their social programs. Cases of snakebite envenomations in the Neotropics are inaccurate due to inadequate disease management from medical records to the choice of treatments. Victims of snakebite envenomation are primarily found in impoverished agricultural areas where remote conditions limit the availability of antivenom. Antivenom serum is the only Food and Drug Administration-approved treatment used up to date. However, it has several disadvantages in terms of safety and effectiveness. This review provides a comprehensive insight dealing with the current epidemiological status of snakebites in the Neotropics and technologies employed in antivenom production. Also, modern biotechnological tools such as transcriptomic, proteomic, immunogenic, high-density peptide microarray and epitope mapping are highlighted for producing new-generation antivenom sera. These results allow us to propose strategic solutions in the Public Health Sector for managing this disease.
Keywords: antivenom, biotechnology, neglected tropical disease, omics, recombinant antibody.
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Affiliation(s)
- Elizabeth Romo
- Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Marbel Torres
- Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador, Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Immunology and Virology Laboratory, Nanoscience and Nanotechnology Center, Universidad de las Fuerzas Armadas, ESPE, Sangolquí, Ecuador
| | - Sarah Martin-Solano
- Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador, Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera de Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública, Universidad Central del Ecuador
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5
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A ShK-like Domain from Steinernema carpocapsae with Bioinsecticidal Potential. Toxins (Basel) 2022; 14:toxins14110754. [PMID: 36356004 PMCID: PMC9699480 DOI: 10.3390/toxins14110754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Entomopathogenic nematodes are used as biological control agents against a broad range of insect pests. We ascribed the pathogenicity of these organisms to the excretory/secretory products (ESP) released by the infective nematode. Our group characterized different virulence factors produced by Steinernema carpocapsae that underlie its success as an insect pathogen. A novel ShK-like peptide (ScK1) from this nematode that presents high sequence similarity with the ShK peptide from a sea anemone was successfully produced recombinantly in Escherichia coli. The secondary structure of ScK1 appeared redox-sensitive, exhibiting a far-UV circular dichroism spectrum consistent with an alpha-helical secondary structure. Thermal denaturation of the ScK1 allowed estimating the melting temperature to 59.2 ± 0.1 °C. The results from toxicity assays using Drosophila melanogaster as a model show that injection of this peptide can kill insects in a dose-dependent manner with an LD50 of 16.9 µM per adult within 24 h. Oral administration of the fusion protein significantly reduced the locomotor activity of insects after 48 h (p < 0.05, Tukey's test). These data show that this nematode expresses insecticidal peptides with potential as next-generation insecticides.
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6
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Herrera-Bravo J, Farías JG, Contreras FP, Herrera-Belén L, Beltrán JF. PEP-PREDNa+: A web server for prediction of highly specific peptides targeting voltage-gated Na+ channels using machine learning techniques. Comput Biol Med 2022; 145:105414. [DOI: 10.1016/j.compbiomed.2022.105414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
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7
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von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022; 11:6588117. [PMID: 35640874 PMCID: PMC9155608 DOI: 10.1093/gigascience/giac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
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Affiliation(s)
- Bjoern M von Reumont
- Goethe University Frankfurt, Institute for Cell Biology and Neuroscience, Department for Applied Bioinformatics, 60438 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany.,Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Naira Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbeli ave. 22, 0028 Yerevan, Armenia
| | - Dimitris Beis
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 11527, Greece
| | - Figen Caliskan
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, TR-26040 Eskisehir, Turkey
| | - Ana Crnković
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maik Damm
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Hannah German
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Trg Republike Hrvatske 14, 10000 Zagreb, Croatia
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nasit Igci
- Nevsehir Haci Bektas Veli University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 50300 Nevsehir, Turkey
| | - Maria P Ikonomopoulou
- Madrid Institute for Advanced Studies in Food, Madrid,E28049, Spain.,The University of Queensland, St Lucia, QLD 4072, Australia
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
| | - Ivan Koludarov
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Tim Lüddecke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Gießen, Germany
| | - Riadh Ben Mansour
- Department of Life Sciences, Faculty of Sciences, Gafsa University, Campus Universitaire Siidi Ahmed Zarrouk, 2112 Gafsa, Tunisia
| | - Maria Vittoria Modica
- Dept. of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - María Eugenia Pachón Ibáñez
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexios Panagiotopoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece.,Animal Biology Division, Department of Biology, University of Patras, Patras, GR-26500, Greece
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Javier Sánchez Céspedes
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andy Sombke
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eivind A B Undheim
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Postboks 1066 Blindern 0316 Oslo, Norway
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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8
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Cardoso V, Brás JLA, Costa IF, Ferreira LMA, Gama LT, Vincentelli R, Henrissat B, Fontes CMGA. Generation of a Library of Carbohydrate-Active Enzymes for Plant Biomass Deconstruction. Int J Mol Sci 2022; 23:ijms23074024. [PMID: 35409382 PMCID: PMC8999789 DOI: 10.3390/ijms23074024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 01/27/2023] Open
Abstract
In nature, the deconstruction of plant carbohydrates is carried out by carbohydrate-active enzymes (CAZymes). A high-throughput (HTP) strategy was used to isolate and clone 1476 genes obtained from a diverse library of recombinant CAZymes covering a variety of sequence-based families, enzyme classes, and source organisms. All genes were successfully isolated by either PCR (61%) or gene synthesis (GS) (39%) and were subsequently cloned into Escherichia coli expression vectors. Most proteins (79%) were obtained at a good yield during recombinant expression. A significantly lower number (p < 0.01) of proteins from eukaryotic (57.7%) and archaeal (53.3%) origin were soluble compared to bacteria (79.7%). Genes obtained by GS gave a significantly lower number (p = 0.04) of soluble proteins while the green fluorescent protein tag improved protein solubility (p = 0.05). Finally, a relationship between the amino acid composition and protein solubility was observed. Thus, a lower percentage of non-polar and higher percentage of negatively charged amino acids in a protein may be a good predictor for higher protein solubility in E. coli. The HTP approach presented here is a powerful tool for producing recombinant CAZymes that can be used for future studies of plant cell wall degradation. Successful production and expression of soluble recombinant proteins at a high rate opens new possibilities for the high-throughput production of targets from limitless sources.
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Affiliation(s)
- Vânia Cardoso
- Centro de Investigação Interdisciplinar em Sanidade Animal—Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (L.M.A.F.); (L.T.G.)
- NZYTech Ltd., Estrada do Paço do Lumiar, Campus do Lumiar, 1649-038 Lisboa, Portugal; (J.L.A.B.); (I.F.C.)
- Correspondence: (V.C.); (C.M.G.A.F.)
| | - Joana L. A. Brás
- NZYTech Ltd., Estrada do Paço do Lumiar, Campus do Lumiar, 1649-038 Lisboa, Portugal; (J.L.A.B.); (I.F.C.)
| | - Inês F. Costa
- NZYTech Ltd., Estrada do Paço do Lumiar, Campus do Lumiar, 1649-038 Lisboa, Portugal; (J.L.A.B.); (I.F.C.)
| | - Luís M. A. Ferreira
- Centro de Investigação Interdisciplinar em Sanidade Animal—Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (L.M.A.F.); (L.T.G.)
| | - Luís T. Gama
- Centro de Investigação Interdisciplinar em Sanidade Animal—Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (L.M.A.F.); (L.T.G.)
| | - Renaud Vincentelli
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Université Aix-Marseille, 13288 Marseille, France; (R.V.); (B.H.)
- Institut National de la Recherche Agronomique, Unité sous Contrat 1408 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Université Aix-Marseille, 13288 Marseille, France; (R.V.); (B.H.)
- Institut National de la Recherche Agronomique, Unité sous Contrat 1408 Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Carlos M. G. A. Fontes
- Centro de Investigação Interdisciplinar em Sanidade Animal—Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (L.M.A.F.); (L.T.G.)
- NZYTech Ltd., Estrada do Paço do Lumiar, Campus do Lumiar, 1649-038 Lisboa, Portugal; (J.L.A.B.); (I.F.C.)
- Correspondence: (V.C.); (C.M.G.A.F.)
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9
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Rivera-de-Torre E, Rimbault C, Jenkins TP, Sørensen CV, Damsbo A, Saez NJ, Duhoo Y, Hackney CM, Ellgaard L, Laustsen AH. Strategies for Heterologous Expression, Synthesis, and Purification of Animal Venom Toxins. Front Bioeng Biotechnol 2022; 9:811905. [PMID: 35127675 PMCID: PMC8811309 DOI: 10.3389/fbioe.2021.811905] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Animal venoms are complex mixtures containing peptides and proteins known as toxins, which are responsible for the deleterious effect of envenomations. Across the animal Kingdom, toxin diversity is enormous, and the ability to understand the biochemical mechanisms governing toxicity is not only relevant for the development of better envenomation therapies, but also for exploiting toxin bioactivities for therapeutic or biotechnological purposes. Most of toxinology research has relied on obtaining the toxins from crude venoms; however, some toxins are difficult to obtain because the venomous animal is endangered, does not thrive in captivity, produces only a small amount of venom, is difficult to milk, or only produces low amounts of the toxin of interest. Heterologous expression of toxins enables the production of sufficient amounts to unlock the biotechnological potential of these bioactive proteins. Moreover, heterologous expression ensures homogeneity, avoids cross-contamination with other venom components, and circumvents the use of crude venom. Heterologous expression is also not only restricted to natural toxins, but allows for the design of toxins with special properties or can take advantage of the increasing amount of transcriptomics and genomics data, enabling the expression of dormant toxin genes. The main challenge when producing toxins is obtaining properly folded proteins with a correct disulfide pattern that ensures the activity of the toxin of interest. This review presents the strategies that can be used to express toxins in bacteria, yeast, insect cells, or mammalian cells, as well as synthetic approaches that do not involve cells, such as cell-free biosynthesis and peptide synthesis. This is accompanied by an overview of the main advantages and drawbacks of these different systems for producing toxins, as well as a discussion of the biosafety considerations that need to be made when working with highly bioactive proteins.
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Affiliation(s)
- Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Esperanza Rivera-de-Torre, ; Andreas H. Laustsen,
| | - Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christoffer V. Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Damsbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Natalie J. Saez
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Yoan Duhoo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Celeste Menuet Hackney
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Esperanza Rivera-de-Torre, ; Andreas H. Laustsen,
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10
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Towards a generic prototyping approach for therapeutically-relevant peptides and proteins in a cell-free translation system. Nat Commun 2022; 13:260. [PMID: 35017494 PMCID: PMC8752827 DOI: 10.1038/s41467-021-27854-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Advances in peptide and protein therapeutics increased the need for rapid and cost-effective polypeptide prototyping. While in vitro translation systems are well suited for fast and multiplexed polypeptide prototyping, they suffer from misfolding, aggregation and disulfide-bond scrambling of the translated products. Here we propose that efficient folding of in vitro produced disulfide-rich peptides and proteins can be achieved if performed in an aggregation-free and thermodynamically controlled folding environment. To this end, we modify an E. coli-based in vitro translation system to allow co-translational capture of translated products by affinity matrix. This process reduces protein aggregation and enables productive oxidative folding and recycling of misfolded states under thermodynamic control. In this study we show that the developed approach is likely to be generally applicable for prototyping of a wide variety of disulfide-constrained peptides, macrocyclic peptides with non-native bonds and antibody fragments in amounts sufficient for interaction analysis and biological activity assessment. Generic approach for rapid prototyping is essential for the progress of synthetic biology. Here the authors modify the cell-free translation system to control protein aggregation and folding and validate the approach by using single conditions for prototyping of various disulfide-constrained polypeptides.
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11
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Stability and Safety of Inhibitor Cystine Knot Peptide, GTx1-15, from the Tarantula Spider Grammostola rosea. Toxins (Basel) 2021; 13:toxins13090621. [PMID: 34564625 PMCID: PMC8473062 DOI: 10.3390/toxins13090621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 12/19/2022] Open
Abstract
Inhibitor cystine knot (ICK) peptides are knotted peptides with three intramolecular disulfide bonds that affect several types of ion channels. Some are proteolytically stable and are promising scaffolds for drug development. GTx1-15 is an ICK peptide that inhibits the voltage-dependent calcium channel Cav3.1 and the voltage-dependent sodium channels Nav1.3 and Nav1.7. As a model molecule to develop an ICK peptide drug, we investigated several important pharmaceutical characteristics of GTx1-15. The stability of GTx1-15 in rat and human blood plasma was examined, and no GTx1-15 degradation was observed in either rat or human blood plasma for 24 h in vitro. GTx1-15 in blood circulation was detected for several hours after intravenous and intramuscular administration, indicating high stability in plasma. The thermal stability of GTx1-15 as examined by high thermal incubation and protein thermal shift assays indicated that GTx1-15 possesses high heat stability. The cytotoxicity and immunogenicity of GTx1-15 were examined using the human monocytic leukemia cell line THP-1. GTx1-15 showed no cytotoxicity or immunogenicity even at high concentrations. These results indicate that GTx1-15 itself is suitable for peptide drug development and as a peptide library scaffold.
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12
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Liu BS, Jiang BR, Hu KC, Liu CH, Hsieh WC, Lin MH, Sung WC. Development of a Broad-Spectrum Antiserum against Cobra Venoms Using Recombinant Three-Finger Toxins. Toxins (Basel) 2021; 13:556. [PMID: 34437427 PMCID: PMC8402450 DOI: 10.3390/toxins13080556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Three-finger toxins (3FTXs) are the most clinically relevant components in cobra (genus Naja) venoms. Administration of the antivenom is the recommended treatment for the snakebite envenomings, while the efficacy to cross-neutralize the different cobra species is typically limited, which is presumably due to intra-specific variation of the 3FTXs composition in cobra venoms. Targeting the clinically relevant venom components has been considered as an important factor for novel antivenom design. Here, we used the recombinant type of long-chain α-neurotoxins (P01391), short-chain α-neurotoxins (P60770), and cardiotoxin A3 (P60301) to generate a new immunogen formulation and investigated the potency of the resulting antiserum against the venom lethality of three medially important cobras in Asia, including the Thai monocled cobra (Naja kaouthia), the Taiwan cobra (Naja atra), and the Thai spitting cobra (Naja Siamensis) snake species. With the fusion of protein disulfide isomerase and the low-temperature settings, the correct disulfide bonds were built on these recombinant 3FTXs (r3FTXs), which were confirmed by the circular dichroism spectra and tandem mass spectrometry. Immunization with r3FTX was able to induce the specific antibody response to the native 3FTXs in cobra venoms. Furthermore, the horse and rabbit antiserum raised by the r3FTX mixture is able to neutralize the venom lethality of the selected three medically important cobras. Thus, the study demonstrated that the r3FTXs are potential immunogens in the development of novel antivenom with broad neutralization activity for the therapeutic treatment of victims involving cobra snakes in countries.
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Affiliation(s)
- Bing-Sin Liu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan; (B.-S.L.); (B.-R.J.); (K.-C.H.); (M.-H.L.)
| | - Bo-Rong Jiang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan; (B.-S.L.); (B.-R.J.); (K.-C.H.); (M.-H.L.)
| | - Kai-Chieh Hu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan; (B.-S.L.); (B.-R.J.); (K.-C.H.); (M.-H.L.)
| | - Chien-Hsin Liu
- Centers for Disease Control, Ministry of Health and Welfare, Taipei 10050, Taiwan; (C.-H.L.); (W.-C.H.)
| | - Wen-Chin Hsieh
- Centers for Disease Control, Ministry of Health and Welfare, Taipei 10050, Taiwan; (C.-H.L.); (W.-C.H.)
| | - Min-Han Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan; (B.-S.L.); (B.-R.J.); (K.-C.H.); (M.-H.L.)
| | - Wang-Chou Sung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 35053, Taiwan; (B.-S.L.); (B.-R.J.); (K.-C.H.); (M.-H.L.)
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13
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Zheng L, Lin Z, Fan H, Chen M, Yu J, Miao Y, Wu B. A fluorescent screening method for optimization of conotoxin expression in Pichia pastoris. Biotechnol Appl Biochem 2021; 69:1611-1621. [PMID: 34337794 DOI: 10.1002/bab.2231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/29/2021] [Indexed: 11/11/2022]
Abstract
Conotoxins are small cysteine-rich peptides secreted by the Conus venom glands, which act on ion channels or membrane receptors with high specificity and potency. Conotoxins are invaluable sources for neuroscience research and drug leads, but their application is hindered by the limited successes in quantitative engineering using either chemical or biotechnological approaches. Here, we explore the Pichia pastoris to express 23 selected conopeptides using a GFP-based fluorescence screen. We found that, in a protease-deficient strain PichiaPink™ Strain 4 (ade2 prb1 pep4), most of the recombinant conopeptides were expressed as two major folding variants including a compact form that was somehow resistant to reduction and high temperature. The GFP-αTxIA was the only one displaying a single band that showed a dose-dependent neurotoxicity on larvae of the insect Plutella xylostella, with a 48-h LD50 lower than 1.12 pmol mg-1 body weight. Furthermore, the recombinant αTxIA after cleavage from the fusion was able to inhibit cell proliferation of the LYCT and HEK293T cell lines with an appearance IC50 of 341 ± 8 and 235 ± 15 nM, respectively. This screening method is straightforward and easy to scale up, providing a versatile tool for further optimization of conotoxin production in the yeast cell.
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Affiliation(s)
- Lei Zheng
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Freshwater Fisheries Research Institute of Fujian Province, Fuzhou, China
| | - Zeyin Lin
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haiping Fan
- Freshwater Fisheries Research Institute of Fujian Province, Fuzhou, China
| | - Mengxue Chen
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiawei Yu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binghua Wu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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14
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Strategies for the Production of Soluble Interferon-Alpha Consensus and Potential Application in Arboviruses and SARS-CoV-2. Life (Basel) 2021; 11:life11060460. [PMID: 34063766 PMCID: PMC8223780 DOI: 10.3390/life11060460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
Biopharmaceutical production is currently a multibillion-dollar industry with high growth perspectives. The research and development of biologically sourced pharmaceuticals are extremely important and a reality in our current healthcare system. Interferon alpha consensus (cIFN) is a non-natural synthetic antiviral molecule that comprises all the most prevalent amino acids of IFN-α into one consensus protein sequence. For clinical use, cIFN is produced in E. coli in the form of inclusion bodies. Here, we describe the use of two solubility tags (Fh8 and DsbC) to improve soluble cIFN production. Furthermore, we analyzed cIFN production in different culture media and temperatures in order to improve biopharmaceutical production. Our results demonstrate that Fh8-cIFN yield was improved when bacteria were cultivated in autoinduction culture medium at 30 °C. After hydrolysis, the recovery of soluble untagged cIFN was 58% from purified Fh8-cIFN molecule, fourfold higher when compared to cIFN recovered from the DsbC-cIFN, which achieved 14% recovery. The biological activity of cIFN was tested on in vitro model of antiviral effect against Zika, Mayaro, Chikungunya and SARS-CoV-2 virus infection in susceptible VERO cells. We show, for the first time, that cIFN has a potent activity against these viruses, being very low amounts of the molecule sufficient to inhibit virus multiplication. Thus, this molecule could be used in a clinical approach to treat Arboviruses and SARS-CoV-2.
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15
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Saikia C, Ben-Nissan G, Reuveny E, Karbat I. Production of recombinant venom peptides as tools for ion channel research. Methods Enzymol 2021; 654:169-201. [PMID: 34120712 DOI: 10.1016/bs.mie.2021.01.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Animal venom is a rich source for peptide toxins that bind and modulate the function of ion channels. Owing to their ability to bind receptor sites on the channel protein with high affinity and specificity, peptide neurotoxins have become an indispensable tool for ion channel research. Recent breakthroughs in structural biology and advances in computer simulations of biomolecules have sparked a new interest in animal toxins as probes of channel protein structure and function. Here, we focus on methods used to produce animal toxins for research purposes using recombinant expression. The specific challenges associated with heterologous production of venom peptides are discussed, and several methods targeting these issues are presented with an emphasis on E. coli based systems. An efficient protocol for the bacterial expression, folding, and purification of recombinant venom peptides is described.
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Affiliation(s)
- Chandamita Saikia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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16
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Herzig V, Cristofori-Armstrong B, Israel MR, Nixon SA, Vetter I, King GF. Animal toxins - Nature's evolutionary-refined toolkit for basic research and drug discovery. Biochem Pharmacol 2020; 181:114096. [PMID: 32535105 PMCID: PMC7290223 DOI: 10.1016/j.bcp.2020.114096] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022]
Abstract
Venomous animals have evolved toxins that interfere with specific components of their victim's core physiological systems, thereby causing biological dysfunction that aids in prey capture, defense against predators, or other roles such as intraspecific competition. Many animal lineages evolved venom systems independently, highlighting the success of this strategy. Over the course of evolution, toxins with exceptional specificity and high potency for their intended molecular targets have prevailed, making venoms an invaluable and almost inexhaustible source of bioactive molecules, some of which have found use as pharmacological tools, human therapeutics, and bioinsecticides. Current biomedically-focused research on venoms is directed towards their use in delineating the physiological role of toxin molecular targets such as ion channels and receptors, studying or treating human diseases, targeting vectors of human diseases, and treating microbial and parasitic infections. We provide examples of each of these areas of venom research, highlighting the potential that venom molecules hold for basic research and drug development.
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Affiliation(s)
- Volker Herzig
- School of Science & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia.
| | | | - Mathilde R Israel
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Samantha A Nixon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia.
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17
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Reynaud S, Ciolek J, Degueldre M, Saez NJ, Sequeira AF, Duhoo Y, Brás JLA, Meudal H, Cabo Díez M, Fernández Pedrosa V, Verdenaud M, Boeri J, Pereira Ramos O, Ducancel F, Vanden Driessche M, Fourmy R, Violette A, Upert G, Mourier G, Beck-Sickinger AG, Mörl K, Landon C, Fontes CMGA, Miñambres Herráiz R, Rodríguez de la Vega RC, Peigneur S, Tytgat J, Quinton L, De Pauw E, Vincentelli R, Servent D, Gilles N. A Venomics Approach Coupled to High-Throughput Toxin Production Strategies Identifies the First Venom-Derived Melanocortin Receptor Agonists. J Med Chem 2020; 63:8250-8264. [PMID: 32602722 DOI: 10.1021/acs.jmedchem.0c00485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Animal venoms are rich in hundreds of toxins with extraordinary biological activities. Their exploitation is difficult due to their complexity and the small quantities of venom available from most venomous species. We developed a Venomics approach combining transcriptomic and proteomic characterization of 191 species and identified 20,206 venom toxin sequences. Two complementary production strategies based on solid-phase synthesis and recombinant expression in Escherichia coli generated a physical bank of 3597 toxins. Screened on hMC4R, this bank gave an incredible hit rate of 8%. Here, we focus on two novel toxins: N-TRTX-Preg1a, exhibiting an inhibitory cystine knot (ICK) motif, and N-BUTX-Ptr1a, a short scorpion-CSαβ structure. Neither N-TRTX-Preg1a nor N-BUTX-Ptr1a affects ion channels, the known targets of their toxin scaffolds, but binds to four melanocortin receptors with low micromolar affinities and activates the hMC1R/Gs pathway. Phylogenetically, these two toxins form new groups within their respective families and represent novel hMC1R agonists, structurally unrelated to the natural agonists.
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Affiliation(s)
- Steve Reynaud
- Université Paris-Sud, 15 Rue Georges Clemenceau, Orsay 91405 France.,Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Justyna Ciolek
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Michel Degueldre
- Mass Spectrometry Laboratory, Université de Liège, Allée du six Aout 11, Quartier Agora, Liege 4000 Belgium.,Department of Analytical Science Biologicals, UCB, Chemin du Foriest, Braine L'Alleud 1420 Belgium
| | - Natalie J Saez
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille 13288 France.,Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, QLD, Australia
| | - Ana Filipa Sequeira
- Universidade de Lisboa, CIISA - Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, Lisboa 1300-477 Portugal.,NZYTech Lda, Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E - R/C, Lisboa 1649-038 Portugal
| | - Yoan Duhoo
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille 13288 France.,Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, QLD, Australia
| | - Joana L A Brás
- Universidade de Lisboa, CIISA - Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, Lisboa 1300-477 Portugal.,NZYTech Lda, Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E - R/C, Lisboa 1649-038 Portugal
| | - Hervé Meudal
- Centre National de la Recherche Scientifique, Centre de Biophysique Moléculaire, rue Charles Sadron, Orléans 45071 France
| | - Miguel Cabo Díez
- Next-Generation Sequencing Laboratory, Sistemas Genómicos Ltd., Ronda de Guglielmo Marconi, 6, Paterna 46980 Spain
| | - Victoria Fernández Pedrosa
- Next-Generation Sequencing Laboratory, Sistemas Genómicos Ltd., Ronda de Guglielmo Marconi, 6, Paterna 46980 Spain
| | - Marion Verdenaud
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Julia Boeri
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Oscar Pereira Ramos
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Frédéric Ducancel
- Université Paris Saclay, CEA, Département IDMIT, 18 route du Panorama, 92265 Fontenay-aux-Roses, France
| | - Margot Vanden Driessche
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Rudy Fourmy
- Alphabiotoxine Laboratory sprl, Barberie 15, Montroeul-au-bois 7911 Belgium
| | - Aude Violette
- Alphabiotoxine Laboratory sprl, Barberie 15, Montroeul-au-bois 7911 Belgium
| | - Grégory Upert
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Gilles Mourier
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | | | - Karin Mörl
- Institute of Biochemistry, Universitat Leipzig, Leipzig 04103 Germany
| | - Céline Landon
- Centre National de la Recherche Scientifique, Centre de Biophysique Moléculaire, rue Charles Sadron, Orléans 45071 France
| | - Carlos M G A Fontes
- Universidade de Lisboa, CIISA - Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, Lisboa 1300-477 Portugal.,NZYTech Lda, Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E - R/C, Lisboa 1649-038 Portugal
| | - Rebeca Miñambres Herráiz
- Next-Generation Sequencing Laboratory, Sistemas Genómicos Ltd., Ronda de Guglielmo Marconi, 6, Paterna 46980 Spain
| | | | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Herestraat 49, Leuven 3000 Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Herestraat 49, Leuven 3000 Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, Université de Liège, Allée du six Aout 11, Quartier Agora, Liege 4000 Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Université de Liège, Allée du six Aout 11, Quartier Agora, Liege 4000 Belgium
| | - Renaud Vincentelli
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Marseille 13288 France
| | - Denis Servent
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
| | - Nicolas Gilles
- Université Paris Saclay, CEA, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette 91191 France
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18
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Bjørn-Yoshimoto WE, Ramiro IBL, Yandell M, McIntosh JM, Olivera BM, Ellgaard L, Safavi-Hemami H. Curses or Cures: A Review of the Numerous Benefits Versus the Biosecurity Concerns of Conotoxin Research. Biomedicines 2020; 8:E235. [PMID: 32708023 PMCID: PMC7460000 DOI: 10.3390/biomedicines8080235] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 01/18/2023] Open
Abstract
Conotoxins form a diverse group of peptide toxins found in the venom of predatory marine cone snails. Decades of conotoxin research have provided numerous measurable scientific and societal benefits. These include their use as a drug, diagnostic agent, drug leads, and research tools in neuroscience, pharmacology, biochemistry, structural biology, and molecular evolution. Human envenomations by cone snails are rare but can be fatal. Death by envenomation is likely caused by a small set of toxins that induce muscle paralysis of the diaphragm, resulting in respiratory arrest. The potency of these toxins led to concerns regarding the potential development and use of conotoxins as biological weapons. To address this, various regulatory measures have been introduced that limit the use and access of conotoxins within the research community. Some of these regulations apply to all of the ≈200,000 conotoxins predicted to exist in nature of which less than 0.05% are estimated to have any significant toxicity in humans. In this review we provide an overview of the many benefits of conotoxin research, and contrast these to the perceived biosecurity concerns of conotoxins and research thereof.
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Affiliation(s)
- Walden E. Bjørn-Yoshimoto
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark; (W.E.B.-Y.); (I.B.L.R.)
| | - Iris Bea L. Ramiro
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark; (W.E.B.-Y.); (I.B.L.R.)
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA;
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - J. Michael McIntosh
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.M.M.); (B.M.O.)
- George E. Whalen Veterans Affairs Medical Center, Salt Lake City, UT 84148, USA
- Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.M.M.); (B.M.O.)
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark; (W.E.B.-Y.); (I.B.L.R.)
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.M.M.); (B.M.O.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
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19
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Chow CY, Absalom N, Biggs K, King GF, Ma L. Venom-derived modulators of epilepsy-related ion channels. Biochem Pharmacol 2020; 181:114043. [PMID: 32445870 DOI: 10.1016/j.bcp.2020.114043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022]
Abstract
Epilepsy is characterised by spontaneous recurrent seizures that are caused by an imbalance between neuronal excitability and inhibition. Since ion channels play fundamental roles in the generation and propagation of action potentials as well as neurotransmitter release at a subset of excitatory and inhibitory synapses, their dysfunction has been linked to a wide variety of epilepsies. Indeed, these unique proteins are the major biological targets for antiepileptic drugs. Selective targeting of a specific ion channel subtype remains challenging for small molecules, due to the high level of homology among members of the same channel family. As a consequence, there is a growing trend to target ion channels with biologics. Venoms are the best known natural source of ion channel modulators, and venom peptides are increasingly recognised as potential therapeutics due to their high selectivity and potency gained through millions of years of evolutionary selection pressure. Here we describe the major ion channel families involved in the pathogenesis of various types of epilepsy, including voltage-gated Na+, K+, Ca2+ channels, Cys-loop receptors, ionotropic glutamate receptors and P2X receptors, and currently available venom-derived peptides that target these channel proteins. Although only a small number of venom peptides have successfully progressed to the clinic, there is reason to be optimistic about their development as antiepileptic drugs, notwithstanding the challenges associated with development of any class of peptide drug.
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Affiliation(s)
- Chun Yuen Chow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nathan Absalom
- Brain and Mind Centre, School of Pharmacy, Faculty of Health and Medicine, The University of Sydney, Sydney, NSW 2050, Australia
| | - Kimberley Biggs
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Linlin Ma
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia.
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20
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Zhou L, Liu Z, Xu G, Li L, Xuan K, Xu Y, Zhang R. Expression of Melittin in Fusion with GST in Escherichia coli and Its Purification as a Pure Peptide with Good Bacteriostatic Efficacy. ACS OMEGA 2020; 5:9251-9258. [PMID: 32363276 PMCID: PMC7191569 DOI: 10.1021/acsomega.0c00085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/23/2020] [Indexed: 05/10/2023]
Abstract
The expression and purification of melittin (MET) in microbials are difficult because of its antibacterial activities. In this work, MET was fused with a glutathione-S-transferase (GST) tag and expressed in Escherichia coli to overcome its lethality to host cells. The fusion protein GST-MET was highly expressed and then purified by glutathione sepharose high-performance affinity chromatography, digested with prescission protease, and further purified by Superdex Peptide 10/300 GL chromatography. Finally, 3.5 mg/L recombinant melittin (rMET) with a purity of >90% was obtained; its antibacterial activities against Gram-positive Bacillus pumilus and Staphylococcus pasteuri were similar to those of commercial MET. A circular dichroism spectroscopic assay showed that the rMET peptide secondary structure was similar to those of the commercial form. To our knowledge, this is the report of the preparation of active pure rMET with no tags. The successful expression and purification of rMET will enable large-scale, industrial biosynthesis of MET.
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Affiliation(s)
- Lixian Zhou
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.
R. China
| | - Zhiyong Liu
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.
R. China
| | - Guanyu Xu
- Xuteli
School, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Lihong Li
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.
R. China
| | - Kaiang Xuan
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.
R. China
| | - Yan Xu
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.
R. China
| | - Rongzhen Zhang
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, School
of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, P.
R. China
- . Tel: +86 510 85197760. Fax: +86 501 85918201
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21
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Nitta KR, Vincentelli R, Jacox E, Cimino A, Ohtsuka Y, Sobral D, Satou Y, Cambillau C, Lemaire P. High-Throughput Protein Production Combined with High- Throughput SELEX Identifies an Extensive Atlas of Ciona robusta Transcription Factor DNA-Binding Specificities. Methods Mol Biol 2020; 2025:487-517. [PMID: 31267468 DOI: 10.1007/978-1-4939-9624-7_23] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Transcription factors (TFs) control gene transcription, binding to specific DNA motifs located in cis-regulatory elements across the genome. The identification of TF-binding motifs is thus an important aspect to understand the role of TFs in gene regulation. SELEX, Systematic Evolution of Ligands by EXponential enrichment, is an efficient in vitro method, which can be used to determine the DNA-binding specificity of TFs. Thanks to the development of high-throughput (HT) DNA cloning system and protein production technology, the classical SELEX assay has be extended to high-throughput scale (HT-SELEX).We report here the detailed protocol for the cloning, production, and purification of 420 Ciona robusta DNA BD. 263 Ciona robusta TF DNA-binding domain proteins were purified in milligram quantities and analyzed by HT-SELEX. The identification of 139 recognition sequences generates an atlas of protein-DNA-binding specificities that is crucial for the understanding of the gene regulatory network (GRN) of Ciona robusta. Overall, our analysis suggests that the Ciona robusta repertoire of sequence-specific transcription factors comprises less than 500 genes. The protocols for high-throughput protein production and HT-SELEX described in this article for the study of Ciona robusta TF DNA-binding specificity are generic and have been successfully applied to a wide range of TFs from other species, including human, mouse, and Drosophila.
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Affiliation(s)
- Kazuhiro R Nitta
- Institute of Developmental Biology of Marseille (IBDM), Aix-Marseille Université/CNRS, Marseille cedex 9, France.,Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille cedex 9, France
| | - Edwin Jacox
- Institute of Developmental Biology of Marseille (IBDM), Aix-Marseille Université/CNRS, Marseille cedex 9, France.,Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier/CNRS, Montpellier cedex 5, France
| | - Agnès Cimino
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, CNRS, Aix-Marseille Université, Marseille cedex 9, France
| | - Yukio Ohtsuka
- Institute of Developmental Biology of Marseille (IBDM), Aix-Marseille Université/CNRS, Marseille cedex 9, France.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Daniel Sobral
- Institute of Developmental Biology of Marseille (IBDM), Aix-Marseille Université/CNRS, Marseille cedex 9, France.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, CNRS, Aix-Marseille Université, Marseille cedex 9, France
| | - Patrick Lemaire
- Institute of Developmental Biology of Marseille (IBDM), Aix-Marseille Université/CNRS, Marseille cedex 9, France. .,Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier/CNRS, Montpellier cedex 5, France.
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22
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Dehghan Z, Ayat H, Mohammad Ahadi A. Expression, Purification and Docking Studies on IMe-AGAP, the First Antitumor-analgesic Like Peptide from Iranian Scorpion Mesobuthus eupeus. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2020; 19:206-216. [PMID: 33680023 PMCID: PMC7757975 DOI: 10.22037/ijpr.2019.15339.13028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Scorpion venom contains different toxins with multiple biological functions. IMe-AGAP is the first Analgesic-Antitumor like Peptide (AGAP) isolated from Iranian scorpion Mesobuthus eupeus. This peptide is similar to AGAP toxin with high analgesic activity, extracted from Chinese scorpion and inhibits NaV1.8 and NaV1.9 voltage-gated sodium channels involved in the pain pathway. In this study, IMe-AGAP was cloned in a prokaryotic expression vector; expression of toxin in Escherichia coli (E. coli) was assayed and then purified. In in-silico studies, peptide sequence was compared with other scorpion analgesic toxins. The structures of IMe-AGAP and sodium channels were modeled using homology modeling. Structural evaluation and stereo-chemical analysis of modeled structures were performed using RAMPAGE web server Ramachandran plots. Hex Server was used to investigate the interactions between IMe-AGAP and S3-S4 and also S5-S6 segments of NaV1.8 and NaV1.9. Binding energies calculation was used for evaluation of protein docking. Soluble expression of IMe-AGAP in bacteria was investigated by SDS-PAGE analysis. Pure recombinant protein was obtained by Ni-NTA affinity chromatography. The results of three-dimensional structure prediction showed βαββ topology for the toxin that is similar to the conserved structure of α-toxins. Comparison analysis between IMe-AGAP and AGAP toxins exhibited high similarity in homology modeling. Docking analysis demonstrated that IMe-AGAP can interact with NaV1.8 and NaV1.9 domains involved in pain. According to the results of homology studies and docking, IMe-AGAP might be a novel potential drug for pain treatment.
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23
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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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24
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Ubiquitous Carbohydrate Binding Modules Decorate 936 Lactococcal Siphophage Virions. Viruses 2019; 11:v11070631. [PMID: 31324000 PMCID: PMC6669499 DOI: 10.3390/v11070631] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 01/29/2023] Open
Abstract
With the availability of an increasing number of 3D structures of bacteriophage components, combined with powerful in silico predictive tools, it has become possible to decipher the structural assembly and functionality of phage adhesion devices. In the current study, we examined 113 members of the 936 group of lactococcal siphophages, and identified a number of Carbohydrate Binding Modules (CBMs) in the neck passage structure and major tail protein, on top of evolved Dit proteins, as recently reported by us. The binding ability of such CBM-containing proteins was assessed through the construction of green fluorescent protein fusion proteins and subsequent binding assays. Two CBMs, one from the phage tail and another from the neck, demonstrated definite binding to their phage-specific host. Bioinformatic analysis of the structural proteins of 936 phages reveals that they incorporate binding modules which exhibit structural homology to those found in other lactococcal phage groups and beyond, indicating that phages utilize common structural “bricks” to enhance host binding capabilities. The omnipresence of CBMs in Siphophages supports their beneficial role in the infection process, as they can be combined in various ways to form appendages with different shapes and functionalities, ensuring their success in host detection in their respective ecological niches.
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25
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Nielsen LD, Foged MM, Albert A, Bertelsen AB, Søltoft CL, Robinson SD, Petersen SV, Purcell AW, Olivera BM, Norton RS, Vasskog T, Safavi-Hemami H, Teilum K, Ellgaard L. The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework. J Biol Chem 2019; 294:8745-8759. [PMID: 30975904 DOI: 10.1074/jbc.ra119.007491] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/04/2019] [Indexed: 12/19/2022] Open
Abstract
Venomous marine cone snails produce peptide toxins (conotoxins) that bind ion channels and receptors with high specificity and therefore are important pharmacological tools. Conotoxins contain conserved cysteine residues that form disulfide bonds that stabilize their structures. To gain structural insight into the large, yet poorly characterized conotoxin H-superfamily, we used NMR and CD spectroscopy along with MS-based analyses to investigate H-Vc7.2 from Conus victoriae, a peptide with a VI/VII cysteine framework. This framework has CysI-CysIV/CysII-CysV/CysIII-CysVI connectivities, which have invariably been associated with the inhibitor cystine knot (ICK) fold. However, the solution structure of recombinantly expressed and purified H-Vc7.2 revealed that although it displays the expected cysteine connectivities, H-Vc7.2 adopts a different fold consisting of two stacked β-hairpins with opposing β-strands connected by two parallel disulfide bonds, a structure homologous to the N-terminal region of the human granulin protein. Using structural comparisons, we subsequently identified several toxins and nontoxin proteins with this "mini-granulin" fold. These findings raise fundamental questions concerning sequence-structure relationships within peptides and proteins and the key determinants that specify a given fold.
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Affiliation(s)
- Lau D Nielsen
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark
| | - Mads M Foged
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark
| | | | - Andreas B Bertelsen
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark
| | - Cecilie L Søltoft
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark
| | - Samuel D Robinson
- the Department of Biology, University of Utah, Salt Lake City, Utah 84112.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Steen V Petersen
- the Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark
| | - Anthony W Purcell
- the Department of Biochemistry and Molecular Biology and Monash Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia, and
| | | | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Terje Vasskog
- the Norut Northern Research Institute, 9294 Tromsø, Norway
| | - Helena Safavi-Hemami
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark.,the Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
| | - Kaare Teilum
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark
| | - Lars Ellgaard
- From the Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen N., Denmark,
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26
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Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space. Proc Natl Acad Sci U S A 2019; 116:6063-6068. [PMID: 30850540 PMCID: PMC6442616 DOI: 10.1073/pnas.1815791116] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Over the last two decades, the number of gene/protein sequences gleaned from sequencing projects of individual genomes and environmental DNA has grown exponentially. Only a tiny fraction of these predicted proteins has been experimentally characterized, and the function of most proteins remains hypothetical or only predicted based on sequence similarity. Despite the development of postgenomic methods, such as transcriptomics, proteomics, and metabolomics, the assignment of function to protein sequences remains one of the main challenges in modern biology. As in all classes of proteins, the growing number of predicted carbohydrate-active enzymes (CAZymes) has not been accompanied by a systematic and accurate attribution of function. Taking advantage of the CAZy database, which groups CAZymes into families and subfamilies based on amino acid similarities, we recombinantly produced 564 proteins selected from subfamilies without any biochemically characterized representatives, from distant relatives of characterized enzymes and from nonclassified proteins that show little similarity with known CAZymes. Screening these proteins for activity on a wide collection of carbohydrate substrates led to the discovery of 13 CAZyme families (two of which were also discovered by others during the course of our work), revealed three previously unknown substrate specificities, and assigned a function to 25 subfamilies.
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27
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Liu Y, Zhang J, Wang R, Wu Y, Wang W, Xin X, Du M, Cao Y, Zhang H. Identification of novel Kv1.3 targeting venom peptides by a single round of autocrine-based selection. Biochem Biophys Res Commun 2019; 509:954-959. [PMID: 30648553 DOI: 10.1016/j.bbrc.2019.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/04/2019] [Indexed: 11/24/2022]
Abstract
Venom peptides are an excellent source of pharmacologically active molecules for ion channels that have been considered as promising drug targets. However, mining venoms that interact with ion channel remains challenging. Previously an autocrine based high throughput selection system was developed to screen venom peptide library but the method includes repetitious selection rounds that may cause loss of valuable hits. To simplify the selection process, next generation sequencing was employed to directly identify the positive hits after a single round of selection. The advantage of the improved system was demonstrated by the discovery of 3 novel Kv1.3 targeting venom peptides among which Kappa-thalatoxin-Tas2a is a potent Kv1.3 antagonist. Therefore, this simplified method is efficient to identify novel venom peptides that target ion channels.
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Affiliation(s)
- Yaohui Liu
- State Key Laboratory of Medicinal Chemical Biology, 94 Weijin Road, Tianjin, 300071, China; College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jiashuo Zhang
- State Key Laboratory of Medicinal Chemical Biology, 94 Weijin Road, Tianjin, 300071, China; College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Ruikun Wang
- State Key Laboratory of Medicinal Chemical Biology, 94 Weijin Road, Tianjin, 300071, China; College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Yaxing Wu
- State Key Laboratory of Medicinal Chemical Biology, 94 Weijin Road, Tianjin, 300071, China; College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Xiu Xin
- State Key Laboratory of Medicinal Chemical Biology, 94 Weijin Road, Tianjin, 300071, China; College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Mingjuan Du
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Youjia Cao
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| | - Hongkai Zhang
- State Key Laboratory of Medicinal Chemical Biology, 94 Weijin Road, Tianjin, 300071, China; College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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28
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de Marco A, Ferrer-Miralles N, Garcia-Fruitós E, Mitraki A, Peternel S, Rinas U, Trujillo-Roldán MA, Valdez-Cruz NA, Vázquez E, Villaverde A. Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 2019; 43:53-72. [PMID: 30357330 DOI: 10.1093/femsre/fuy038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Vassilika Vouton, 70013 Heraklion, Crete, Greece.,Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology Hellas (FORTH), N. Plastira 100, Vassilika Vouton, 70013 Heraklion, Crete, Greece
| | | | - Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
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Monitoring the Disulfide Bonds of Folding Isomers of Synthetic CTX A3 Polypeptide Using MS-Based Technology. Toxins (Basel) 2019; 11:toxins11010052. [PMID: 30658470 PMCID: PMC6356385 DOI: 10.3390/toxins11010052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 12/19/2022] Open
Abstract
Native disulfide formation is crucial to the process of disulfide-rich protein folding in vitro. As such, analysis of the disulfide bonds can be used to track the process of the folding reaction; however, the diverse structural isomers interfere with characterization due to the non-native disulfide linkages. Previously, a mass spectrometry (MS) based platform coupled with peptide demethylation and an automatic disulfide bond searching engine demonstrated the potential to screen disulfide-linked peptides for the unambiguous assignment of paired cysteine residues of toxin components in cobra venom. The developed MS-based platform was evaluated to analyze the disulfide bonds of structural isomers during the folding reaction of synthetic cardiotoxin A3 polypeptide (syn-CTX A3), an important medical component in cobra venom. Through application of this work flow, a total of 13 disulfide-linked peptides were repeatedly identified across the folding reaction, and two of them were found to contain cysteine pairings, like those found in native CTX A3. Quantitative analysis of these disulfide-linked peptides showed the occurrence of a progressive disulfide rearrangement that generates a native disulfide bond pattern on syn-CTX A3 folded protein. The formation of these syn-CTX A3 folded protein reaches a steady level in the late stage of the folding reaction. Biophysical and cell-based assays showed that the collected syn-CTX A3 folded protein have a β-sheet secondary structure and cytotoxic activity similar to that of native CTX A3. In addition, the immunization of the syn-CTX A3 folded proteins could induce neutralization antibodies against the cytotoxic activity of native CTX A3. In contrast, these structure activities were poorly observed in the other folded isomers with non-native disulfide bonds. The study highlights the ability of the developed MS platform to assay isomers with heterogeneous disulfide bonds, providing insight into the folding mechanism of the bioactive protein generation.
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Duhoo Y, Sequeira AF, Saez NJ, Turchetto J, Ramond L, Peysson F, Brás JLA, Gilles N, Darbon H, Fontes CMGA, Vincentelli R. High-Throughput Production of Oxidized Animal Toxins in Escherichia coli. Methods Mol Biol 2019; 2025:165-190. [PMID: 31267452 DOI: 10.1007/978-1-4939-9624-7_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
High-throughput production (HTP) of synthetic genes is becoming an important tool to explore the biological function of the extensive genomic and meta-genomic information currently available from various sources. One such source is animal venom, which contains thousands of novel bioactive peptides with potential uses as novel therapeutics to treat a plethora of diseases as well as in environmentally benign bioinsecticide formulations. Here, we describe a HTP platform for recombinant bacterial production of oxidized disulfide-rich proteins and peptides from animal venoms. High-throughput, host-optimized, gene synthesis and subcloning, combined with robust HTP expression and purification protocols, generate a semiautomated pipeline for the accelerated production of proteins and peptides identified from genomic or transcriptomic libraries. The platform has been applied to the production of thousands of animal venom peptide toxins for the purposes of drug discovery, but has the power to be universally applicable for high-level production of various and diverse target proteins in soluble form. This chapter details the HTP protocol for gene synthesis and production, which supported high levels of peptide expression in the E. coli periplasm using a cleavable DsbC fusion. Finally, target proteins and peptides are purified using automated HTP methods, before undergoing quality control and screening.
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Affiliation(s)
- Yoan Duhoo
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Ana Filipa Sequeira
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal.,NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do paço do Lumiar, Lisbon, Portugal
| | - Natalie J Saez
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
| | - Jeremy Turchetto
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Laurie Ramond
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Fanny Peysson
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Joana L A Brás
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do paço do Lumiar, Lisbon, Portugal
| | - Nicolas Gilles
- CEA/DRF/Joliot, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France
| | - Hervé Darbon
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal.,NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do paço do Lumiar, Lisbon, Portugal
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille cedex 9, France.
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31
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Saez NJ, Herzig V. Versatile spider venom peptides and their medical and agricultural applications. Toxicon 2018; 158:109-126. [PMID: 30543821 DOI: 10.1016/j.toxicon.2018.11.298] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023]
Abstract
Spiders have been evolving complex and diverse repertoires of peptides in their venoms with vast pharmacological activities for more than 300 million years. Spiders use their venoms for prey capture and defense, hence they contain peptides that target both prey (mainly arthropods) and predators (other arthropods or vertebrates). This includes peptides that potently and selectively modulate a range of targets such as ion channels, receptors and signaling pathways involved in physiological processes. The contribution of these targets in particular disease pathophysiologies makes spider venoms a valuable source of peptides with potential therapeutic use. In addition, peptides with insecticidal activities, used for prey capture, can be exploited for the development of novel bioinsecticides for agricultural use. Although we have already reviewed potential applications of spider venom peptides as therapeutics (in 2010) and as bioinsecticides (in 2012), a considerable number of research articles on both topics have been published since, warranting an updated review. Here we explore the most recent research on the use of spider venom peptides for both medical and agricultural applications.
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Affiliation(s)
- Natalie J Saez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
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32
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Munawar A, Ali SA, Akrem A, Betzel C. Snake Venom Peptides: Tools of Biodiscovery. Toxins (Basel) 2018; 10:toxins10110474. [PMID: 30441876 PMCID: PMC6266942 DOI: 10.3390/toxins10110474] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 01/09/2023] Open
Abstract
Nature endowed snakes with a lethal secretion known as venom, which has been fine-tuned over millions of years of evolution. Snakes utilize venom to subdue their prey and to survive in their natural habitat. Venom is known to be a very poisonous mixture, consisting of a variety of molecules, such as carbohydrates, nucleosides, amino acids, lipids, proteins and peptides. Proteins and peptides are the major constituents of the dry weight of snake venoms and are of main interest for scientific investigations as well as for various pharmacological applications. Snake venoms contain enzymatic and non-enzymatic proteins and peptides, which are grouped into different families based on their structure and function. Members of a single family display significant similarities in their primary, secondary and tertiary structures, but in many cases have distinct pharmacological functions and different bioactivities. The functional specificity of peptides belonging to the same family can be attributed to subtle variations in their amino acid sequences. Currently, complementary tools and techniques are utilized to isolate and characterize the peptides, and study their potential applications as molecular probes, and possible templates for drug discovery and design investigations.
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Affiliation(s)
- Aisha Munawar
- Department of Chemistry, University of Engineering and Technology, Lahore 54890, Pakistan.
| | - Syed Abid Ali
- H.E. J. Research Institute of Chemistry, (ICCBS), University of Karachi, Karachi 75270, Pakistan.
| | - Ahmed Akrem
- Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan.
| | - Christian Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, University of Hamburg, 22607 Hamburg, Germany.
- Laboratory for Structural Biology of Infection and Inflammation, DESY, Build. 22a, Notkestr. 85, 22603 Hamburg, Germany.
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Hayes S, Vincentelli R, Mahony J, Nauta A, Ramond L, Lugli GA, Ventura M, van Sinderen D, Cambillau C. Functional carbohydrate binding modules identified in evolved dits from siphophages infecting various Gram-positive bacteria. Mol Microbiol 2018; 110:777-795. [DOI: 10.1111/mmi.14124] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Stephen Hayes
- School of Microbiology; University College Cork; Cork Ireland
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
| | - Jennifer Mahony
- School of Microbiology; University College Cork; Cork Ireland
| | - Arjen Nauta
- FrieslandCampina; Amersfoort The Netherlands
| | - Laurie Ramond
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
| | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Life Sciences; University of Parma; Parma Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences; University of Parma; Parma Italy
| | - Douwe van Sinderen
- School of Microbiology; University College Cork; Cork Ireland
- APC Microbiome Ireland, University College Cork; Cork Ireland
| | - Christian Cambillau
- School of Microbiology; University College Cork; Cork Ireland
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
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Engineering varied serine protease inhibitors by converting P1 site of BF9, a weakly active Kunitz-type animal toxin. Int J Biol Macromol 2018; 120:1190-1197. [PMID: 30172807 DOI: 10.1016/j.ijbiomac.2018.08.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/14/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022]
Abstract
Although there were a lot of weakly active animal toxins in the venoms, their values and applications are still mysterious, such as BF9, which is a Kunitz-type toxin isolated from the venom of the elapid snake Bungarus fasciatus. Here, we used BF9 to be a molecular scaffold, and engineered eight BF9-derived peptides by changing P1 site Asn17 of BF9, such as BF9-N17Y and BF9-N17T designed from the polar subfamily, BF9-N17L and BF9-N17G designed from the Non-polar subfamily, BF9-N17D designed from acidic subfamily, and BF9-N17H, BF9-N17K and BF9-N17R designed from basic subfamily. Through enzyme inhibitor experiment assays, we found a potent and selective chymotrypsin inhibitor BF9-N17Y, a potent and selective coagulation factor XIa inhibitor BF9-N17H, and two highly potent coagulation factor XIa inhibitors BF9-N17K and BF9-N17. APTT and PT assays further showed that BF9-N17H, BF9-N17K and BF9-N17R were three novel anticoagulants with selectively intrinsic coagulation pathway inhibitory activity. Considering that natural weakly active animal toxins are also a huge peptide resource, our present work might open a new window about pharmacological applications of weakly active animal toxins, which might be good templates for potent and selective molecular probe and lead drug designs.
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35
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Toxins as tools: Fingerprinting neuronal pharmacology. Neurosci Lett 2018; 679:4-14. [DOI: 10.1016/j.neulet.2018.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/09/2018] [Accepted: 02/02/2018] [Indexed: 12/30/2022]
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36
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Safavi-Hemami H, Brogan SE, Olivera BM. Pain therapeutics from cone snail venoms: From Ziconotide to novel non-opioid pathways. J Proteomics 2018; 190:12-20. [PMID: 29777871 DOI: 10.1016/j.jprot.2018.05.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/15/2018] [Indexed: 01/04/2023]
Abstract
There have been numerous attempts to develop non-opioid drugs for severe pain, but the vast majority of these efforts have failed. A notable exception is Ziconotide (Prialt®), approved by the FDA in 2004. In this review, we summarize the present status of Ziconotide as a therapeutic drug and introduce a wider framework: the potential of venom peptides from cone snails as a resource providing a continuous pipeline for the discovery of non-opioid pain therapeutics. An auxiliary theme that we hope to develop is that these venoms, already a validated starting point for non-opioid drug leads, should also provide an opportunity for identifying novel molecular targets for future pain drugs. This review comprises several sections: the first focuses on Ziconotide as a therapeutic (including a historical retrospective and a clinical perspective); followed by sections on other promising Conus venom peptides that are either in clinical or pre-clinical development. We conclude with a discussion on why the outlook for discovery appears exceptionally promising. The combination of new technologies in diverse fields, including the development of novel high-content assays and revolutionary advancements in transcriptomics and proteomics, puts us at the cusp of providing a continuous pipeline of non-opioid drug innovations for pain. SIGNIFICANCE: The current opioid epidemic is the deadliest drug crisis in American history. Thus, this review on the discovery of non-opioid pain therapeutics and pathways from cone snail venoms is significant and timely.
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Affiliation(s)
| | - Shane E Brogan
- Anesthesiology, University of Utah, Salt Lake City, UT, United States; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Baldomero M Olivera
- Departments of Biology, University of Utah, Salt Lake City, UT, United States
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37
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Abstract
Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This “venomic” approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution. The main challenge for venomics is the effective integration of transcriptomics, proteomics, and pharmacological data and the efficient analysis of big datasets. Novel database search tools and visualisation techniques are now being introduced that facilitate data exploration, with ongoing advances in related omics fields being expected to further enhance venomics studies. Despite these challenges and future opportunities, cone snail venomics has already exponentially expanded the number of novel venom peptide sequences identified from the species investigated, although most novel conotoxins remain to be pharmacologically characterised. Therefore, efficient high-throughput peptide production systems and/or banks of miniaturized discovery assays are required to overcome this bottleneck and thus enhance cone snail venom bioprospecting and accelerate the identification of novel drug leads.
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Starobova H, S. W. A. H, Lewis RJ, Vetter I. Transcriptomics in pain research: insights from new and old technologies. Mol Omics 2018; 14:389-404. [DOI: 10.1039/c8mo00181b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Physiological and pathological pain involves a complex interplay of multiple cell types and signaling pathways.
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Affiliation(s)
- H. Starobova
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
| | - Himaya S. W. A.
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
| | - R. J. Lewis
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
| | - I. Vetter
- Centre for Pain Research
- Institute for Molecular Bioscience
- University of Queensland
- St Lucia
- Australia
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39
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Sabalza M, Barber CA, Abrams WR, Montagna R, Malamud D. Zika Virus Specific Diagnostic Epitope Discovery. J Vis Exp 2017. [PMID: 29286404 DOI: 10.3791/56784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-density peptide microarrays allow screening of more than six thousand peptides on a single standard microscopy slide. This method can be applied for drug discovery, therapeutic target identification, and developing of diagnostics. Here, we present a protocol to discover specific Zika virus (ZIKV) diagnostic peptides using a high-density peptide microarray. A human serum sample validated for ZIKV infection was incubated with a high-density peptide microarray containing the entire ZIKV protein translated into 3,423 unique 15 linear amino acid (aa) residues with a 14-aa residue overlap printed in duplicate. Staining with different secondary antibodies within the same array, we detected peptides that bind to Immunoglobulin M (IgM) and Immunoglobulin G (IgG) antibodies present in serum. These peptides were selected for further validation experiments. In this protocol, we describe the strategy followed to design, process, and analyze a high-density peptide microarray.
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Affiliation(s)
- Maite Sabalza
- Department of Basic Sciences and Craniofacial Development, New York University College of Dentistry;
| | - Cheryl A Barber
- Department of Basic Sciences and Craniofacial Development, New York University College of Dentistry
| | - William R Abrams
- Department of Basic Sciences and Craniofacial Development, New York University College of Dentistry
| | | | - Daniel Malamud
- Department of Basic Sciences and Craniofacial Development, New York University College of Dentistry; Department of Medicine, New York University Langone School of Medicine
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40
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