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Mortelecque J, Zejneli O, Bégard S, Simões MC, ElHajjar L, Nguyen M, Cantrelle FX, Hanoulle X, Rain JC, Colin M, Gomes CM, Buée L, Landrieu I, Danis C, Dupré E. A selection and optimization strategy for single-domain antibodies targeting the PHF6 linear peptide within the tau intrinsically disordered protein. J Biol Chem 2024; 300:107163. [PMID: 38484799 PMCID: PMC11007443 DOI: 10.1016/j.jbc.2024.107163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
The use of variable domain of the heavy-chain of the heavy-chain-only antibodies (VHHs) as disease-modifying biomolecules in neurodegenerative disorders holds promises, including targeting of aggregation-sensitive proteins. Exploitation of their clinical values depends however on the capacity to deliver VHHs with optimal physico-chemical properties for their specific context of use. We described previously a VHH with high therapeutic potential in a family of neurodegenerative diseases called tauopathies. The activity of this promising parent VHH named Z70 relies on its binding within the central region of the tau protein. Accordingly, we carried out random mutagenesis followed by yeast two-hybrid screening to obtain optimized variants. The VHHs selected from this initial screen targeted the same epitope as VHH Z70 as shown using NMR spectroscopy and had indeed improved binding affinities according to dissociation constant values obtained by surface plasmon resonance spectroscopy. The improved affinities can be partially rationalized based on three-dimensional structures and NMR data of three complexes consisting of an optimized VHH and a peptide containing the tau epitope. Interestingly, the ability of the VHH variants to inhibit tau aggregation and seeding could not be predicted from their affinity alone. We indeed showed that the in vitro and in cellulo VHH stabilities are other limiting key factors to their efficacy. Our results demonstrate that only a complete pipeline of experiments, here described, permits a rational selection of optimized VHH variants, resulting in the selection of VHH variants with higher affinities and/or acting against tau seeding in cell models.
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Affiliation(s)
- Justine Mortelecque
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Orgeta Zejneli
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France; Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Séverine Bégard
- Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Margarida C Simões
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Lea ElHajjar
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Marine Nguyen
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - François-Xavier Cantrelle
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Xavier Hanoulle
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | | | - Morvane Colin
- Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Cláudio M Gomes
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luc Buée
- Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France.
| | - Isabelle Landrieu
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
| | - Clément Danis
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France; Univ. Lille, Inserm, CHU-Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Elian Dupré
- CNRS EMR9002 - BSI - Integrative Structural Biology, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
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Yu X, Li S, Feng H, Liao X, Xing XH, Bai Z, Liu X, Zhang C. CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion. Metab Eng 2023; 75:192-204. [PMID: 36572334 DOI: 10.1016/j.ymben.2022.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/25/2022]
Abstract
Genome-scale target identification promises to guide microbial cell factory engineering for higher-titer production of biomolecules such as recombinant proteins (r-protein), but challenges remain due to the need not only for comprehensive genotypic perturbation but also in conjunction with high-throughput phenotypic screening strategies. Here, we developed a CRISPRi-microfluidics screening platform to systematically identify crucial gene targets that can be engineered to enhance r-protein secretion in Corynebacterium glutamicum. We created a CRISPR interference (CRISPRi) library containing 46,549 single-guide RNAs, where we aimed to unbiasedly target all genes for repression. Meanwhile, we developed a highly efficient droplet-based microfluidics system integrating the FlAsH-tetracysteine assay that enables screening of millions of strains to identify potential knockdowns conducive to nanobody VHH secretion. Among our highest-ranking candidates are a slew of previously unknown targets involved in transmembrane transport, amino-acid metabolism and redox regulation. Guided by these findings, we eventually constructed a hyperproducer for multiple proteins via combinatorial engineering of redox-response transcription factors. As the near-universal applicability of CRISPRi technology and the FlAsH-based screening platform, this procedure might be expanded to include a varied variety of microbial species and recombinant proteins.
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Affiliation(s)
- Xinyu Yu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Shuang Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xihao Liao
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Zhonghu Bai
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiuxia Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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The current state of amyloidosis therapeutics and the potential role of fluorine in their treatment. Biochimie 2022; 202:123-135. [PMID: 35963462 DOI: 10.1016/j.biochi.2022.08.003] [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: 02/16/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022]
Abstract
Amyloidosis, commonly known as amyloid-associated diseases, is characterized by improperly folded proteins accumulating in tissues and eventually causing organ damage, which is linked to several disorders ranging from neurodegenerative to peripheral diseases. It has an enormous societal and financial impact on the global health sector. Due to the complexity of protein misfolding and intertwined aggregation, there are no effective disease-modifying medications at present, and the condition is likely mis/non-diagnosed half of the time. Nonetheless, over the last two decades, substantial research into aggregation processes has revealed the possibilities of new intervention approaches. On the other hand, fluorine has been a rising star in therapeutic development for numerous neurodegenerative illnesses and other peripheral diseases. In this study, we revised and emphasized the possible significance of fluorine-modified therapeutic molecules and fluorine-modified nanoparticles (NPs) in the modulation of amyloidogenic proteins, including insulin, amyloid beta peptide (Aβ), prion protein (PrP), transthyretin (TTR) and Huntingtin (htt).
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Skottrup PD, Døssing H, Andersen NW, Buch-Rasmussen L. Nanobody-based microfluidic human Fc assay for preclinical plasma quantification of IgG1/1.1 and IgG1-Fc-conjugates. J Immunol Methods 2022; 502:113214. [PMID: 34998814 DOI: 10.1016/j.jim.2022.113214] [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: 10/15/2021] [Revised: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Therapeutic antibodies and Fc-conjugates are becoming increasingly popular for disease management and accurate and sensitive pharmacokinetic measurements are critical in lead candidate selection in pre-clinical drug discovery. METHODS AND STUDY DESIGN Human Fc-specific intact monoclonal antibodies, polyclonal antibodies, Fab fragments, aptamers, affibodies and nanobodies were screened for potential as biotinylated capture moieties in a microfluidic assay. Test compounds were Bevacizumab, Rituximab, Infliximab as well as an in-house IgG1.1 and an IgG1-drug conjugate. RESULTS Capture molecules were tested for specificity in plasma matrices from beagle dog, rat, mouse, pig, rhesus monkey and cynomolgus monkey. We find that the llama nanobody provides the best selectivity across across species. The assay usability were verified in cynomolgus monkey pharmacokinetic studies of in-house IgG1.1 and IgG1-fusion molecules. CONCLUSION The presented generic nanobody-based assay may find relevance in preclinical testing of future human Fc-containing drug conjugates devoid of Fab fragments and intact monoclonal antibodies.
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Affiliation(s)
- Peter Durand Skottrup
- Novo Nordisk A/S, Global Research Technologies, Research Bioanalysis, Novo Nordisk Park, DK-2760 Måløv, Denmark.
| | - Holger Døssing
- Novo Nordisk A/S, Global Research Technologies, Research Bioanalysis, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Natasja Weismann Andersen
- Novo Nordisk A/S, Global Research Technologies, Research Bioanalysis, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Linda Buch-Rasmussen
- Novo Nordisk A/S, Global Research Technologies, Research Bioanalysis, Novo Nordisk Park, DK-2760 Måløv, Denmark
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Soleimanizadeh A, Dinter H, Schindowski K. Central Nervous System Delivery of Antibodies and Their Single-Domain Antibodies and Variable Fragment Derivatives with Focus on Intranasal Nose to Brain Administration. Antibodies (Basel) 2021; 10:antib10040047. [PMID: 34939999 PMCID: PMC8699001 DOI: 10.3390/antib10040047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
IgG antibodies are some of the most important biopharmaceutical molecules with a high market volume. In spite of the fact that clinical therapies with antibodies are broadly utilized in oncology, immunology and hematology, their delivery strategies and biodistribution need improvement, their limitations being due to their size and poor ability to penetrate into tissues. In view of their small size, there is a rising interest in derivatives, such as single-domain antibodies and single-chain variable fragments, for clinical diagnostic but also therapeutic applications. Smaller antibody formats combine several benefits for clinical applications and can be manufactured at reduced production costs compared with full-length IgGs. Moreover, such formats have a relevant potential for targeted drug delivery that directs drug cargo to a specific tissue or across the blood–brain barrier. In this review, we give an overview of the challenges for antibody drug delivery in general and focus on intranasal delivery to the central nervous system with antibody formats of different sizes.
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Affiliation(s)
- Arghavan Soleimanizadeh
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Faculty of Medicine, University of Ulm, 89081 Ulm, Germany
| | - Heiko Dinter
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Department of Pharmacy and Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Katharina Schindowski
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Correspondence:
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Kulkarni SS, Falzarano D. Unique aspects of adaptive immunity in camelids and their applications. Mol Immunol 2021; 134:102-108. [PMID: 33751993 DOI: 10.1016/j.molimm.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/21/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023]
Abstract
Members of the Camelidae have unique adaptive immunological features that are not widely observed in other species. All camelids are known to have three distinct IgG isotypes - IgG1, IgG2 and IgG3. While IgG1 has a conventional antibody structure, both IgG2 and IgG3 are devoid of light chains and instead possess hypervariable regions in their heavy chain (VHH), while lacking the typical CH1 domain found in heavy chains. VHH domains are increasingly being utilized as "next generation" antibodies, as they have unique biochemical and structural properties including high pH stability as well as a lower molecular weight allowing for increased tissue penetration. These features of VHH domains offer a number of advantages for both biotechnology and clinical applications and are commonly termed "nanobodies". A second unique aspect of the camelid adaptive response is involves T cell-mediated immunity. Characterization of gamma delta (ꝩδ) T cells in camelid species has found they use somatic hypermutation in their T cell receptor gamma (TRG) and delta (TRD) loci to increase the structural stability of their ꝩδ T receptor. The use of somatic hyper mutation to increase the diversity of their T cell repertoire, is a feature that has not been observed in other mammalian species. In addition, in alpacas there is a unique subset of ꝩδ T cells called Vꝩ9Vδ2 T cells. Activation of these cells is dependent upon phosphoantigen (PAg)-mediated interaction with B7-like butyrophilin molecules (BTN-3). This makes alpacas the first species outside of primates to be identified with this unique subset and activation mechanism. Here we review some fundamentals of camelid adaptive immunity that make them distinct from other vertebrate species and their potential applications to human therapies.
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Affiliation(s)
- Swarali S Kulkarni
- Vaccine and Infectious Disease Organization and Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization and Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
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Vettore N, Moray J, Brans A, Herman R, Charlier P, Kumita JR, Kerff F, Dobson CM, Dumoulin M. Characterisation of the structural, dynamic and aggregation properties of the W64R amyloidogenic variant of human lysozyme. Biophys Chem 2021; 271:106563. [PMID: 33640796 DOI: 10.1016/j.bpc.2021.106563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
The accumulation in vital organs of amyloid fibrils made of mutational variants of lysozyme (HuL) is associated with a human systemic amyloid disease. The detailed comparison of the in vitro properties of the I56T and D67H amyloidogenic variants to those of the T70N non-amyloidogenic variant and the wild-type (WT) protein suggested that the deposition of large amounts of aggregated disease-related lysozyme variants is initiated by the formation of transient intermediate species. The ability to populate such intermediates is essentially due to the destabilisation of the protein and the loss of the global structural cooperativity under physiologically relevant conditions. Here, we report the characterisation of a third naturally occurring amyloidogenic lysozyme variant, W64R, in comparison with the I56T and WT proteins. The X-ray crystal structure of the W64R variant at 1.15 Å resolution is very similar to that of the WT protein; a few interactions within the β-domain and at the interface between the α- and β-domains differ, however, from those in the WT protein. Consequently, the W64R mutation destabilizes the protein to an extent that is similar to that observed for the I56T and D67H mutations. The ΔG°NU(H2O) is reduced by 24 kJ·mol-1 and the Tm is about 12 °C lower than that of the WT protein. Under native conditions, the W64R and I56T proteins are readily digested by proteinase K, while the WT protein remains intact. These results suggest that the two variant proteins transiently populate similar partially unfolded states in which proteinase K cleavage sites are accessible to the protease. Moreover, the in vitro aggregation properties of the W64R protein are similar to those of the I56T variant. Altogether, these results indicate that the properties of the W64R protein are astonishingly similar to those of the I56T variant. They further corroborate the idea that HuL variants associated with the disease are those whose stability and global structural cooperativity are sufficiently reduced to allow the formation of aggregation prone partially folded intermediates under physiological conditions.
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Affiliation(s)
- Nicola Vettore
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Joël Moray
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Alain Brans
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Raphaël Herman
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Paulette Charlier
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Janet R Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Frédéric Kerff
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mireille Dumoulin
- Centre for Protein Engineering, InBioS, Department of Life Sciences, University of Liège, (Sart-Tilman) 4000 Liège, Belgium.
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Scafi M, Valleix S, Benyamine A, Jean E, Harlé JR, Rossi P, Daniel L, Schleinitz N, Granel B. L’amylose à lysozyme. Rev Med Interne 2019; 40:323-329. [DOI: 10.1016/j.revmed.2018.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/29/2018] [Indexed: 11/25/2022]
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El Turk F, De Genst E, Guilliams T, Fauvet B, Hejjaoui M, Di Trani J, Chiki A, Mittermaier A, Vendruscolo M, Lashuel HA, Dobson CM. Exploring the role of post-translational modifications in regulating α-synuclein interactions by studying the effects of phosphorylation on nanobody binding. Protein Sci 2019; 27:1262-1274. [PMID: 29603451 DOI: 10.1002/pro.3412] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Abstract
Intracellular deposits of α-synuclein in the form of Lewy bodies are major hallmarks of Parkinson's disease (PD) and a range of related neurodegenerative disorders. Post-translational modifications (PTMs) of α-synuclein are increasingly thought to be major modulators of its structure, function, degradation and toxicity. Among these PTMs, phosphorylation near the C-terminus at S129 has emerged as a dominant pathogenic modification as it is consistently observed to occur within the brain and cerebrospinal fluid (CSF) of post-mortem PD patients, and its level appears to correlate with disease progression. Phosphorylation at the neighboring tyrosine residue Y125 has also been shown to protect against α-synuclein toxicity in a Drosophila model of PD. In the present study we address the potential roles of C-terminal phosphorylation in modulating the interaction of α-synuclein with other protein partners, using a single domain antibody fragment (NbSyn87) that binds to the C-terminal region of α-synuclein with nanomolar affinity. The results reveal that phosphorylation at S129 has negligible effect on the binding affinity of NbSyn87 to α-synuclein while phosphorylation at Y125, only four residues away, decreases the binding affinity by a factor of 400. These findings show that, despite the fact that α-synuclein is intrinsically disordered in solution, selective phosphorylation can modulate significantly its interactions with other molecules and suggest how this particular form of modification could play a key role in regulating the normal and aberrant function of α-synuclein.
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Affiliation(s)
- Farah El Turk
- Centre for Mosfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom.,Department of Chemistry, McGill University, Montreal, Quebec, H3A 2K6, Canada
| | - Erwin De Genst
- Centre for Mosfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Tim Guilliams
- Centre for Mosfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Bruno Fauvet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH 1015, Switzerland
| | - Mirva Hejjaoui
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH 1015, Switzerland
| | - Justin Di Trani
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 2K6, Canada
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH 1015, Switzerland
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 2K6, Canada
| | - Michele Vendruscolo
- Centre for Mosfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH 1015, Switzerland
| | - Christopher M Dobson
- Centre for Mosfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
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Kim DY, Kandalaft H, Hussack G, Raphael S, Ding W, Kelly JF, Henry KA, Tanha J. Evaluation of a noncanonical Cys40-Cys55 disulfide linkage for stabilization of single-domain antibodies. Protein Sci 2019; 28:881-888. [PMID: 30803088 DOI: 10.1002/pro.3595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/01/2019] [Accepted: 02/21/2019] [Indexed: 12/27/2022]
Abstract
Incorporation of noncanonical disulfide linkages into single-domain antibodies (sdAbs) has been shown to enhance thermostability and other properties. Here, we evaluated the effects of introducing a novel disulfide linkage formed between Cys residues at IMGT positions 40 and 55 on the melting temperatures (T m s), reversibility of thermal unfolding, solubility, and antigen-binding affinities of three types of sdAbs (VH H, VH , and VL domains). The Cys40-Cys55 disulfide linkage was tolerated by 9/9 VH Hs, 12/12 VH s, and 2/11 VL s tested and its formation was confirmed by mass spectrometry. Using circular dichroism, we found that the Cys40-Cys55 disulfide linkage increased sdAb T m by an average of 10.0°C (range: 0-21.8°C). However, enhanced thermostability came at the cost of a partial loss of refolding ability upon thermal denaturation as well as, for some sdAbs, significantly decreased solubility and antigen-binding affinity. Thus, Cys40/Cys55 can be added to the panel of known locations for introducing stabilizing noncanonical disulfide linkages into antibody variable domains, although its effects should be tested empirically for individual sdAbs.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Hiba Kandalaft
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Shalini Raphael
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Wen Ding
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - John F Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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Ali A, Baby B, Vijayan R. From Desert to Medicine: A Review of Camel Genomics and Therapeutic Products. Front Genet 2019; 10:17. [PMID: 30838017 PMCID: PMC6389616 DOI: 10.3389/fgene.2019.00017] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Camels have an important role in the lives of human beings, especially in arid regions, due to their multipurpose role and unique ability to adapt to harsh conditions. In spite of its enormous economic, cultural, and biological importance, the camel genome has not been widely studied. The size of camel genome is roughly 2.38 GB, containing over 20,000 genes. The unusual genetic makeup of the camel is the main reason behind its ability to survive under extreme environmental conditions. The camel genome harbors several unique variations which are being investigated for the treatment of several disorders. Various natural products from camels have also been tested and prescribed as adjunct therapy to control the progression of ailments. Interestingly, the camel employs unique immunological and molecular mechanisms against pathogenic agents and pathological conditions. Here, we broadly review camel classification, distribution and breed as well as recent progress in the determination of the camel genome, its size, genetic distribution, response to various physiological conditions, immunogenetics and the medicinal potential of camel gene products.
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Affiliation(s)
| | | | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
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12
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Giorgetti S, Greco C, Tortora P, Aprile FA. Targeting Amyloid Aggregation: An Overview of Strategies and Mechanisms. Int J Mol Sci 2018; 19:E2677. [PMID: 30205618 PMCID: PMC6164555 DOI: 10.3390/ijms19092677] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/02/2018] [Accepted: 09/05/2018] [Indexed: 12/26/2022] Open
Abstract
Amyloids result from the aggregation of a set of diverse proteins, due to either specific mutations or promoting intra- or extra-cellular conditions. Structurally, they are rich in intermolecular β-sheets and are the causative agents of several diseases, both neurodegenerative and systemic. It is believed that the most toxic species are small aggregates, referred to as oligomers, rather than the final fibrillar assemblies. Their mechanisms of toxicity are mostly mediated by aberrant interactions with the cell membranes, with resulting derangement of membrane-related functions. Much effort is being exerted in the search for natural antiamyloid agents, and/or in the development of synthetic molecules. Actually, it is well documented that the prevention of amyloid aggregation results in several cytoprotective effects. Here, we portray the state of the art in the field. Several natural compounds are effective antiamyloid agents, notably tetracyclines and polyphenols. They are generally non-specific, as documented by their partially overlapping mechanisms and the capability to interfere with the aggregation of several unrelated proteins. Among rationally designed molecules, we mention the prominent examples of β-breakers peptides, whole antibodies and fragments thereof, and the special case of drugs with contrasting transthyretin aggregation. In this framework, we stress the pivotal role of the computational approaches. When combined with biophysical methods, in several cases they have helped clarify in detail the protein/drug modes of interaction, which makes it plausible that more effective drugs will be developed in the future.
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Affiliation(s)
- Sofia Giorgetti
- Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Via Taramelli 3b, 27100 Pavia, Italy.
| | - Claudio Greco
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy.
| | - Paolo Tortora
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
- Milan Center for Neuroscience (Neuro-MI), 20126 Milano, Italy.
| | - Francesco Antonio Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV. J Virol 2018; 92:JVI.00837-18. [PMID: 29950421 PMCID: PMC6146697 DOI: 10.1128/jvi.00837-18] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 12/22/2022] Open
Abstract
Therapeutic development is critical for preventing and treating continual MERS-CoV infections in humans and camels. Because of their small size, nanobodies (Nbs) have advantages as antiviral therapeutics (e.g., high expression yield and robustness for storage and transportation) and also potential limitations (e.g., low antigen-binding affinity and fast renal clearance). Here, we have developed novel Nbs that specifically target the receptor-binding domain (RBD) of MERS-CoV spike protein. They bind to a conserved site on MERS-CoV RBD with high affinity, blocking RBD's binding to MERS-CoV receptor. Through engineering a C-terminal human Fc tag, the in vivo half-life of the Nbs is significantly extended. Moreover, the Nbs can potently cross-neutralize the infections of diverse MERS-CoV strains isolated from humans and camels. The Fc-tagged Nb also completely protects humanized mice from lethal MERS-CoV challenge. Taken together, our study has discovered novel Nbs that hold promise as potent, cost-effective, and broad-spectrum anti-MERS-CoV therapeutic agents. The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) continues to infect humans and camels, calling for efficient, cost-effective, and broad-spectrum strategies to control its spread. Nanobodies (Nbs) are single-domain antibodies derived from camelids and sharks and are potentially cost-effective antivirals with small size and great expression yield. In this study, we developed a novel neutralizing Nb (NbMS10) and its human-Fc-fused version (NbMS10-Fc), both of which target the MERS-CoV spike protein receptor-binding domain (RBD). We further tested their receptor-binding affinity, recognizing epitopes, cross-neutralizing activity, half-life, and efficacy against MERS-CoV infection. Both Nbs can be expressed in yeasts with high yield, bind to MERS-CoV RBD with high affinity, and block the binding of MERS-CoV RBD to the MERS-CoV receptor. The binding site of the Nbs on the RBD was mapped to be around residue Asp539, which is part of a conserved conformational epitope at the receptor-binding interface. NbMS10 and NbMS10-Fc maintained strong cross-neutralizing activity against divergent MERS-CoV strains isolated from humans and camels. Particularly, NbMS10-Fc had significantly extended half-life in vivo; a single-dose treatment of NbMS10-Fc exhibited high prophylactic and therapeutic efficacy by completely protecting humanized mice from lethal MERS-CoV challenge. Overall, this study proves the feasibility of producing cost-effective, potent, and broad-spectrum Nbs against MERS-CoV and has produced Nbs with great potentials as anti-MERS-CoV therapeutics. IMPORTANCE Therapeutic development is critical for preventing and treating continual MERS-CoV infections in humans and camels. Because of their small size, nanobodies (Nbs) have advantages as antiviral therapeutics (e.g., high expression yield and robustness for storage and transportation) and also potential limitations (e.g., low antigen-binding affinity and fast renal clearance). Here, we have developed novel Nbs that specifically target the receptor-binding domain (RBD) of MERS-CoV spike protein. They bind to a conserved site on MERS-CoV RBD with high affinity, blocking RBD's binding to MERS-CoV receptor. Through engineering a C-terminal human Fc tag, the in vivo half-life of the Nbs is significantly extended. Moreover, the Nbs can potently cross-neutralize the infections of diverse MERS-CoV strains isolated from humans and camels. The Fc-tagged Nb also completely protects humanized mice from lethal MERS-CoV challenge. Taken together, our study has discovered novel Nbs that hold promise as potent, cost-effective, and broad-spectrum anti-MERS-CoV therapeutic agents.
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14
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Abstract
Single-domain antibodies (sdAbs), the autonomous variable domains of heavy chain-only antibodies produced naturally by camelid ungulates and cartilaginous fishes, have evolved to bind antigen using only three complementarity-determining region (CDR) loops rather than the six present in conventional VH:VL antibodies. It has been suggested, based on limited evidence, that sdAbs may adopt paratope structures that predispose them to preferential recognition of recessed protein epitopes, but poor or non-recognition of protuberant epitopes and small molecules. Here, we comprehensively surveyed the evidence in support of this hypothesis. We found some support for a global structural difference in the paratope shapes of sdAbs compared with those of conventional antibodies: sdAb paratopes have smaller molecular surface areas and diameters, more commonly have non-canonical CDR1 and CDR2 structures, and have elongated CDR3 length distributions, but have similar amino acid compositions and are no more extended (interatomic distance measured from CDR base to tip) than conventional antibody paratopes. Comparison of X-ray crystal structures of sdAbs and conventional antibodies in complex with cognate antigens showed that sdAbs and conventional antibodies bury similar solvent-exposed surface areas on proteins and form similar types of non-covalent interactions, although these are more concentrated in the compact sdAb paratope. Thus, sdAbs likely have privileged access to distinct antigenic regions on proteins, but only owing to their small molecular size and not to general differences in molecular recognition mechanism. The evidence surrounding the purported inability of sdAbs to bind small molecules was less clear. The available data provide a structural framework for understanding the evolutionary emergence and function of autonomous heavy chain-only antibodies.
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Affiliation(s)
- Kevin A Henry
- a Human Health Therapeutics Research Centre , National Research Council Canada , Ottawa , Ontario , Canada
| | - C Roger MacKenzie
- a Human Health Therapeutics Research Centre , National Research Council Canada , Ottawa , Ontario , Canada.,b School of Environmental Sciences , University of Guelph , Guelph , Ontario , Canada
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15
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Griffin JWD, Bradshaw PC. In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme. BMC STRUCTURAL BIOLOGY 2018; 18:9. [PMID: 30029603 PMCID: PMC6053722 DOI: 10.1186/s12900-018-0088-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
Background Amyloidogenic proteins are most often associated with neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, but there are more than two dozen human proteins known to form amyloid fibrils associated with disease. Lysozyme is an antimicrobial protein that is used as a general model to study amyloid fibril formation. Studies aimed at elucidating the process of amyloid formation of lysozyme tend to focus on partial unfolding of the native state due to the relative instability of mutant amyloidogenic variants. While this is well supported, the data presented here suggest the native structure of the variants may also play a role in primary nucleation. Results Three-dimensional structural analysis identified lysozyme residues 21, 62, 104, and 122 as displaced in both amyloidogenic variants compared to wild type lysozyme. Residue interaction network (RIN) analysis found greater clustering of residues 112–117 in amyloidogenic variants of lysozyme compared to wild type. An analysis of the most energetically favored predicted dimers and trimers provided further evidence for a role for residues 21, 62, 104, 122, and 112–117 in amyloid formation. Conclusions This study used lysozyme as a model to demonstrate the utility of combining 3D structural analysis with RIN analysis for studying the general process of amyloidogenesis. Results indicated that binding of two or more amyloidogenic lysozyme mutants may be involved in amyloid nucleation by placing key residues (21, 62, 104, 122, and 112–117) in proximity before partial unfolding occurs. Identifying residues in the native state that may be involved in amyloid formation could provide novel drug targets to prevent a range of amyloidoses.
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Affiliation(s)
- Jeddidiah W D Griffin
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
| | - Patrick C Bradshaw
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
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16
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He T, Zhu J, Nie Y, Hu R, Wang T, Li P, Zhang Q, Yang Y. Nanobody Technology for Mycotoxin Detection in the Field of Food Safety: Current Status and Prospects. Toxins (Basel) 2018; 10:E180. [PMID: 29710823 PMCID: PMC5983236 DOI: 10.3390/toxins10050180] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 01/18/2023] Open
Abstract
Mycotoxins, which are toxic, carcinogenic, and/or teratogenic, have posed a threat to food safety and public health. Sensitive and effective determination technologies for mycotoxin surveillance are required. Immunoassays have been regarded as useful supplements to chromatographic techniques. However, conventional antibodies involved in immunoassays are difficult to be expressed recombinantly and are susceptible to harsh environments. Nanobodies (or VHH antibodies) are antigen-binding sites of the heavy-chain antibodies produced from Camelidae. They are found to be expressed easily in prokaryotic or eukaryotic expression systems, more robust in extreme conditions, and facile to be used as surrogates for artificial antigens. These properties make them the promising and environmentally friendly immunoreagents in the next generation of immunoassays. This review briefly describes the latest developments in the area of nanobodies used in mycotoxin detection. Moreover, by integrating the introduction of the principle of nanobodies production and the critical assessment of their performance, this paper also proposes the prospect of nanobodies in the field of food safety in the foreseeable future.
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Affiliation(s)
- Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Ting Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Peiwu Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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17
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Liu JL, Shriver-Lake LC, Anderson GP, Zabetakis D, Goldman ER. Selection, characterization, and thermal stabilization of llama single domain antibodies towards Ebola virus glycoprotein. Microb Cell Fact 2017; 16:223. [PMID: 29233140 PMCID: PMC5726015 DOI: 10.1186/s12934-017-0837-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/28/2017] [Indexed: 12/26/2022] Open
Abstract
Background A key advantage of recombinant antibody technology is the ability to optimize and tailor reagents. Single domain antibodies (sdAbs), the recombinantly produced variable domains derived from camelid and shark heavy chain antibodies, provide advantages of stability and solubility and can be further engineered to enhance their properties. In this study, we generated sdAbs specific for Ebola virus envelope glycoprotein (GP) and increased their stability to expand their utility for use in austere locals. Ebola virus is extremely virulent and causes fatal hemorrhagic fever in ~ 50 percent of the cases. The viral GP binds to host cell receptors to facilitate viral entry and thus plays a critical role in pathogenicity. Results An immune phage display library containing more than 107 unique clones was developed from a llama immunized with a combination of killed Ebola virus and recombinantly produced GP. We panned the library to obtain GP binding sdAbs and isolated sdAbs from 5 distinct sequence families. Three GP binders with dissociation constants ranging from ~ 2 to 20 nM, and melting temperatures from ~ 57 to 72 °C were selected for protein engineering in order to increase their stability through a combination of consensus sequence mutagenesis and the addition of a non-canonical disulfide bond. These changes served to increase the melting temperatures of the sdAbs by 15–17 °C. In addition, fusion of a short positively charged tail to the C-terminus which provided ideal sites for the chemical modification of these sdAbs resulted in improved limits of detection of GP and Ebola virus like particles while serving as tracer antibodies. Conclusions SdAbs specific for Ebola GP were selected and their stability and functionality were improved utilizing protein engineering. Thermal stability of antibody reagents may be of particular importance when operating in austere locations that lack reliable refrigeration. Future efforts can evaluate the potential of these isolated sdAbs as candidates for diagnostic or therapeutic applications for Ebola. Electronic supplementary material The online version of this article (10.1186/s12934-017-0837-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinny L Liu
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Lisa C Shriver-Lake
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - George P Anderson
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Dan Zabetakis
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Ellen R Goldman
- US Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, 4555 Overlook Ave SW, Washington, DC, 20375, USA.
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18
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Henry KA, Kandalaft H, Lowden MJ, Rossotti MA, van Faassen H, Hussack G, Durocher Y, Kim DY, Tanha J. A disulfide-stabilized human V L single-domain antibody library is a source of soluble and highly thermostable binders. Mol Immunol 2017; 90:190-196. [PMID: 28820969 DOI: 10.1016/j.molimm.2017.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/18/2022]
Abstract
We have previously shown that incorporation of a second intradomain disulfide linkage into camelid VHH and human VH/VL single-domain antibodies confers increased thermostability. Here, we explored the effects of introducing an additional disulfide linkage, formed between Cys48 and Cys64 (Kabat numbering), into a phage-displayed synthetic human VL library. In comparison to an identical library bearing only the highly conserved Cys23-Cys88 disulfide linkage, the disulfide-stabilized VL library tolerated a similar degree of randomization but retained a higher level of functional diversity after selection with protein L. Both libraries yielded soluble, antigen-specific VLs that recognized a model antigen (maltose-binding protein) with similar affinities, in the micromolar range; however, the disulfide-stabilized antigen-specific VLs were much more thermostable (average ΔTm ∼10°C) than non-disulfide-stabilized VLs. This work provides proof-of-concept for building synthetic antibody libraries using disulfide-constrained immunoglobulin domains, thus avoiding pitfalls of post-hoc disulfide linkage engineering such as impaired antigen binding and reduced expression yield.
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Affiliation(s)
- Kevin A Henry
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Hiba Kandalaft
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Michael J Lowden
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Martin A Rossotti
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Henk van Faassen
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Yves Durocher
- Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Royalmount Avenue, Montréal, Québec, H4P 2R2, Canada
| | - Dae Young Kim
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada; School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
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19
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Goldman ER, Liu JL, Zabetakis D, Anderson GP. Enhancing Stability of Camelid and Shark Single Domain Antibodies: An Overview. Front Immunol 2017; 8:865. [PMID: 28791022 PMCID: PMC5524736 DOI: 10.3389/fimmu.2017.00865] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/07/2017] [Indexed: 11/13/2022] Open
Abstract
Single domain antibodies (sdAbs) are gaining a reputation as superior recognition elements as they combine the advantages of the specificity and affinity found in conventional antibodies with high stability and solubility. Melting temperatures (Tms) of sdAbs cover a wide range from below 50 to over 80°C. Many sdAbs have been engineered to increase their Tm, making them stable until exposed to extreme temperatures. SdAbs derived from the variable heavy chains of camelid and shark heavy chain-only antibodies are termed VHH and VNAR, respectively, and generally exhibit some ability to refold and bind antigen after heat denaturation. This ability to refold varies from 0 to 100% and is a property dependent on both intrinsic factors of the sdAb and extrinsic conditions such as the sample buffer ionic strength, pH, and sdAb concentration. SdAbs have also been engineered to increase their solubility and refolding ability, which enable them to function even after exposure to temperatures that exceed their melting point. In addition, efforts to improve their stability at extreme pH and in the presence of chemical denaturants or proteases have been undertaken. Multiple routes have been employed to engineer sdAbs with these enhanced stabilities. The methods utilized to achieve these goals include grafting complementarity-determining regions onto stable frameworks, introduction of non-canonical disulfide bonds, random mutagenesis combined with stringent selection, point mutations such as inclusion of negative charges, and genetic fusions. Increases of up to 20°C have been realized, pushing the Tm of some sdAbs to over 90°C. Herein, we present an overview of the work done to stabilize sdAbs derived from camelids and sharks. Utilizing these various strategies sdAbs have been stabilized without significantly compromising their affinity, thereby providing superior reagents for detection, diagnostic, and therapeutic applications.
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Affiliation(s)
- Ellen R Goldman
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - Jinny L Liu
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - Dan Zabetakis
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
| | - George P Anderson
- Center for BioMolecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States
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20
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Skottrup PD. Structural insights into a high affinity nanobody:antigen complex by homology modelling. J Mol Graph Model 2017; 76:305-312. [PMID: 28779687 DOI: 10.1016/j.jmgm.2017.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 12/30/2022]
Abstract
Porphyromonas gingivalis is a major periodontitis-causing pathogens. P. gingivalis secrete a cysteine protease termed RgpB, which is specific for Arg-Xaa bonds in substrates. Recently, a nanobody-based assay was used to demonstrate that RgpB could represent a novel diagnostic target, thereby simplifying. P. gingivalis detection. The nanobody, VHH7, had a high binding affinity and was specific for RgpB, when tested towards the highly identical RgpA. In this study a homology model of VHH7 was build. The complementarity determining regions (CDR) comprising the paratope residues responsible for RgpB binding were identified and used as input to the docking. Furthermore, residues likely involved in the RgpB epitope was identified based upon RgpB:RgpA alignment and analysis of residue surface accessibility. CDR residues and putitative RgpB epitope residues were used as input to an information-driven flexible docking approach using the HADDOCK server. Analysis of the VHH7:RgpB model demonstrated that the epitope was found in the immunoglobulin-like domain and residue pairs located at the molecular paratope:epitope interface important for complex stability was identified. Collectively, the VHH7 homology model and VHH7:RgpB docking supplies knowledge of the residues involved in the high affinity interaction. This information could prove valuable in the design of an antibody-drug conjugate for specific RgpB targeting.
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Affiliation(s)
- Peter Durand Skottrup
- Department of Clinical Biochemistry, Copenhagen University Hospital, Kettegård Alle 30, DK-2650 Hvidovre, Denmark.
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21
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Ahn M, Hagan CL, Bernardo-Gancedo A, De Genst E, Newby FN, Christodoulou J, Dhulesia A, Dumoulin M, Robinson CV, Dobson CM, Kumita JR. The Significance of the Location of Mutations for the Native-State Dynamics of Human Lysozyme. Biophys J 2017; 111:2358-2367. [PMID: 27926837 PMCID: PMC5153563 DOI: 10.1016/j.bpj.2016.10.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 11/27/2022] Open
Abstract
The conversion of human lysozyme into amyloid fibrils is associated with a rare but fatal hereditary form of nonneuropathic systemic amyloidosis. The accumulation of large amounts of aggregated protein is thought to be initiated by the formation of transient intermediate species of disease-related lysozyme variants, essentially due to the loss of global cooperativity under physiologically relevant conditions. Interestingly, all five naturally occurring, amyloidogenic, single-point mutations are located in the β-domain of lysozyme, the region that is predominantly unfolded during the formation of the transient intermediate species. Given the lack of known naturally occurring, amyloidogenic, single-point mutations in the α-domain, we chose three specific mutations to address the effects that location may have on native-state dynamics, as studied by hydrogen-deuterium (HD) exchange experiments analyzed by NMR spectroscopy, and mass spectrometry. We compared the effect of a destabilizing α-domain mutation (I23A) with that of the well-characterized I59T β-domain variant. We also investigated the effect of a mutation that has minor effects on native-state stability at the domain interface (I56V) and compared it with that of a variant with similar stability within the C-helix (I89V). We show that when variants have similar reduced native-state stabilities, the location of the mutation (I23A versus I59T) is crucial to the native-state dynamics, with the α-domain mutation having a significantly lower ability to populate transient intermediate species under physiologically relevant conditions. Interestingly, the mutation at the interface (I56V) has a greater effect in facilitating the formation of transient intermediate species at elevated temperatures compared with the variants containing α-domain mutations, even though this mutation results in only minor changes to the native-state stability of lysozyme. These findings reveal that the location of specific mutations is an important factor in determining the native-state dynamical properties of human lysozyme in the context of its propensity to populate the aggregation-prone transient intermediate species associated with pathogenic amyloid formation.
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Affiliation(s)
- Minkoo Ahn
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Christine L Hagan
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francisco N Newby
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, United Kingdom
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBios, Institute of Chemistry, University of Liege, Liege (Sart Tilman), Belgium
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Janet R Kumita
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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Ankarcrona M, Winblad B, Monteiro C, Fearns C, Powers ET, Johansson J, Westermark GT, Presto J, Ericzon BG, Kelly JW. Current and future treatment of amyloid diseases. J Intern Med 2016; 280:177-202. [PMID: 27165517 PMCID: PMC4956553 DOI: 10.1111/joim.12506] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There are more than 30 human proteins whose aggregation appears to cause degenerative maladies referred to as amyloid diseases or amyloidoses. These disorders are named after the characteristic cross-β-sheet amyloid fibrils that accumulate systemically or are localized to specific organs. In most cases, current treatment is limited to symptomatic approaches and thus disease-modifying therapies are needed. Alzheimer's disease is a neurodegenerative disorder with extracellular amyloid β-peptide (Aβ) fibrils and intracellular tau neurofibrillary tangles as pathological hallmarks. Numerous clinical trials have been conducted with passive and active immunotherapy, and small molecules to inhibit Aβ formation and aggregation or to enhance Aβ clearance; so far such clinical trials have been unsuccessful. Novel strategies are therefore required and here we will discuss the possibility of utilizing the chaperone BRICHOS to prevent Aβ aggregation and toxicity. Type 2 diabetes mellitus is symptomatically treated with insulin. However, the underlying pathology is linked to the aggregation and progressive accumulation of islet amyloid polypeptide as fibrils and oligomers, which are cytotoxic. Several compounds have been shown to inhibit islet amyloid aggregation and cytotoxicity in vitro. Future animal studies and clinical trials have to be conducted to determine their efficacy in vivo. The transthyretin (TTR) amyloidoses are a group of systemic degenerative diseases compromising multiple organ systems, caused by TTR aggregation. Liver transplantation decreases the generation of misfolded TTR and improves the quality of life for a subgroup of this patient population. Compounds that stabilize the natively folded, nonamyloidogenic, tetrameric conformation of TTR have been developed and the drug tafamidis is available as a promising treatment.
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Affiliation(s)
- M Ankarcrona
- Department of Neurobiology Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - B Winblad
- Department of Neurobiology Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - C Monteiro
- Department of Chemistry, The Skaggs Institute for Chemical Biology, La Jolla, CA, USA.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - C Fearns
- Department of Chemistry, The Skaggs Institute for Chemical Biology, La Jolla, CA, USA.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - E T Powers
- Department of Chemistry, The Skaggs Institute for Chemical Biology, La Jolla, CA, USA
| | - J Johansson
- Department of Neurobiology Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - G T Westermark
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - J Presto
- Department of Neurobiology Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - B-G Ericzon
- Division of Transplantation Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - J W Kelly
- Department of Chemistry, The Skaggs Institute for Chemical Biology, La Jolla, CA, USA.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
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Leung WH, So PK, Wong WT, Lo WH, Chan PH. Ethylenediamine-modified amyloid fibrils of hen lysozyme with stronger adsorption capacity as rapid nano-biosorbents for removal of chromium(vi) ions. RSC Adv 2016. [DOI: 10.1039/c6ra15238d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The development of amine-fortified amyloid fibrils of hen lysozyme as biosorbents for Cr(vi) removal is reported. Through –COO−/ethylenediamine conjugation, the nanofibers have higher net positive charge, offering rapid and stronger charge-based absorption of Cr(vi).
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Affiliation(s)
- Wai-Hong Leung
- State Key Laboratory of Chirosciences
- Department of Applied Biology and Chemical Technology
- The Hong Kong Polytechnic University
- Kowloon
- P. R. China
| | - Pui-Kin So
- State Key Laboratory of Chirosciences
- Department of Applied Biology and Chemical Technology
- The Hong Kong Polytechnic University
- Kowloon
- P. R. China
| | - Wai-Ting Wong
- State Key Laboratory of Chirosciences
- Department of Applied Biology and Chemical Technology
- The Hong Kong Polytechnic University
- Kowloon
- P. R. China
| | - Wai-Hung Lo
- State Key Laboratory of Chirosciences
- Department of Applied Biology and Chemical Technology
- The Hong Kong Polytechnic University
- Kowloon
- P. R. China
| | - Pak-Ho Chan
- State Key Laboratory of Chirosciences
- Department of Applied Biology and Chemical Technology
- The Hong Kong Polytechnic University
- Kowloon
- P. R. China
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24
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Yim SS, Choi JW, Lee RJ, Lee YJ, Lee SH, Kim SY, Jeong KJ. Development of a new platform for secretory production of recombinant proteins inCorynebacterium glutamicum. Biotechnol Bioeng 2015; 113:163-72. [DOI: 10.1002/bit.25692] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/23/2015] [Accepted: 06/22/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Sung Sun Yim
- Department of Chemical and Biomolecular Engineering; BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
| | - Jae Woong Choi
- Department of Chemical and Biomolecular Engineering; BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
| | - Roo Jin Lee
- Department of Chemical and Biomolecular Engineering; BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
| | - Yong Jae Lee
- Department of Chemical and Biomolecular Engineering; BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
| | - Se Hwa Lee
- Department of Chemical and Biomolecular Engineering; BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
| | - So Young Kim
- Bio R&D Center; CJ CheilJedang, 92 Gayang-dong, Gangseo-gu; Seoul 175-724 Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering; BK21 Plus program, KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
- Institute for the BioCentury; KAIST, 291 Daehak-ro, Yuseong-gu; Daejeon 305-701 Republic of Korea
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25
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Kaczmarek JZ, Skottrup PD. Selection and characterization of camelid nanobodies towards urokinase-type plasminogen activator. Mol Immunol 2015; 65:384-90. [DOI: 10.1016/j.molimm.2015.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 01/17/2023]
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26
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Pain C, Dumont J, Dumoulin M. Camelid single-domain antibody fragments: Uses and prospects to investigate protein misfolding and aggregation, and to treat diseases associated with these phenomena. Biochimie 2015; 111:82-106. [DOI: 10.1016/j.biochi.2015.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/23/2015] [Indexed: 12/19/2022]
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27
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Liu Z, García-Díaz B, Catacchio B, Chiancone E, Vogel HJ. Protecting Gram-negative bacterial cell envelopes from human lysozyme: Interactions with Ivy inhibitor proteins from Escherichia coli and Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:3032-46. [PMID: 25838125 DOI: 10.1016/j.bbamem.2015.03.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 11/15/2022]
Abstract
Lysozymes play an important role in host defense by degrading peptidoglycan in the cell envelopes of pathogenic bacteria. Several Gram-negative bacteria can evade this mechanism by producing periplasmic proteins that inhibit the enzymatic activity of lysozyme. The Escherichia coli inhibitor of vertebrate lysozyme, Ivyc and its Pseudomonas aeruginosa homolog, Ivyp1 have been shown to be potent inhibitors of hen egg white lysozyme (HEWL). Since human lysozyme (HL) plays an important role in the innate immune response, we have examined the binding of HL to Ivyc and Ivyp1. Our results show that Ivyp1 is a weaker inhibitor of HL than Ivyc even though they inhibit HEWL with similar potency. Calorimetry experiments confirm that Ivyp1 interacts more weakly with HL than HEWL. Analytical ultracentrifugation studies revealed that Ivyp1 in solution is a monomer and forms a 30kDa heterodimer with both HL and HEWL, while Ivyc is a homodimer that forms a tetramer with both enzymes. The interaction of Ivyp1 with HL was further characterized by NMR chemical shift perturbation experiments. In addition to the characteristic His-containing Ivy inhibitory loop that binds into the active site of lysozyme, an extended loop (P2) between the final two beta-strands also participates in forming protein-protein interactions. The P2 loop is not conserved in Ivyc and it constitutes a flexible region in Ivyp1 that becomes more rigid in the complex with HL. We conclude that differences in the electrostatic interactions at the binding interface between Ivy inhibitors and distinct lysozymes determine the strength of this interaction. This article is part of a Special Issue entitled: Bacterial Resistance to Antimicrobial Peptides.
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Affiliation(s)
- Zhihong Liu
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Beatriz García-Díaz
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Bruno Catacchio
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro, 5-00185 Roma, Italy
| | - Emilia Chiancone
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro, 5-00185 Roma, Italy
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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28
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Kim DY, Hussack G, Kandalaft H, Tanha J. Mutational approaches to improve the biophysical properties of human single-domain antibodies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1983-2001. [DOI: 10.1016/j.bbapap.2014.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/05/2014] [Accepted: 07/11/2014] [Indexed: 01/06/2023]
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29
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Kim DY, To R, Kandalaft H, Ding W, van Faassen H, Luo Y, Schrag JD, St-Amant N, Hefford M, Hirama T, Kelly JF, MacKenzie R, Tanha J. Antibody light chain variable domains and their biophysically improved versions for human immunotherapy. MAbs 2014; 6:219-35. [PMID: 24423624 PMCID: PMC3929445 DOI: 10.4161/mabs.26844] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We set out to gain deeper insight into the potential of antibody light chain variable domains (VLs) as immunotherapeutics. To this end, we generated a naïve human VL phage display library and, by using a method previously shown to select for non-aggregating antibody heavy chain variable domains (VHs), we isolated a diversity of VL domains by panning the library against B cell super-antigen protein L. Eight domains representing different germline origins were shown to be non-aggregating at concentrations as high as 450 µM, indicating VL repertoires are a rich source of non-aggregating domains. In addition, the VLs demonstrated high expression yields in E. coli, protein L binding and high reversibility of thermal unfolding. A side-by-side comparison with a set of non-aggregating human VHs revealed that the VLs had similar overall profiles with respect to melting temperature (Tm), reversibility of thermal unfolding and resistance to gastrointestinal proteases. Successful engineering of a non-canonical disulfide linkage in the core of VLs did not compromise the non-aggregation state or protein L binding properties. Furthermore, the introduced disulfide bond significantly increased their Tms, by 5.5–17.5 °C, and pepsin resistance, although it somewhat reduced expression yields and subtly changed the structure of VLs. Human VLs and engineered versions may make suitable therapeutics due to their desirable biophysical features. The disulfide linkage-engineered VLs may be the preferred therapeutic format because of their higher stability, especially for oral therapy applications that necessitate high resistance to the stomach’s acidic pH and pepsin.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Rebecca To
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Hiba Kandalaft
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Wen Ding
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Henk van Faassen
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Yan Luo
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Joseph D Schrag
- Human Health Therapeutics; National Research Council Canada; Montréal, QC Canada
| | - Nadereh St-Amant
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Mary Hefford
- Centre for Vaccine Evaluation; Biologics and Genetic Therapies Directorate;, Health Canada; Ottawa, ON Canada
| | - Tomoko Hirama
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - John F Kelly
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada
| | - Roger MacKenzie
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics; National Research Council Canada; Ottawa, ON Canada; School of Environmental Sciences; Ontario Agricultural College; University of Guelph; Guelph, ON Canada; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa, ON Canada
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30
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De Genst E, Messer A, Dobson CM. Antibodies and protein misfolding: From structural research tools to therapeutic strategies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1907-1919. [PMID: 25194824 DOI: 10.1016/j.bbapap.2014.08.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/21/2014] [Accepted: 08/27/2014] [Indexed: 01/24/2023]
Abstract
Protein misfolding disorders, including the neurodegenerative conditions Alzheimer's disease (AD) and Parkinson's disease (PD) represent one of the major medical challenges or our time. The underlying molecular mechanisms that govern protein misfolding and its links with disease are very complex processes, involving the formation of transiently populated but highly toxic molecular species within the crowded environment of the cell and tissue. Nevertheless, much progress has been made in understanding these events in recent years through innovative experiments and therapeutic strategies, and in this review we present an overview of the key roles of antibodies and antibody fragments in these endeavors. We discuss in particular how these species are being used in combination with a variety of powerful biochemical and biophysical methodologies, including a range of spectroscopic and microscopic techniques applied not just in vitro but also in situ and in vivo, both to gain a better understanding of the mechanistic nature of protein misfolding and aggregation and also to design novel therapeutic strategies to combat the family of diseases with which they are associated. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Affiliation(s)
- Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Anne Messer
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA; Department of Biomedical Sciences, University at Albany, Albany, NY 12208, USA
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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31
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Hagihara Y, Saerens D. Engineering disulfide bonds within an antibody. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2016-2023. [PMID: 25038323 DOI: 10.1016/j.bbapap.2014.07.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/23/2014] [Accepted: 07/09/2014] [Indexed: 01/11/2023]
Abstract
Antibodies have evolved to function in oxidative, extracellular environments. A pair of cysteines in close proximity will oxidatively react to form a disulfide bond that fixes and stabilizes the tertiary structure of a protein. Immunoglobulin G (IgG) includes several disulfide bonds, and the patterns of inter-chain disulfide bonds characterize different IgG sub-classes. Moreover, the Ig-fold domains are characterized by a buried intra-domain disulfide bond, which is important for its structural stability. However, the intra-domain disulfide bond can be replaced without crucial effects on the structure and function, if the domain structure is intrinsically stable or has been stabilized by protein engineering. In previous studies, disulfide bonds were removed by amino-acid substitution indicating that Val and/or Ala (i.e. Ala-Ala, Ala-Val, Val-Ala, and Val-Ala) pairs were preferred for cysteine replacement in the Ig-fold domain. As such, these mutations may be useful for the intracellular use of antibodies. Recently, additional intra-domain disulfide bonds have been shown to stabilize Ig-fold domains and whole IgGs. In heavy chain variable or light chain variable domains, the introduction of additional disulfide bonds into the framework region did not reduce antigen-binding affinity, suggesting that generating disulfide bonds may be a method for stabilizing IgG and antibody fragments, such as the antigen-binding fragment, and single-chain and single-domain antibodies. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Affiliation(s)
- Yoshihisa Hagihara
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka Ikeda, Osaka 563-8577, Japan.
| | - Dirk Saerens
- Vrije Universiteit Brussel, Research Group Cellular & Molecular Immunology, Pleinlaan 2, 1050 Brussels, Belgium
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32
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Lee CC, Perchiacca JM, Tessier PM. Toward aggregation-resistant antibodies by design. Trends Biotechnol 2013; 31:612-20. [DOI: 10.1016/j.tibtech.2013.07.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/30/2013] [Accepted: 07/05/2013] [Indexed: 12/19/2022]
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33
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De Genst E, Chan PH, Pardon E, Hsu STD, Kumita JR, Christodoulou J, Menzer L, Chirgadze DY, Robinson CV, Muyldermans S, Matagne A, Wyns L, Dobson CM, Dumoulin M. A nanobody binding to non-amyloidogenic regions of the protein human lysozyme enhances partial unfolding but inhibits amyloid fibril formation. J Phys Chem B 2013; 117:13245-13258. [PMID: 23919586 PMCID: PMC4612432 DOI: 10.1021/jp403425z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the effects of the interaction of two camelid antibody fragments, generally called nanobodies, namely cAb-HuL5 and a stabilized and more aggregation-resistant variant cAb-HuL5G obtained by protein engineering, on the properties of two amyloidogenic variants of human lysozyme, I56T and D67H, whose deposition in vital organs including the liver, kidney, and spleen is associated with a familial non-neuropathic systemic amyloidosis. Both NMR spectroscopy and X-ray crystallographic studies reveal that cAb-HuL5 binds to the α-domain, one of the two lobes of the native lysozyme structure. The binding of cAb-HuL5/cAb-HuL5G strongly inhibits fibril formation by the amyloidogenic variants; it does not, however, suppress the locally transient cooperative unfolding transitions, characteristic of these variants, in which the β-domain and the C-helix unfold and which represents key early intermediate species in the formation of amyloid fibrils. Therefore, unlike two other nanobodies previously described, cAb-HuL5/cAb-HuL5G does not inhibit fibril formation via the restoration of the global cooperativity of the native structure of the lysozyme variants to that characteristic of the wild-type protein. Instead, it inhibits a subsequent step in the assembly of the fibrils, involving the unfolding and structural reorganization of the α-domain. These results show that nanobodies can protect against the formation of pathogenic aggregates at different stages in the structural transition of a protein from the soluble native state into amyloid fibrils, illustrating their value as structural probes to study the molecular mechanisms of amyloid fibril formation. Combined with their amenability to protein engineering techniques to improve their stability and solubility, these findings support the suggestion that nanobodies can potentially be developed as therapeutics to combat protein misfolding diseases.
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Affiliation(s)
- Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pak-Ho Chan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P.R. China
| | - Els Pardon
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Laboratory of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Shang-Te D. Hsu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
- Institute of Biological Chemistry, Academia Sinica, No 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, No 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Gower Street, London WC1E 6BT, U.K
| | - Linda Menzer
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
| | - Dimitri Y. Chirgadze
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
| | - Serge Muyldermans
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Research Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
| | - Lode Wyns
- Department of Structural Biology, Vlaams Interuniversitair Instituut voor Biotechnologie VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Laboratory of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Mireille Dumoulin
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institute of Chemistry, University of Liege, B-4000 Liege (Sart Tilman), Belgium
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34
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Nanobodies Raised against Monomeric α-Synuclein Distinguish between Fibrils at Different Maturation Stages. J Mol Biol 2013; 425:2397-411. [DOI: 10.1016/j.jmb.2013.01.040] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 01/12/2023]
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35
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Abstract
The deposition of peptides and proteins as amyloid fibrils is a common feature of nearly 50 medical -disorders affecting the brain or a variety of other organs and tissues. These disorders, which include Alzheimer's disease, Parkinson's disease, the prion diseases, and type II diabetes, have an enormous impact on the public health and economy of the modern world. Extensive research is therefore taking place to determine the underlying molecular mechanisms and determinants of the pathological conversion of amyloidogenic proteins from their soluble forms into fibrillar structures. The use of molecular probes and biophysical techniques, such as X-ray crystallography and particularly NMR spectroscopy, are allowing detailed analysis of the mechanism of fibril formation and of the underlying structural and chemical features of the associated pathogenicity. Nanobodies, the antigen-binding domains derived from camelid heavy-chain antibodies, are excellent tools to probe protein aggregation as a result of their exquisite specificity and high affinity and stability, along with their ease of expression and small size; the latter in particular allows them to be used very efficiently in combination with NMR spectroscopy and X-ray crystallography. In this chapter we present an overview of how nanobodies are being used to obtain detailed information on the mechanisms of amyloid formation and on the nature and origin of their links with human diseases.
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Affiliation(s)
- Erwin De Genst
- Department of Chemistry, University of Cambridge, Cambridge, UK.
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36
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Abstract
Solubility and stability are amongst the factors contributing to the therapeutic efficacy of biologics. Human antibody heavy chain variable domains, VHs, are one class of biologics; improving VH biophysical properties is the focus of significant protein engineering efforts. Here, we describe an efficacy engineering approach which involves the introduction of a disulfide linkage in the VH core and which improves both VH solubility and stability. More specifically, we describe protocols for generation of disulfide engineered human VHs and their characterization in terms of disulfide linkage formation, non-aggregation, and stability. Our solubility/stability engineering approach may be applied to other VHs.
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37
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Lee YH, Goto Y. Kinetic intermediates of amyloid fibrillation studied by hydrogen exchange methods with nuclear magnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1307-23. [DOI: 10.1016/j.bbapap.2012.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/28/2023]
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38
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Ahn M, De Genst E, Kaminski Schierle GS, Erdelyi M, Kaminski CF, Dobson CM, Kumita JR. Analysis of the native structure, stability and aggregation of biotinylated human lysozyme. PLoS One 2012; 7:e50192. [PMID: 23166837 PMCID: PMC3500338 DOI: 10.1371/journal.pone.0050192] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/22/2012] [Indexed: 11/29/2022] Open
Abstract
Fibril formation by mutational variants of human lysozyme is associated with a fatal form of hereditary non-neuropathic systemic amyloidosis. Defining the mechanistic details of lysozyme aggregation is of crucial importance for understanding the origin and progression of this disease and related misfolding conditions. In this study, we show that a biotin moiety can be introduced site-specifically at Lys33 of human lysozyme. We demonstrate, using biophysical techniques, that the structure and stability of the native-state of the protein are not detectably altered by this modification, and that the ability to form amyloid fibrils is unchanged. By taking advantage of biotin-avidin interactions, we show that super-resolution fluorescence microscopy can generate detailed images of the mature fibrils. This methodology can readily enable the introduction of additional probes into the protein, thereby providing the means through which to understand, in detail, the nature of the aggregation process of lysozyme and its variants under a variety of conditions.
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Affiliation(s)
- Minkoo Ahn
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Miklos Erdelyi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
- National Physics Laboratory, Teddington, United Kingdom
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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Gavrin LK, Denny RA, Saiah E. Small Molecules That Target Protein Misfolding. J Med Chem 2012; 55:10823-43. [DOI: 10.1021/jm301182j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lori Krim Gavrin
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Rajiah Aldrin Denny
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
| | - Eddine Saiah
- BioTherapeutics
Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge,
Massachusetts 02140, United States
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40
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Kim DY, Kandalaft H, Ding W, Ryan S, van Faassen H, Hirama T, Foote SJ, MacKenzie R, Tanha J. Disulfide linkage engineering for improving biophysical properties of human VH domains. Protein Eng Des Sel 2012; 25:581-9. [PMID: 22942392 DOI: 10.1093/protein/gzs055] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To enhance their therapeutic potential, human antibody heavy chain variable domains (V(H)s) would benefit from increased thermostability. The highly conserved disulfide linkage that connects Cys23 and Cys104 residues in the core of V(H) domains is crucial to their stability and function. It has previously been shown that the introduction of a second disulfide linkage can increase the thermostability of camelid heavy-chain antibody variable domains (V(H)Hs). Using four model domains we demonstrate that this strategy is also applicable to human V(H) domains. The introduced disulfide linkage, formed between Cys54 and Cys78 residues, increased the thermostability of V(H)s by 14-18°C. In addition, using a novel hexa-histidine capture technology, circular dichroism, turbidity, size exclusion chromatography and multiangle light scattering measurements, we demonstrate reduced V(H) aggregation in domains with the Cys54-Cys78 disulfide linkage. However, we also found that the engineered disulfide linkage caused conformational changes, as indicated by reduced binding of the V(H)s to protein A. This indicates that it may be prudent to use the synthetic V(H) libraries harboring the engineered disulfide linkage before screening for affinity reagents. Such strategies may increase the number of thermostable binders.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON, Canada K1A 0R6
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41
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Johnson SM, Connelly S, Fearns C, Powers ET, Kelly JW. The transthyretin amyloidoses: from delineating the molecular mechanism of aggregation linked to pathology to a regulatory-agency-approved drug. J Mol Biol 2012; 421:185-203. [PMID: 22244854 PMCID: PMC3350832 DOI: 10.1016/j.jmb.2011.12.060] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 12/22/2011] [Accepted: 12/29/2011] [Indexed: 12/31/2022]
Abstract
Transthyretin (TTR) is one of the many proteins that are known to misfold and aggregate (i.e., undergo amyloidogenesis) in vivo. The process of TTR amyloidogenesis causes nervous system and/or heart pathology. While several of these maladies are associated with mutations that destabilize the native TTR quaternary and/or tertiary structure, wild-type TTR amyloidogenesis also leads to the degeneration of postmitotic tissue. Over the past 20 years, much has been learned about the factors that influence the propensity of TTR to aggregate. This biophysical information led to the development of a therapeutic strategy, termed "kinetic stabilization," to prevent TTR amyloidogenesis. This strategy afforded the drug tafamidis which was recently approved by the European Medicines Agency for the treatment of TTR familial amyloid polyneuropathy, the most common familial TTR amyloid disease. Tafamidis is the first and currently the only medication approved to treat TTR familial amyloid polyneuropathy. Here we review the biophysical basis for the kinetic stabilization strategy and the structure-based drug design effort that led to this first-in-class pharmacologic agent.
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Affiliation(s)
- Steven M. Johnson
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
| | - Stephen Connelly
- Department of Molecular Biology, La Jolla, California 92037, USA
| | - Colleen Fearns
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Evan T. Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
| | - Jeffery W. Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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42
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Analysis of heavy-chain antibody responses and resistance to Parelaphostrongylus tenuis in experimentally infected alpacas. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2012; 19:1019-26. [PMID: 22593238 DOI: 10.1128/cvi.00178-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The parasitic nematode Parelaphostrongylus tenuis is an important cause of neurologic disease of camelids in central and eastern North America. The aim of this study was to determine whether alpacas develop resistance to disease caused by P. tenuis in response to a previous infection or a combination of controlled infection and immunization. Alpacas were immunized with a homogenate of third-stage larvae (L3) and simultaneously implanted subcutaneously with diffusion chambers containing 20 live L3. Sham-treated animals received adjuvant alone and empty chambers. The protocol was not effective in inducing resistance to oral challenge with 10 L3, and disease developed between 60 and 71 days following infection. Immediately following the onset of neurologic disease, affected animals were treated with a regimen of anthelmintic and anti-inflammatory drugs, and all recovered. One year later, a subset of alpacas from this experiment was challenged with 20 L3 and the results showed that prior infection induced resistance to disease. Primary and secondary infections induced production of conventional and heavy-chain IgGs that reacted with soluble antigens in L3 homogenates but did not consistently recognize a recombinant form of a parasite-derived aspartyl protease inhibitor. Thus, the latter antigen may not be a good candidate for serology-based diagnostic tests. Antibody responses to parasite antigens occurred in the absence of overt disease, demonstrating that P. tenuis infection can be subclinical in a host that has been considered to be highly susceptible to disease. The potential for immunoprophylaxis to be effective in preventing disease caused by P. tenuis was supported by evidence of resistance to reinfection.
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Hussack G, Mackenzie CR, Tanha J. Characterization of single-domain antibodies with an engineered disulfide bond. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 911:417-29. [PMID: 22886266 DOI: 10.1007/978-1-61779-968-6_25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Camelidae single-domain antibodies (VHHs) represent a unique class of emerging therapeutics. Similar to other recombinant antibody fragments (e.g., Fabs, scFvs), VHHs are amenable to library screening and selection, but benefit from superior intrinsic biophysical properties such as high refolding efficiency, high solubility, no tendency for aggregation, resistance to proteases and chemical denaturants, and high expression, making them ideal agents for antibody-based drug design. Despite these favorable biophysical characteristics, further improvements to VHH stability are desirable when considering applications in adverse environments like high heat, low humidity, pH extremes, and the acidic, protease-rich gastrointestinal tract. Recently, the introduction of a disulfide bond into the hydrophobic core of camelid VHHs increased antibody thermal and conformational stability. Here, we present additional protocols for characterizing the effects of the introduced disulfide bond on a panel of llama VHHs. Specifically, we employ mass spectrometry fingerprinting analysis of VHH peptides to confirm the presence of the introduced disulfide bond, size exclusion chromatography, and surface plasmon resonance to examine the effects on aggregation state and target affinity, and circular dichroism spectroscopy and protease digestion assays to assess the effects on thermal and proteolytic stability. The disulfide bond stabilization strategy can be incorporated into antibody library design and should lead to hyperstabilized single-domain antibodies (VHHs, VHs), and possibly Fabs and scFvs, if selection pressures such as denaturants or proteases are introduced during antibody selection.
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Affiliation(s)
- Greg Hussack
- Institute for Biological Sciences, National Research Council Canada, Ottawa, ON, Canada.
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Hussack G, Hirama T, Ding W, MacKenzie R, Tanha J. Engineered single-domain antibodies with high protease resistance and thermal stability. PLoS One 2011; 6:e28218. [PMID: 22140551 PMCID: PMC3227653 DOI: 10.1371/journal.pone.0028218] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/03/2011] [Indexed: 11/28/2022] Open
Abstract
The extreme pH and protease-rich environment of the upper gastrointestinal tract is a major obstacle facing orally-administered protein therapeutics, including antibodies. Through protein engineering, several Clostridium difficile toxin A-specific heavy chain antibody variable domains (VHHs) were expressed with an additional disulfide bond by introducing Ala/Gly54Cys and Ile78Cys mutations. Mutant antibodies were compared to their wild-type counterparts with respect to expression yield, non-aggregation status, affinity for toxin A, circular dichroism (CD) structural signatures, thermal stability, protease resistance, and toxin A-neutralizing capacity. The mutant VHHs were found to be well expressed, although with lower yields compared to wild-type counterparts, were non-aggregating monomers, retained low nM affinity for toxin A, albeit the majority showed somewhat reduced affinity compared to wild-type counterparts, and were capable of in vitro toxin A neutralization in cell-based assays. Far-UV and near-UV CD spectroscopy consistently showed shifts in peak intensity and selective peak minima for wild-type and mutant VHH pairs; however, the overall CD profile remained very similar. A significant increase in the thermal unfolding midpoint temperature was observed for all mutants at both neutral and acidic pH. Digestion of the VHHs with the major gastrointestinal proteases, at biologically relevant concentrations, revealed a significant increase in pepsin resistance for all mutants and an increase in chymotrypsin resistance for the majority of mutants. Mutant VHH trypsin resistance was similar to that of wild-type VHHs, although the trypsin resistance of one VHH mutant was significantly reduced. Therefore, the introduction of a second disulfide bond in the hydrophobic core not only increases VHH thermal stability at neutral pH, as previously shown, but also represents a generic strategy to increase VHH stability at low pH and impart protease resistance, with only minor perturbations in target binding affinities. These are all desirable characteristics for the design of protein-based oral therapeutics.
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Affiliation(s)
- Greg Hussack
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Tomoko Hirama
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
| | - Wen Ding
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
| | - Roger MacKenzie
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jamshid Tanha
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Kumita JR, Helmfors L, Williams J, Luheshi LM, Menzer L, Dumoulin M, Lomas DA, Crowther DC, Dobson CM, Brorsson AC. Disease-related amyloidogenic variants of human lysozyme trigger the unfolded protein response and disturb eye development in Drosophila melanogaster. FASEB J 2011; 26:192-202. [PMID: 21965601 PMCID: PMC3250245 DOI: 10.1096/fj.11-185983] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have created a Drosophila model of lysozyme amyloidosis to investigate the in vivo behavior of disease-associated variants. To achieve this objective, wild-type (WT) protein and the amyloidogenic variants F57I and D67H were expressed in Drosophila melanogaster using the UAS-gal4 system and both the ubiquitous and retinal expression drivers Act5C-gal4 and gmr-gal4. The nontransgenic w(1118) Drosophila line was used as a control throughout. We utilized ELISA experiments to probe lysozyme protein levels, scanning electron microscopy for eye phenotype classification, and immunohistochemistry to detect the unfolded protein response (UPR) activation. We observed that expressing the destabilized F57I and D67H lysozymes triggers UPR activation, resulting in degradation of these variants, whereas the WT lysozyme is secreted into the fly hemolymph. Indeed, the level of WT was up to 17 times more abundant than the variant proteins. In addition, the F57I variant gave rise to a significant disruption of the eye development, and this correlated to pronounced UPR activation. These results support the concept that the onset of familial amyloid disease is linked to an inability of the UPR to degrade completely the amyloidogenic lysozymes prior to secretion, resulting in secretion of these destabilized variants, thereby leading to deposition and associated organ damage.
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Affiliation(s)
- Janet R Kumita
- Department of Chemistry, University of Cambridge, Cambridge, UK
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46
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Skottrup PD, Leonard P, Kaczmarek JZ, Veillard F, Enghild JJ, O'Kennedy R, Sroka A, Clausen RP, Potempa J, Riise E. Diagnostic evaluation of a nanobody with picomolar affinity toward the protease RgpB from Porphyromonas gingivalis. Anal Biochem 2011; 415:158-67. [PMID: 21569755 DOI: 10.1016/j.ab.2011.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 12/23/2022]
Abstract
Porphyromonas gingivalis is one of the major periodontitis-causing pathogens. P. gingivalis secretes a group of proteases termed gingipains, and in this study we have used the RgpB gingipain as a biomarker for P. gingivalis. We constructed a naive camel nanobody library and used phage display to select one nanobody toward RgpB with picomolar affinity. The nanobody was used in an inhibition assay for detection of RgpB in buffer as well as in saliva. The nanobody was highly specific for RgpB given that it did not bind to the homologous gingipain HRgpA. This indicated the presence of a binding epitope within the immunoglobulin-like domain of RgpB. A subtractive inhibition assay was used to demonstrate that the nanobody could bind native RgpB in the context of intact cells. The nanobody bound exclusively to the P. gingivalis membrane-bound RgpB isoform (mt-RgpB) and to secreted soluble RgpB. Further cross-reactivity studies with P. gingivalis gingipain deletion mutants showed that the nanobody could discriminate between native RgpB and native Kgp and RgpA in complex bacterial samples. This study demonstrates that RgpB can be used as a specific biomarker for P. gingivalis detection and that the presented nanobody-based assay could supplement existing methods for P. gingivalis detection.
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Affiliation(s)
- Peter Durand Skottrup
- Department of Pharmacology and Pharmacotherapy, Faculty of Pharmaceutical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Rahbarizadeh F, Ahmadvand D, Sharifzadeh Z. Nanobody; an old concept and new vehicle for immunotargeting. Immunol Invest 2011; 40:299-338. [PMID: 21244216 DOI: 10.3109/08820139.2010.542228] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The use of antibodies in cancer therapy has come a long way since the day Paul Ehrlich described the concept and Kohler and Milstein devised the hybridoma technology to bring this theory to reality. The synthesis of murine monoclonal antibodies (mAbs) was the first success in this field, leading to the invention of chimerization, the production of variable fragments (Fv) with the progression to domain antibodies (dAb) and later humanization technologies to maximize the clinical utility of murine mAbs. It was just by chance that dAbs were found to exist in ?heavy chain? immunoglobulins from Camelidae family and cartilaginous fish. These unique antibody fragments interact with antigen by virtue of only one single variable domain, referred to as VHH or nanobody. Several characteristics make nanobody use superior to the abovementioned antibodies. They are non-immunogenic and show high thermal and chemical stability. There are several reports of raising specific nanobodies against enzymes, haptens, pathogens, toxins and tumor markers, which are outlined in this paper. All these characteristics make them strong candidates as targeting agents for cancer therapy.
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Affiliation(s)
- Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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Abstract
Approximately 500 million years ago, two types of recombinatorial adaptive immune systems (AISs) arose in vertebrates. The jawed vertebrates diversify their repertoire of immunoglobulin domain-based T and B cell antigen receptors mainly through the rearrangement of V(D)J gene segments and somatic hypermutation, but none of the fundamental AIS recognition elements in jawed vertebrates have been found in jawless vertebrates. Instead, the AIS of jawless vertebrates is based on variable lymphocyte receptors (VLRs) that are generated through recombinatorial usage of a large panel of highly diverse leucine-rich-repeat (LRR) sequences. Whereas the appearance of transposon-like, recombination-activating genes contributed uniquely to the origin of the AIS in jawed vertebrates, the use of activation-induced cytidine deaminase for receptor diversification is common to both the jawed and jawless vertebrates. Despite these differences in anticipatory receptor construction, the basic AIS design featuring two interactive T and B lymphocyte arms apparently evolved in an ancestor of jawed and jawless vertebrates within the context of preexisting innate immunity and has been maintained since as a consequence of powerful and enduring selection, most probably for pathogen defense purposes.
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Affiliation(s)
- Masayuki Hirano
- Emory Vaccine Center, Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
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49
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Saerens D. Isolation and optimization of camelid single-domain antibodies: Dirk Saerens’ work on nanobodies. World J Biol Chem 2010; 1:235-8. [PMID: 21537479 PMCID: PMC3083966 DOI: 10.4331/wjbc.v1.i7.235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 07/01/2010] [Accepted: 07/08/2010] [Indexed: 02/05/2023] Open
Abstract
It is well established that all camelids have unique antibodies circulating in their blood. Unlike antibodies from all other species, these special antibodies are devoid of light chains, and are composed of a heavy chain homodimer. These so-called heavy-chain antibodies (HCAbs) are expressed after a V-D-J rearrangement and require dedicated constant gamma genes. An immune response is raised in these HCAbs following a classical immunization protocol. These HCAbs are easily purified from serum, and their antigen-binding fragment interacts with parts of the target that are less antigenic to conventional antibodies. The antigen binding site of the dromedary HCAb comprises one single domain, referred to as VHH or nanobody (Nb), therefore, a strategy was designed to clone the Nb repertoire of an immunized dromedary and to select the Nb with specificity for our target antigens. The monoclonal Nb is produced well in bacteria, is very stable and highly soluble, and it binds the antigen with high affinity and specificity. Currently, the recombinant Nb has been developed successfully for research purposes, as a probe in biosensors, to diagnose infections, or to treat diseases such as cancer or trypanosomiasis.
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Affiliation(s)
- Dirk Saerens
- Dirk Saerens, Department of Cellular and Molecular Immunology, Vrije Universiteits Brussel-Vlaams Instituut voor Biotechnology, Pleinlaan 2, B-1050 Brussel, Belgium
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50
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De Genst EJ, Guilliams T, Wellens J, O'Day EM, Waudby CA, Meehan S, Dumoulin M, Hsu STD, Cremades N, Verschueren KHG, Pardon E, Wyns L, Steyaert J, Christodoulou J, Dobson CM. Structure and properties of a complex of α-synuclein and a single-domain camelid antibody. J Mol Biol 2010; 402:326-43. [PMID: 20620148 DOI: 10.1016/j.jmb.2010.07.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 10/19/2022]
Abstract
The aggregation of the intrinsically disordered protein α-synuclein to form fibrillar amyloid structures is intimately associated with a variety of neurological disorders, most notably Parkinson's disease. The molecular mechanism of α-synuclein aggregation and toxicity is not yet understood in any detail, not least because of the paucity of structural probes through which to study the behavior of such a disordered system. Here, we describe an investigation involving a single-domain camelid antibody, NbSyn2, selected by phage display techniques to bind to α-synuclein, including the exploration of its effects on the in vitro aggregation of the protein under a variety of conditions. We show using isothermal calorimetric methods that NbSyn2 binds specifically to monomeric α-synuclein with nanomolar affinity and by means of NMR spectroscopy that it interacts with the four C-terminal residues of the protein. This latter finding is confirmed by the determination of a crystal structure of NbSyn2 bound to a peptide encompassing the nine C-terminal residues of α-synuclein. The NbSyn2:α-synuclein interaction is mediated mainly by side-chain interactions while water molecules cross-link the main-chain atoms of α-synuclein to atoms of NbSyn2, a feature we believe could be important in intrinsically disordered protein interactions more generally. The aggregation behavior of α-synuclein at physiological pH, including the morphology of the resulting fibrillar structures, is remarkably unaffected by the presence of NbSyn2 and indeed we show that NbSyn2 binds strongly to the aggregated as well as to the soluble forms of α-synuclein. These results give strong support to the conjecture that the C-terminal region of the protein is not directly involved in the mechanism of aggregation and suggest that binding of NbSyn2 could be a useful probe for the identification of α-synuclein aggregation in vitro and possibly in vivo.
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Affiliation(s)
- Erwin J De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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