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Gondelaud F, Bouakil M, Le Fèvre A, Miele AE, Chirot F, Duclos B, Liwo A, Ricard-Blum S. Extended disorder at the cell surface: The conformational landscape of the ectodomains of syndecans. Matrix Biol Plus 2021; 12:100081. [PMID: 34505054 PMCID: PMC8416954 DOI: 10.1016/j.mbplus.2021.100081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 10/26/2022] Open
Abstract
Syndecans are membrane proteoglycans regulating extracellular matrix assembly, cell adhesion and signaling. Their ectodomains can be shed from the cell surface, and act as paracrine and autocrine effectors or as competitors of full-length syndecans. We report the first biophysical characterization of the recombinant ectodomains of the four human syndecans using biophysical techniques, and show that they behave like flexible random-coil intrinsically disordered proteins, and adopt several conformation ensembles in solution. We have characterized their conformational landscapes using native mass spectrometry (MS) and ion-mobility MS, and demonstrated that the syndecan ectodomains explore the majority of their conformational landscape, from minor compact, globular-like, conformations to extended ones. We also report that the ectodomain of syndecan-4, corresponding to a natural isoform, is able to dimerize via a disulfide bond. We have generated a three-dimensional model of the C-terminus of this dimer, which supports the dimerization via a disulfide bond. Furthermore, we have mapped the NXIP adhesion motif of syndecans and their sequences involved in the formation of ternary complexes with integrins and growth factor receptors on the major conformations of their ectodomains, and shown that these sequences are not accessible in all the conformations, suggesting that only some of them are biologically active. Lastly, although the syndecan ectodomains have a far lower number of amino acid residues than their membrane partners, their intrinsic disorder and flexibility allow them to adopt extended conformations, which have roughly the same size as the cell surface receptors (e.g., integrins and growth factor receptors) they bind to.
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Key Words
- CCS, collision cross section
- CD, circular dichroism
- CSD, charge state distribution
- Cell-matrix interactions
- Conformations
- DLS, dynamic light scattering
- DTT, dithiothreitol
- ED, ectodomain
- ESI-IM-MS, electrospray ionization - ion mobility - mass spectrometry
- ESI-MS, electrospray ionization - mass spectrometry
- GAG, glycosaminoglycan
- IDP, intrinsically disordered protein
- Intrinsically disordered proteins
- MoRF, molecular recognition feature
- PAGE, polyacrylamide gel electrophoresis
- PMG, pre-molten globule
- RC, random-coil
- SASA, solvent accessible surface area
- SAXS, small angle X-ray scattering
- SDC, syndecan
- SDS, sodium dodecyl sulfate
- SEC, size exclusion chromatography
- Syndecans
- TFE, trifluoroethanol
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Affiliation(s)
- Frank Gondelaud
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
| | - Mathilde Bouakil
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, Cité Lyonnaise de l'Environnement et de l'Analyse, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Aurélien Le Fèvre
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Adriana Erica Miele
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
| | - Fabien Chirot
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Bertrand Duclos
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
| | - Adam Liwo
- Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne cedex, France
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Alameldin S, Costina V, Abdel-Baset HA, Nitschke K, Nuhn P, Neumaier M, Hedtke M. Coupling size exclusion chromatography to ultracentrifugation improves detection of exosomal proteins from human plasma by LC-MS. Pract Lab Med 2021; 26:e00241. [PMID: 34258353 DOI: 10.1016/j.plabm.2021.e00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Objectives Exosomes are small lipid bilayer vesicles that are defined by their endocytic origin and size range of 30–140 nm. They are constantly produced by different cell types, by both healthy and abnormal cells, and can be isolated from almost all body fluids. Little information exists in isolating exosomes from plasma due to the complexity of its content and the presence of contaminating plasma proteins. Design and methods We carried-out liquid chromatography-mass spectrometry (LC-MS/MS) analyses of plasma-derived vesicles from 4 healthy donors obtained by 2 coupled methodologies: Ultracentrifugation (UC) coupled with size-exclusion chromatography (SEC) to isolate and subsequently enrich exosomes. We compared the proteins detected by UC alone and UC coupled with SEC. Results In the coupled UC + SEC methodology we found 52.25% more proteins enriched in exosomes as CD9, Annexins, YWHAZ (14-3-3 family) and others, than by using UC alone. There is also a reduction of 98.8% of contaminating plasma proteins by coupling UC and SEC in comparison to using UC alone. Conclusions We conclude that exosomes can be successfully isolated from plasma using a very simple combination of standard methods, which could largely improve the proteomics profiling of plasma exosomes. Isolating exosomes with the least possible contaminants is very important for their clinical application. Isolating exosomes from human plasma faces considerable challenges. There is no ideal single isolation technique until this date. Exosomes can be successfully isolated from plasma using a combination of Ultracentrifugation and SEC.
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Key Words
- AGO2, Argonaute protein
- CSF, cerebrospinal fluid
- EVs, extracellular vesicles
- Exosomes
- FDR, false discovery rate
- Human plasma
- ILVs, intraluminal vesicles
- MVBs, multivesicular bodies
- Mass spectrometry
- SEC, size exclusion chromatography
- Size-exclusion chromatography
- UC, ultracentrifugation
- Ultracentrifugation
- cfNAs, Cell-free nucleic acids
- ctDNA, circulating tumor DNA
- miRNA, microRNA
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Sui L, Guo HC. Enhanced recombinant expression and purification of human IRAP for biochemical and crystallography studies. Biochem Biophys Rep 2021; 27:101042. [PMID: 34169156 PMCID: PMC8207215 DOI: 10.1016/j.bbrep.2021.101042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Insulin-regulated aminopeptidase (IRAP) in humans is a membrane bound enzyme that has multiple functions. It was first described as a companion protein of the insulin-responsive glucose transporter, Glut4, in specialized vesicles. The protein has subsequently been shown to be identical to the oxytocinase/aminopeptidase or the angiotensin IV (Ang IV) receptor (AT4 receptor). Some AT4 ligand peptides, such as Ang IV and LVV-hemorphin-7, have been shown to act as IRAP inhibitors that exert memory-enhancing properties. As such IRAP has been a target for developing cognitive enhancers. To facilitate detailed mechanistic studies of IRAP catalysis and inhibition, and to pave the way for biophysical and structural studies of IRAP in complex with peptide inhibitors, we report here an optimized expression and purification system using High Five insect cells. We also report biochemical characterizations of the purified recombinant IRAP with a standard aminopeptidase substrate and an optimized IRAP peptide inhibitor with a Ki of 98 nM.
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Key Words
- AT4, Ang IV receptor
- Ang IV, angiotensin IV
- Cognitive enhancers
- Crystallization
- ERAP, endoplasmic reticulum aminopeptidase
- Expression and purification
- IEX, ion exchange chromatography
- IMAC, immobilized metal ion affinity chromatography
- IRAP, insulin-regulated aminopeptidase
- Insulin-regulated aminopeptidase (IRAP)
- L-AMC, leucine 7-amido-4-methylcoumarin
- LVV-H7, LVV-hemorphin-7
- MHC-I, major histocompatibility complex class I
- Peptide inhibitor
- SEC, size exclusion chromatography
- Substrate affinity
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Affiliation(s)
- Lufei Sui
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA, 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA, 01854, USA
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Hirschi S, Kalbermatter D, Ucurum Z, Fotiadis D. Cryo-electron microscopic and X-ray crystallographic analysis of the light-driven proton pump proteorhodopsin reveals a pentameric assembly. J Struct Biol X 2020; 4:100024. [PMID: 32647827 PMCID: PMC7337067 DOI: 10.1016/j.yjsbx.2020.100024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/30/2022]
Abstract
Affinity tag-free isolation of proteorhodopsin (PR) by ion exchange and size exclusion chromatography. Biochemical and computational analysis indicate a single, pentameric PR population. Highly pure and homogeneous PR enables growth of 3D crystals. X-ray crystallography and cryo-electron microscopy reveal pentameric assembly of PR.
The green-light absorbing proteorhodopsin (GPR) is the prototype of bacterial light-driven proton pumps. It has been the focus of continuous research since its discovery 20 years ago and has sparked the development and application of various biophysical techniques. However, a certain controversy and ambiguity about the oligomeric assembly of GPR still remains. We present here the first tag-free purification of pentameric GPR. The combination of ion exchange and size exclusion chromatography yields homogeneous and highly pure untagged pentamers from GPR overexpressing Escherichia coli. The presented purification procedure provides native-like protein and excludes the need for affinity purification tags. Importantly, three-dimensional protein crystals of GPR were successfully grown and analyzed by X-ray crystallography. These results together with data from single particle cryo-electron microscopy provide direct evidence for the pentameric stoichiometry of purified GPR.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - David Kalbermatter
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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Powers KT, Gildenberg MS, Washington MT. Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations. Comput Struct Biotechnol J 2019; 17:570-578. [PMID: 31073392 PMCID: PMC6495069 DOI: 10.1016/j.csbj.2019.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 01/03/2023] Open
Abstract
Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational flexibility of such systems using hybrid approaches. One particularly fruitful strategy has been the combination of small-angle X-ray scattering (SAXS) and molecular simulations. In this article, we provide a brief overview of SAXS and molecular simulations and then discuss two general approaches for combining SAXS data and molecular simulations: minimal ensemble approaches and full ensemble approaches. In minimal ensemble approaches, one selects a minimal ensemble of structures from the simulations that best fit the SAXS data. In full ensemble approaches, one validates a full ensemble of structures from the simulations using SAXS data. We argue that full ensemble models are more realistic than minimal ensemble searches models and that full ensemble approaches should be used wherever possible. Conformationally flexible proteins are a major challenge for structural biologists. Flexible proteins can be examined by combining molecular simulations and SAXS. Minimal ensemble searches are a common way of combining simulations and SAXS. Full ensemble methods use SAXS to validate simulations without curve fitting. Full ensemble models are more realistic than minimal ensemble searches models.
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Key Words
- BD, Brownian dynamics
- CG, coarse-grained
- Cryo-EM, cryo-electron microscopy
- DNA polymerase
- DNA replication
- Dmax, maximal distance
- LD, Langevin dynamics
- MD, molecular dynamics
- Minimal ensemble search
- NMR, nuclear magnetic resonance
- PCNA, proliferating cell nuclear antigen
- Pol η, DNA polymerase eta
- Protein structure
- RPA, replication protein A
- Rg, radius of gyration
- SANS
- SANS, small-angle neutron scattering
- SAXS
- SAXS, small-angle X-ray scattering
- SEC, size exclusion chromatography
- SUMO, small ubiquitin-like modifie
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Affiliation(s)
- Kyle T Powers
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States of America
| | - Melissa S Gildenberg
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States of America
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States of America
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Chura-Chambi RM, Fraga TR, da Silva LB, Yamamoto BB, Isaac L, Barbosa AS, Morganti L. Leptospira interrogans thermolysin refolded at high pressure and alkaline pH displays proteolytic activity against complement C3. ACTA ACUST UNITED AC 2018; 19:e00266. [PMID: 29992100 PMCID: PMC6036645 DOI: 10.1016/j.btre.2018.e00266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/23/2018] [Accepted: 06/16/2018] [Indexed: 11/30/2022]
Abstract
Enzymes from the thermolysin family are crucial factors in the pathogenesis of several diseases caused by bacteria and are potential targets for therapeutic interventions. Thermolysin encoded by the gene LIC13322 of the causative agent of leptospirosis, Leptospira interrogans, was shown to cleave proteins from the Complement System. However, the production of this recombinant protein using traditional refolding processes with high levels of denaturing reagents for thermolysin inclusion bodies (TL-IBs) solubilization results in poor recovery and low proteolytic activity probably due to improper refolding of the protein. Based on the assumption that leptospiral proteases play a crucial role during infection, the aim of this work was to obtain a functional recombinant thermolysin for future studies on the role of these metalloproteases on leptospiral infection. The association of high hydrostatic pressure (HHP) and alkaline pH was utilized for thermolysin refolding. Incubation of a suspension of TL-IBs at HHP and a pH of 11.0 is non-denaturing but effective for thermolysin solubilization. Soluble protein does not reaggregate by dialysis to pH 8.0. A volumetric yield of 46 mg thermolysin/L of bacterial culture and a yield of near 100% in relation to the total thermolysin present in TL-IBs were obtained. SEC-purified thermolysin suffers fragmentation, likely due to autoproteolysis and presents proteolytic activity against complement C3 α-chain, possibly by a generation of a C3b-like molecule. The proteolytic activity of thermolysin against C3 was time and dose-dependent. The experience gained in this study shall help to establish efficient HHP-based processes for refolding of bioactive proteins from IBs.
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Affiliation(s)
- Rosa Maria Chura-Chambi
- Instituto de Pesquisas Energéticas e Nucleares IPEN-CNEN/SP, Centro de Biotecnologia, Av. Prof. Lineu Prestes, 2242, CEP 05508-000, São Paulo, SP, Brazil
| | - Tatiana Rodrigues Fraga
- Instituto de Ciências Biomédicas, Universidade de São Paulo, Departamento de Imunologia, Av. Prof. Lineu Prestes, 1374, CEP 05508-900, São Paulo, SP, Brazil
| | - Ludmila Bezerra da Silva
- Instituto Butantan, Laboratório de Bacteriologia, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | - Bruno Bernardi Yamamoto
- Instituto Butantan, Laboratório de Bacteriologia, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | - Lourdes Isaac
- Instituto de Ciências Biomédicas, Universidade de São Paulo, Departamento de Imunologia, Av. Prof. Lineu Prestes, 1374, CEP 05508-900, São Paulo, SP, Brazil
| | - Angela Silva Barbosa
- Instituto Butantan, Laboratório de Bacteriologia, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | - Ligia Morganti
- Instituto de Pesquisas Energéticas e Nucleares IPEN-CNEN/SP, Centro de Biotecnologia, Av. Prof. Lineu Prestes, 2242, CEP 05508-000, São Paulo, SP, Brazil
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Lata K, Afsar M, Ramachandran R. Biochemical characterization and novel inhibitor identification of Mycobacterium tuberculosis Endonuclease VIII 2 (Rv3297). Biochem Biophys Rep 2017; 12:20-28. [PMID: 28955788 PMCID: PMC5613217 DOI: 10.1016/j.bbrep.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/10/2017] [Accepted: 07/29/2017] [Indexed: 12/03/2022] Open
Abstract
Nei2 (Rv3297) is a DNA Base Excision Repair (BER) glycosylase that is essential for survival of Mycobacterium tuberculosis in primates. We show that MtbNei2 is a bifunctional glycosylase that specifically acts on oxidized pyrimidine-containing single-stranded, double-stranded, 5’/3’ fork and bubble DNA substrates. MtbNei2 possesses Uracil DNA glycosylase activity unlike E. coli Nei. Mutational studies demonstrate that Pro2 and Glu3 located in the active site are essential for glycosylase activity of MtbNei2. Mutational analysis demonstrated that an unstructured C-terminal zinc finger domain that was important for activity in E. coli Nei and Fpg, was not required for the glycosylase activity of MtbNei2. Lastly, we screened the NCI natural product compound database and identified three natural product inhibitors with IC50 values ranging between 41.8 μM-92.7 μM against MtbNei2 in in vitro inhibition assays. Surface Plasmon Resonance (SPR) experiments showed that the binding affinity of the best inhibitor, NSC31867, was 74 nM. The present results set the stage for exploiting this important target in developing new therapeutic strategies that target Mycobacterial BER. Biochemical characterization of MtbNei2 (Rv3297). Pro2 and Glu3 residues are essential for MtbNei2 activity. Zinc finger domain is dispensable for activity. 3 natural product inhibitors identified against MtbNei2.
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Key Words
- AP, apurinic/apyrimidinic
- BER
- BER inhibitors
- BER, base excision repair
- EcoFpg, E. coli Formamidopyrimidine glycosylase
- EcoNei, E. coli Endonuclease VIII
- Endonuclease VIII 2
- Glycosylases
- MDR, multidrug resistance
- Mtb, Mycobacterium tuberculosis
- MtbNei2, M. tuberculosis Endonuclease VIII 2
- MtbNei2ΔZNF, M. tuberculosis zinc finger domain deleted mutant
- NSC250430 (Pubchem CID: 317611)
- NSC31867 (Pubchem CID: 233380)
- NSC345647 (Pubchem CID: 53277)
- ROS
- ROS, reactive oxygen species
- SEC, size exclusion chromatography
- TB, tuberculosis
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Narai-Kanayama A, Hanaishi T, Aso K. Mechanistic investigation of capability of enzymatically synthesized polycysteine to cross-link proteins. Biochem Biophys Rep 2016; 7:338-346. [PMID: 28955924 PMCID: PMC5613652 DOI: 10.1016/j.bbrep.2016.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/13/2016] [Accepted: 07/15/2016] [Indexed: 11/29/2022] Open
Abstract
Background Previously, we had reported that α-chymotrypsin–catalyzed polymerization of l-cysteine ethyl ester in a frozen buffer provided poly-l-cysteine (PLCys) in good yield, of which degree of polymerization had been determined to be 6–11. Almost all of SH groups in PLCys were in free forms. Such a multi-thiol peptide may cross-link proteins through thiol/disulfide (SH/SS) exchange reactions, considering the knowledge that other synthetic multi-thiol additives changes properties of protein materials. Methods This study explored the capability of PLCys to cross-link proteins using lysozyme as a model protein which has four disulfide bonds but no free SH group. The protein was incubated with PLCys at neutral pH and at below 70 °C to avoid PLCys-independent, β-elimination-mediated cross-linkings. Protein polymerization was analyzed by SDS-PAGE and SEC. PLCys peptides involved in the protein polymer, which were released by reduction with dithiothreitol, were analyzed by RP-HPLC. Conclusions Addition of urea and thermal treatment at 60 °C caused PLCys-induced lysozyme polymerization. Compared with free cysteine, a higher level of PLCys was required for the polymerization probably due to its low water solubility. RP-HPLC analyses suggested that PLCys played a role in the protein polymerization as a cross-linker. General significance Enzymatically synthesized PLCys shows promise as a peptidic cross-linker for the production of protein polymers with novel physiochemical properties and functionalities.
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Key Words
- Cys-OEt, l-cysteine ethyl ester
- DMSO, dimethyl sulfoxide
- DP, degree of polymerization
- DTNB, 5,5′-dithiobis (2-nitrobenzoic acid)
- DTT, dithiothreitol
- Disulfide bond
- IAM, iodoacetamide
- Lysozyme
- MALDI-TOF MS, matrix assisted laser deso′rption/ionization time of flight mass spectrometry
- PLCys, poly-l-cysteine
- Poly-l-cysteine
- Protein cross-linking
- S-CM, S-carbamoylmethyl
- SEC, size exclusion chromatography
- SH/SS exchange
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Affiliation(s)
- Asako Narai-Kanayama
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo 180-8602, Japan
| | - Tomoko Hanaishi
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo 180-8602, Japan
| | - Keiichi Aso
- Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo 180-8602, Japan
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Kelly RL, Sun T, Jain T, Caffry I, Yu Y, Cao Y, Lynaugh H, Brown M, Vásquez M, Wittrup KD, Xu Y. High throughput cross-interaction measures for human IgG1 antibodies correlate with clearance rates in mice. MAbs 2016; 7:770-7. [PMID: 26047159 PMCID: PMC4622737 DOI: 10.1080/19420862.2015.1043503] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although improvements in technology for the isolation of potential therapeutic antibodies have made the process increasingly predictable, the development of biologically active monoclonal antibodies (mAbs) into drugs can often be impeded by developability issues such as poor expression, solubility, and promiscuous cross-reactivity. Establishing early stage developability screening assays capable of predicting late stage behavior is therefore of high value to minimize development risks. Toward this goal, we selected a panel of 16 monoclonal antibodies (mAbs) representing different developability profiles, in terms of self- and cross-interaction propensity, and examined their downstream behavior from expression titer to accelerated stability and pharmacokinetics in mice. Clearance rates showed significant rank-order correlations to 2 cross-interaction related assays, with the closest correlation to a non-specificity assay on the surface of yeast. Additionally, 2 self-association assays correlated with each other but not to mouse clearance rate. This case study suggests that combining assays capable of high throughput screening of self- and cross-interaction early in the discovery stage could significantly lower downstream development risks.
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Affiliation(s)
- Ryan L Kelly
- a Department of Biological Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology ; Cambridge , MA , USA
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Abstract
Monoclonal antibodies and antibody-like molecules represent a fast-growing class of bio-therapeutics that has rapidly transformed patient care in a variety of disease indications. The discovery of antibodies that bind to particular targets with high affinity is now a routine exercise and a variety of in vitro and in vivo techniques are available for this purpose. However, it is still challenging to identify antibodies that, in addition to having the desired biological effect, also express well, remain soluble at different pH levels, remain stable at high concentrations, can withstand high shear stress, and have minimal non-specific interactions. Many promising antibody programs have ultimately failed in development due to the problems associated with one of these factors. Here, we present a simple high-performance liquid chromatography (HPLC)-based screening method to assess these developability factors earlier in discovery process. This method is robust and requires only microgram quantities of proteins. Briefly, we show that for antibodies injected on a commercially available pre-packed Zenix HPLC column, the retention times are inversely related to their colloidal stability with antibodies prone to precipitation or aggregation retained longer on the column with broader peaks. By simply varying the salt content of running buffer, we were also able to estimate the nature of interactions between the antibodies and the column. We believe this approach should generally be applicable to assessment of the developability of other classes of bio-therapeutic molecules, and that the addition of this simple tool early in the discovery process will lead to selection of molecules with improved developability characteristics.
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Affiliation(s)
- Neeraj Kohli
- a Merrimack Pharmaceuticals, Inc. ; Cambridge , MA , USA
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Reusch U, Duell J, Ellwanger K, Herbrecht C, Knackmuss SH, Fucek I, Eser M, McAleese F, Molkenthin V, Gall FL, Topp M, Little M, Zhukovsky EA. A tetravalent bispecific TandAb (CD19/CD3), AFM11, efficiently recruits T cells for the potent lysis of CD19(+) tumor cells. MAbs 2016; 7:584-604. [PMID: 25875246 DOI: 10.1080/19420862.2015.1029216] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
To harness the potent tumor-killing capacity of T cells for the treatment of CD19(+) malignancies, we constructed AFM11, a humanized tetravalent bispecific CD19/CD3 tandem diabody (TandAb) consisting solely of Fv domains. The molecule exhibits good manufacturability and stability properties. AFM11 has 2 binding sites for CD3 and 2 for CD19, an antigen that is expressed from early B cell development through differentiation into plasma cells, and is an attractive alternative to CD20 as a target for the development of therapeutic antibodies to treat B cell malignancies. Comparison of the binding and cytotoxicity of AFM11 with those of a tandem scFv bispecific T cell engager (BiTE) molecule targeting the same antigens revealed that AFM11 elicited more potent in vitro B cell lysis. Though possessing high affinity to CD3, the TandAb mediates serial-killing of CD19(+) cells with little dependence of potency or efficacy upon effector:target ratio, unlike the BiTE. The advantage of the TandAb over the BiTE was most pronounced at lower effector:target ratios. AFM11 mediated strictly target-dependent T cell activation evidenced by CD25 and CD69 induction, proliferation, and cytokine release, notwithstanding bivalent CD3 engagement. In a NOD/scid xenograft model, AFM11 induced dose-dependent growth inhibition of Raji tumors in vivo, and radiolabeled TandAb exhibited excellent localization to tumor but not to normal tissue. After intravenous administration in mice, half-life ranged from 18.4 to 22.9 h. In a human ex vivo B-cell chronic lymphocytic leukemia study, AFM11 exhibited substantial cytotoxic activity in an autologous setting. Thus, AFM11 may represent a promising therapeutic for treatment of CD19(+) malignancies with an advantageous safety risk profile and anticipated dosing regimen.
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Key Words
- ALL
- AUCtot, total area under the curve
- B-ALL, B-precursor acute lymphoblastic leukemia
- BBB, blood-brain barrier
- BiTE, bispecific T cell engager
- CAR, chimeric antigen receptor
- CCS, cell culture supernatant
- CD, cluster of differentiation
- CD3
- CDR, complementarity determining region
- CHO, Chinese hamster ovary
- CL, clearance
- CLL, chronic lymphocytic leukemia
- CNS, central nervous system
- Cmax, maximal concentration
- DMSO, dimethyl sulfoxide
- E:T, effector:target
- EC50, half maximal effective concentration
- ECL, electrochemiluminescence
- F, fluorescence
- FACS, fluorescence-activated cell sorting
- FCS, fetal calf serum
- FR, framework region
- Fab, fragment antigen-binding
- Fc, fragment crystallizable
- FcRn, neonatal Fc receptor
- FcgR, Fc gamma receptor
- Fv, variable fragment
- HMF, high molecular weight forms
- HSA, human serum albumin
- His, histidine
- IFN, interferon
- IL, interleukin
- IgG, immunoglobulin G
- KD, dissociation constant
- LMF, low molecular weight forms
- MSD, MesoScale Discovery
- MWCO, molecular weight cut-off
- NHL, non-Hodgkin lymphoma
- NK, natural killer
- NOD/scid, nonobese diabetic/severe combined immunodeficiency
- Non-Hodgkin lymphoma
- ORR, overall response rate
- PBMC, peripheral blood mononuclear cell
- PBS, phosphate buffered saline
- PES, polyethersulfone
- PHA, phytohemagglutinin
- PI, propidium iodide
- SABC, standardized antibody binding capacity
- SD, standard deviation
- SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis
- SE-HPLC, size exclusion high-pressure liquid chromatography
- SEC, size exclusion chromatography
- SPR, surface plasmon resonance
- T cells
- TNF, tumor necrosis factor
- TandAb, tandem diabody
- VH, variable heavy
- VL, variable light
- Vss, volume of distribution at steady state
- WBA, whole body autoradiography
- bispecific antibodies
- ctrl., control
- i.v., intravenous
- ka, association rate constant
- kd, dissociation rate constant
- s.c., subcutaneous
- scFv, single-chain variable fragment
- t1/2, terminal elimination half-life
- w/o, without
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Affiliation(s)
- Uwe Reusch
- a Affimed Therapeutics AG ; Heidelberg , Germany
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Wu X, Sereno AJ, Huang F, Zhang K, Batt M, Fitchett JR, He D, Rick HL, Conner EM, Demarest SJ. Protein design of IgG/TCR chimeras for the co-expression of Fab-like moieties within bispecific antibodies. MAbs 2015; 7:364-76. [PMID: 25611120 DOI: 10.1080/19420862.2015.1007826] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Immunoglobulins and T cell receptors (TCRs) share common sequences and structures. With the goal of creating novel bispecific antibodies (BsAbs), we generated chimeric molecules, denoted IgG_TCRs, where the Fv regions of several antibodies were fused to the constant domains of the α/β TCR. Replacing CH1 with Cα and CL with Cβ, respectively, was essential for achieving at least partial heavy chain/light chain assembly. Further optimization of the linker regions between the variable and constant domains, as well as replacement of the large FG loop of Cβ with a canonical β-turn, was necessary to consistently obtain full heavy chain/light chain assembly. The optimized IgG_TCR molecules were evaluated biophysically and shown to maintain the binding properties of their parental antibodies. A few BsAbs were generated by co-expressing native Fabs and IgG_TCR Fabs within the same molecular construct. We demonstrate that the IgG_TCR designs steered each of the light chains within the constructs to specifically pair with their cognate heavy chain counterparts. We did find that even with complete constant domain specificity between the CH1/CL and Cα/Cβ domains of the Fabs, strong variable domain interactions can dominate the pairing specificity and induce some mispairing. Overall, the IgG_TCR designs described here are a first step toward the generation of novel BsAbs that may be directed toward the treatment of multi-faceted and complex diseases.
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Key Words
- DSC, differential scanning calorimetry
- FG loop
- HC, heavy chain
- Ha, heavy chain containing Ca in place of CH1
- Hb, heavy chain containing Cb in place of CH1
- LC, light chain
- La, heavy chain containing Ca in place of CL
- Lb, heavy chain containing Cb in place of CL
- RU, resonance units
- SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis
- SEC, size exclusion chromatography
- SPR, surface plasmon resonance
- T cell receptor
- TCR, T cell receptor
- bispecific antibody
- protein chimera
- protein design
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Affiliation(s)
- Xiufeng Wu
- a Eli Lilly Biotechnology Center ; San Diego , CA USA
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Yang Y, Guo Q, Xia M, Li Y, Peng X, Liu T, Tong X, Xu J, Guo H, Qian W, Hou S, Dai J, Wang H, Liu R, Guo Y. Generation and characterization of a target-selectively activated antibody against epidermal growth factor receptor with enhanced anti-tumor potency. MAbs 2015; 7:440-50. [PMID: 25679409 DOI: 10.1080/19420862.2015.1008352] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Panitumumab, as a commercially available antibody, is an effective anticancer therapeutic against epidermal growth factor receptor (EGFR), although it exerts weak antibody-dependent cell-mediated cytotoxicity (ADCC) activity owing to its IgG2 nature. Here, we firstly engineered panitumumab by grafting its variable region into an IgG1 backbone. The engineered panitumumab (denoted as Pan) retained binding activity identical to the parental antibody while exhibiting stronger ADCC activity in vitro and more potent antitumor effect in vivo. To further enhance the target selectivity of Pan, we generated Pan-P by tethering an epitope-blocking peptide to Pan via a tumor-specific protease selective linker. Pan-P showed almost 40-fold weaker affinity compared with Pan, but functional activity was restored to a similar extent as Pan when Pan-P was selectively activated by urokinase-type plasminogen activator (uPA). More importantly, targeted localization of Pan-P was observed in tumor samples from colorectal cancer (CRC) patients and tumor-bearing nude mice, strongly indicating that specific activation also existed ex vivo and in vivo. Furthermore, Pan-P also exhibited effective in vivo antitumor potency similar to Pan. Taken together, our data evidence the enhanced antitumor potency and excellent target selectivity of Pan-P, suggesting its potential use for minimizing on-target toxicity in anti-EGFR therapy.
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Key Words
- ADCC
- ADCC, antibody-dependent cell-mediated cytotoxicity
- CCK-8, Cell Counting Kit 8Yun
- CI, confidence interval
- CRC, colorectal cancer
- ECD, extracellular domain
- EGFR
- EGFR VIII, EGFR Type III Variant
- EGFR, epidermal growth factor receptor
- ELISA, enzyme-linked immunosorbent assay
- HC, heavy chain
- IgG, Immunoglobulin G
- LC, light chain
- Probody™
- SEC, size exclusion chromatography
- SPR, surface plasmon resonance
- TKI, tyrosine kinase inhibitor
- mAb, monoclonal antibody
- monoclonal antibody
- panitumumab
- target-selective activation
- uPA, urokinase-type plasminogen activator
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Affiliation(s)
- Yun Yang
- a PLA General Hospital Cancer Center ; PLA School of Medicine ; Beijing , China
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Chng J, Wang T, Nian R, Lau A, Hoi KM, Ho SCL, Gagnon P, Bi X, Yang Y. Cleavage efficient 2A peptides for high level monoclonal antibody expression in CHO cells. MAbs 2015; 7:403-12. [PMID: 25621616 DOI: 10.1080/19420862.2015.1008351] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Linking the heavy chain (HC) and light chain (LC) genes required for monoclonal antibodies (mAb) production on a single cassette using 2A peptides allows control of LC and HC ratio and reduces non-expressing cells. Four 2A peptides derived from the foot-and-mouth disease virus (F2A), equine rhinitis A virus (E2A), porcine teschovirus-1 (P2A) and Thosea asigna virus (T2A), respectively, were compared for expression of 3 biosimilar IgG1 mAbs in Chinese hamster ovary (CHO) cell lines. HC and LC were linked by different 2A peptides both in the absence and presence of GSG linkers. Insertion of a furin recognition site upstream of 2A allowed removal of 2A residues that would otherwise be attached to the HC. Different 2A peptides exhibited different cleavage efficiencies that correlated to the mAb expression level. The relative cleavage efficiency of each 2A peptide remains similar for expression of different IgG1 mAbs in different CHO cells. While complete cleavage was not observed for any of the 2A peptides, GSG linkers did enhance the cleavage efficiency and thus the mAb expression level. T2A with the GSG linker (GT2A) exhibited the highest cleavage efficiency and mAb expression level. Stably amplified CHO DG44 pools generated using GT2A had titers 357, 416 and 600 mg/L for the 3 mAbs in shake flask batch cultures. Incomplete cleavage likely resulted in incorrectly processed mAb species and aggregates, which were removed with a chromatin-directed clarification method and protein A purification. The vector and methods presented provide an easy process beneficial for both mAb development and manufacturing.
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Key Words
- 2A peptide
- CHO
- CHO, Chinese hamster ovary
- E2A, 2A peptide derived from the equine rhinitis virus
- F2A, 2A peptide derived from the foot-and-mouth disease virus
- G, glycine
- GE2A, E2A with the GSG linker
- GF2A, F2A with the GSG linker
- GFP, green fluorescence protein
- GP2A, P2A with the GSG linker
- GSG linker
- GT2A, T2A with the GSG linker
- HC, heavy chain
- HT, hypoxanthine and thymine
- IRES, internal ribosome entry site
- IgG, immunoglobulin G
- K, lysine
- LC, light chain
- MS, mass spectrometry
- MTX, methotrexate
- P, proline
- P2A, 2A peptide derived from the porcine teschovirus-1
- PFM, protein-free medium
- PVDF, polyvinylidene difluoride
- SEC, size exclusion chromatography
- T2A, 2A peptide derived from the Thosea asigna virus
- cleavage efficiency
- furin
- mAb, monoclonal antibody
- monoclonal antibody
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Affiliation(s)
- Jake Chng
- a Bioprocessing Technology Institute; Agency for Science , Technology and Research (A*STAR) ; Singapore
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15
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Mendler CT, Friedrich L, Laitinen I, Schlapschy M, Schwaiger M, Wester HJ, Skerra A. High contrast tumor imaging with radio-labeled antibody Fab fragments tailored for optimized pharmacokinetics via PASylation. MAbs 2015; 7:96-109. [PMID: 25484039 PMCID: PMC4622060 DOI: 10.4161/19420862.2014.985522] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although antigen-binding fragments (Fabs) of antibodies constitute established tracers for in vivo radiodiagnostics, their functionality is hampered by a very short circulation half-life. PASylation, the genetic fusion with a long, conformationally disordered amino acid chain comprising Pro, Ala and Ser, provides a convenient way to expand protein size and, consequently, retard renal filtration. Humanized αHER2 and αCD20 Fabs were systematically fused with 100 to 600 PAS residues and produced in E. coli. Cytofluorimetric titration analysis on tumor cell lines confirmed that antigen-binding activities of the parental antibodies were retained. The radio-iodinated PASylated Fabs were studied by positron emission tomography (PET) imaging and biodistribution analysis in mouse tumor xenograft models. While the unmodified αHER2 and αCD20 Fabs showed weak tumor uptake (0.8% and 0.2% ID/g, respectively; 24 h p.i.) tumor-associated radioactivity was boosted with increasing PAS length (up to 9 and 26-fold, respectively), approaching an optimum for Fab-PAS400. Remarkably, 6- and 5-fold higher tumor-to-blood ratios compared with the unmodified Fabs were measured in the biodistribution analysis (48 h p.i.) for αHER2 Fab-PAS100 and Fab-PAS200, respectively. These findings were confirmed by PET studies, showing high imaging contrast in line with tumor-to-blood ratios of 12.2 and 5.7 (24 h p.i.) for αHER2 Fab-PAS100 and Fab-PAS200. Even stronger tumor signals were obtained with the corresponding αCD20 Fabs, both in PET imaging and biodistribution analysis, with an uptake of 2.8% ID/g for Fab-PAS100vs. 0.24% ID/g for the unmodified Fab. Hence, by engineering Fabs via PASylation, plasma half-life can be tailored to significantly improve tracer uptake and tumor contrast, thus optimally matching reagent/target interactions.
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Key Words
- ABD, albumin binding domain
- CD20
- CDC, complement-dependent cytotoxicity
- CDR, complementarity-determining region
- CLL, chronic lymphocytic leukemia
- DMEM, Dulbecco's modified Eagle medium
- EPR, enhanced permeability and retention effect
- FACS, fluorescence-activated cell sorting
- FBS, fetal bovine serum
- Fab, antigen-binding fragment
- FcRn, neonatal Fc receptor
- HER2
- HER2, human epidermal growth factor receptor 2
- ID, injected dose
- IDA, iminodiacetic acid
- Ig, immunoglobulin
- MIP, maximum intensity projection
- NHL, non-Hodgkin lymphoma
- PEGylation
- PET, positron emission tomography
- PK, pharmacokinetics
- RIT, radioimmuno therapy
- SEC, size exclusion chromatography
- SPECT, single photon emission computed tomography
- TLC, thin layer chromatography
- antibody fragment
- mAb, monoclonal antibody
- p.i., post injection
- plasma half-life
- protein tracer
- scFv, single-chain variable antibody fragment
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Affiliation(s)
- Claudia T Mendler
- a Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie ; Technische Universität München ; Freising-Weihenstephan , Germany
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16
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Scott RA, Rogers R, Balland A, Brady LJ. Rapid identification of an antibody DNA construct rearrangement sequence variant by mass spectrometry. MAbs 2015; 6:1453-63. [PMID: 25484040 DOI: 10.4161/mabs.36222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
During cell line development for an IgG1 antibody candidate (mAb1), a C-terminal extension was identified in 2 product candidate clones expressed in CHO-K1 cell line. The extension was initially observed as the presence of anomalous new peaks in these clones after analysis by cation exchange chromatography (CEX-HPLC) and reduced capillary electrophoresis (rCE-SDS). Reduced mass analysis of these CHO-K1 clones revealed that a larger than expected mass was present on a sub-population of the heavy chain species, which could not be explained by any known chemical or post-translational modifications. It was suspected that this additional mass on the heavy chain was due to the presence of an additional amino acid sequence. To identify the suspected additional sequence, de novo sequencing in combination with proteomic searching was performed against translated DNA vectors for the heavy chain and light chain. Peptides unique to the clones containing the extension were identified matching short sequences (corresponding to 9 and 35 amino acids, respectively) from 2 non-coding sections of the light chain vector construct. After investigation, this extension was observed to be due to the re-arrangement of the DNA construct, with the addition of amino acids derived from the light chain vector non-translated sequence to the C-terminus of the heavy chain. This observation showed the power of proteomic mass spectrometric techniques to identify an unexpected antibody sequence variant using de novo sequencing combined with database searching, and allowed for rapid identification of the root cause for new peaks in the cation exchange and rCE-SDS assays.
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Key Words
- C-terminal extension
- CAN, acetonitrile
- CEX, cation exchange
- CHO, Chinese hamster ovary
- DNA, deoxyribonucleic acid
- DTT, dithiothreitol
- Da, Dalton
- FDR, false discovery rate
- HC, heavy chain
- HPLC, high performance liquid chromatography
- LC, light chain
- MS, mass spectrometer
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- NCBI, National Center for Biotechnology Information
- NCG, non-concensus glycosylation
- PSM, peptide-spectrum matches
- RP-UPLC, reversed phase ultra-high pressure liquid chromatography
- SEC, size exclusion chromatography
- TFA, trifluoracetic acid
- TOF, time of flight mass spectrometer
- UV, ultraviolet
- aa, amino acids
- mass spectrometry
- ppm, parts per million
- rCE-SDS, reduced capillary electrophoresis-sodium dodecyl sulfate
- sequence variant
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Liu L, Chen J, Yang B, Wang Y. Oligomer-dependent and -independent chaperone activity of sHsps in different stressed conditions. FEBS Open Bio 2015; 5:155-62. [PMID: 25834780 DOI: 10.1016/j.fob.2015.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/20/2015] [Accepted: 02/28/2015] [Indexed: 12/12/2022] Open
Abstract
A great number of studies have proven that sHsps protect cells by inhibiting protein aggregation under heat stress, while little is known about their function to protect cells under acid stress. In this work, we show that Hsp20.1 and Hsp14.1 oligomers dissociated to smaller oligomeric species or even dimer/monomer at low pH (pH 4.0 and pH 2.0), whereas no prominent quaternary structural changes were seen at 50 °C. Both oligomers and smaller oligomeric species exhibited abilities to suppress client aggregation at low pH and at 50 °C. These results suggest that sHsps may function in different modes in different stressed conditions.
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Stracke J, Emrich T, Rueger P, Schlothauer T, Kling L, Knaupp A, Hertenberger H, Wolfert A, Spick C, Lau W, Drabner G, Reiff U, Koll H, Papadimitriou A. A novel approach to investigate the effect of methionine oxidation on pharmacokinetic properties of therapeutic antibodies. MAbs 2014; 6:1229-42. [PMID: 25517308 PMCID: PMC4622569 DOI: 10.4161/mabs.29601] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Preserving the chemical and structural integrity of therapeutic antibodies during manufacturing and storage is a major challenge during pharmaceutical development. Oxidation of Fc methionines Met252 and Met428 is frequently observed, which leads to reduced affinity to FcRn and faster plasma clearance if present at high levels. Because oxidation occurs in both positions simultaneously, their individual contribution to the concomitant changes in pharmacokinetic properties has not been clearly established. A novel pH-gradient FcRn affinity chromatography method was applied to isolate three antibody oxidation variants from an oxidized IgG1 preparation based on their FcRn binding properties. Physico-chemical characterization revealed that the three oxidation variants differed predominantly in the number of oxMet252 per IgG (0, 1, or 2), but not significantly in the content of oxMet428. Corresponding to the increase in oxMet252 content, stepwise reduction of FcRn affinity in vitro, as well as faster clearance and shorter terminal half-life, in huFcRn-transgenic mice were observed. A single Met252 oxidation per antibody had no significant effect on pharmacokinetics (PK) compared with unmodified IgG. Importantly, only molecules with both heavy chains oxidized at Met252 exhibited significantly faster clearance. In contrast, Met428 oxidation had no apparent negative effect on PK and even led to somewhat improved FcRn binding and slower clearance. This minor effect, however, seemed to be abrogated by the dominant effect of Met252 oxidation. The novel approach of functional chromatographic separation of IgG oxidation variants followed by physico-chemical and biological characterization has yielded the first experimentally-backed explanation for the unaltered PK properties of antibody preparations containing relatively high Met252 and Met428 oxidation levels.
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Key Words
- AUC, area under the concentration-time curve
- Antibody
- ESI-MS, electrospray ionization mass spectrometry
- Fab, antigen-binding fragment
- Fc, crystallizable fragment
- FcRn
- FcRn, neonatal Fc receptor
- HRP, horseradish peroxidase
- IgG, immunoglobulin G
- Met, methionine
- Met252
- Met428
- PK, pharmacokinetic
- RU, response units
- SEC, size exclusion chromatography
- SPR, surface plasmon resonance
- affinity chromatography
- column
- degradation
- m/z, mass-to-charge ratio
- mAb, monoclonal antibody
- methionine oxidation
- neonatal Fc receptor
- pH gradient
- pharmacokinetics
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Affiliation(s)
- Jan Stracke
- a Biochemical and Analytical Research; Large Molecule Research ; Roche Pharma Research and Early Development (pRED); Roche Innovation Center ; Penzberg , Germany
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Gamble M, Künze G, Brancale A, Wilson KS, Jones DD. The role of substrate specificity and metal binding in defining the activity and structure of an intracellular subtilisin. FEBS Open Bio 2012; 2:209-15. [PMID: 23650602 PMCID: PMC3642151 DOI: 10.1016/j.fob.2012.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 11/25/2022] Open
Abstract
The dimeric intracellular subtilisin proteases (ISPs) found throughout Gram-positive bacteria are a structurally distinct class of the subtilase family. Unlike the vast majority of subtilisin-like proteases, the ISPs function exclusively within the cell, contributing the majority of observed cellular proteolytic activity. Given that they are active within the cell, little is known about substrate specificity and the role of stress signals such as divalent metal ions in modulating ISP function. We demonstrate that both play roles in defining the proteolytic activity of Bacillus clausii ISP and propose the molecular basis of their effects. Enzyme kinetics reveal that one particular synthetic tetrapeptide substrate, Phe-Ala-Ala-Phe-pNA, is hydrolysed with a catalytic efficiency ∼100-fold higher than any other tested. Heat-denatured whole proteins were found to be better substrates for ISP than the native forms. Substrate binding simulations suggest that the S1, S2 and S4 sites form defined binding pockets. The deep S1 cavity and wide S4 site are fully occupied by the hydrophobic aromatic side-chains of Phe. Divalent metal ions, probably Ca2+, are proposed to be important for ISP activity through structural changes. The presence of >0.01 mM EDTA inactivates ISP, with CD and SEC suggesting that the protein becomes less structured and potentially monomeric. Removal of Ca2+ at sites close to the dimer interface and the S1 pocket are thought to be responsible for the effect. These studies provide a new insight into the potential physiological function of ISPs, by reconciling substrate specificity and divalent metal binding to associate ISP with the unfolded protein response under stress conditions.
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Affiliation(s)
- Michael Gamble
- School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
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