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Guérin M, Vandevenne M, Brans A, Matagne A, Marquant R, Prost E, Octave S, Avalle B, Maffucci I, Padiolleau-Lefèvre S. Production, purification, and quality assessment of borrelial proteins CspZ from Borrelia burgdorferi and FhbA from Borrelia hermsii. Appl Microbiol Biotechnol 2024; 108:425. [PMID: 39042328 PMCID: PMC11266248 DOI: 10.1007/s00253-024-13195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 07/24/2024]
Abstract
Borrelia, spirochetes transmitted by ticks, are the etiological agents of numerous multisystemic diseases, such as Lyme borreliosis (LB) and tick-borne relapsing fever (TBRF). This study focuses on two surface proteins from two Borrelia subspecies involved in these diseases: CspZ, expressed by Borrelia burgdorferi sensu stricto (also named BbCRASP-2 for complement regulator-acquiring surface protein 2), and the factor H binding A (FhbA), expressed by Borrelia hermsii. Numerous subspecies of Borrelia, including these latter, are able to evade the immune defenses of a variety of potential vertebrate hosts in a number of ways. In this context, previous data suggested that both surface proteins play a role in the immune evasion of both Borrelia subspecies by interacting with key regulators of the alternative pathway of the human complement system, factor H (FH) and FH-like protein 1 (FHL-1). The recombinant proteins, CspZ and FhbA, were expressed in Escherichia coli and purified by one-step metal-affinity chromatography, with yields of 15 and 20 mg or pure protein for 1 L of cultured bacteria, respectively. The purity was evaluated by SDS-PAGE and HPLC and is close to about 95%. The mass of CspZ and FhbA was checked by mass spectrometry (MS). Proper folding of CspZ and FhbA was confirmed by circular dichroism (CD), and their biological activity, namely their interaction with purified FH from human serum (recombinant FH15-20 and recombinant FHL-1), was characterized by SPR. Such a study provides the basis for the biochemical characterization of the studied proteins and their biomolecular interactions which is a necessary prerequisite for the development of new approaches to improve the current diagnosis of LB and TBRF. KEY POINTS: • DLS, CD, SEC-MALS, NMR, HPLC, and MS are tools for protein quality assessment • Borrelia spp. possesses immune evasion mechanisms, including human host complement • CspZ and FhbA interact with high affinity (pM to nM) to human FH and rFHL-1.
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Affiliation(s)
- Mickaël Guérin
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Marylène Vandevenne
- Robotein®, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, Liège, 4000, Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Liège, Sart- Tilman), 4000, Belgium
| | - Alain Brans
- Protein Factory, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, Liège, 4000, Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Liège, Sart- Tilman), 4000, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Sart-Tilman, Liège, 4000, Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, Liège, Sart- Tilman), 4000, Belgium
| | - Rodrigue Marquant
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Elise Prost
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Stéphane Octave
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Bérangère Avalle
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Irene Maffucci
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France
| | - Séverine Padiolleau-Lefèvre
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, Compiègne, 60203, France.
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2
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Petrovskiy DV, Nikolsky KS, Kulikova LI, Rudnev VR, Butkova TV, Malsagova KA, Kopylov AT, Kaysheva AL. PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models. Sci Rep 2024; 14:15000. [PMID: 38951578 PMCID: PMC11217302 DOI: 10.1038/s41598-024-65861-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024] Open
Abstract
The primary objective of analyzing the data obtained in a mass spectrometry-based proteomic experiment is peptide and protein identification, or correct assignment of the tandem mass spectrum to one amino acid sequence. Comparison of empirical fragment spectra with the theoretical predicted one or matching with the collected spectra library are commonly accepted strategies of proteins identification and defining of their amino acid sequences. Although these approaches are widely used and are appreciably efficient for the well-characterized model organisms or measured proteins, they cannot detect novel peptide sequences that have not been previously annotated or are rare. This study presents PowerNovo tool for de novo sequencing of proteins using tandem mass spectra acquired in a variety of types of mass analyzers and different fragmentation techniques. PowerNovo involves an ensemble of models for peptide sequencing: model for detecting regularities in tandem mass spectra, precursors, and fragment ions and a natural language processing model, which has a function of peptide sequence quality assessment and helps with reconstruction of noisy sequences. The results of testing showed that the performance of PowerNovo is comparable and even better than widely utilized PointNovo, DeepNovo, Casanovo, and Novor packages. Also, PowerNovo provides complete cycle of processing (pipeline) of mass spectrometry data and, along with predicting the peptide sequence, involves the peptide assembly and protein inference blocks.
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3
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Harvey IB, Chilewski SD, Bhosale D, Tobia SE, Gray C, Gleason C, Haulenbeek J. Overcoming Lot-to-Lot Variability in Protein Activity Using Epitope-Specific Calibration-Free Concentration Analysis. Anal Chem 2024; 96:6275-6281. [PMID: 38600735 PMCID: PMC11044105 DOI: 10.1021/acs.analchem.3c05607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Concentration determination is a fundamental hallmark of protein reagent characterization, providing a means to ensure reproducibility and unify measurements from various assays. However, lot-to-lot differences in protein activity often still occur, leading to uncertainty in the accuracy of downstream measurements. Here, we postulate that those differences are caused by a misrepresentation of the protein concentration as measured by traditional total protein techniques, which can include multiple types of inactive protein species. To overcome this, we developed a standardized method to quantify a protein's active concentration via calibration-free concentration analysis (CFCA). As a pilot study, we compare the biophysical and immunoassay responses from three batches of recombinant soluble lymphocyte-activation gene 3 (sLAG3), as defined by either their total or active concentrations. Defining the sLAG3 reagents by their assay-specific concentration improved consistency in reported kinetic binding parameters and decreased immunoassay lot-to-lot coefficients of variation (CVs) by over 600% compared to the total protein concentration. These findings suggest that the total concentration of a protein reagent may not be the ideal metric to correlate in-assay signals between lots, and by instead quantifying the concentrations of a reagent's assay-specific epitopes, CFCA may prove a useful tool in overcoming lot-to-lot variability.
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Affiliation(s)
- Ian B. Harvey
- Translational
Sciences and Diagnostics, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
| | - Shannon D. Chilewski
- Translational
Sciences and Diagnostics, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
| | - Devyani Bhosale
- Translational
Sciences and Diagnostics, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
| | - Sarah E. Tobia
- Translational
Sciences and Diagnostics, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
| | - Christopher Gray
- Translational
Sciences and Diagnostics, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
| | - Carol Gleason
- Global
Biometrics and Data Sciences, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
| | - Jonathan Haulenbeek
- Translational
Sciences and Diagnostics, Bristol-Myers
Squibb, Princeton, New Jersey 08540, United States
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4
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Zuber PK, Said N, Hilal T, Wang B, Loll B, González-Higueras J, Ramírez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH. Concerted transformation of a hyper-paused transcription complex and its reinforcing protein. Nat Commun 2024; 15:3040. [PMID: 38589445 PMCID: PMC11001881 DOI: 10.1038/s41467-024-47368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
RfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an α-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a β-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.
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Affiliation(s)
- Philipp K Zuber
- Biochemistry IV-Biophysical Chemistry, Universität Bayreuth, Bayreuth, Germany
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nelly Said
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tarek Hilal
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
- Research Center of Electron Microscopy and Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany
| | - Bing Wang
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Bernhard Loll
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | | | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany.
| | - Stefan H Knauer
- Biochemistry IV-Biophysical Chemistry, Universität Bayreuth, Bayreuth, Germany.
- Bristol-Myers Squibb GmbH & Co. KGaA, Munich, Germany.
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5
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Eweje F, Walsh ML, Ahmad K, Ibrahim V, Alrefai A, Chen J, Chaikof EL. Protein-based nanoparticles for therapeutic nucleic acid delivery. Biomaterials 2024; 305:122464. [PMID: 38181574 PMCID: PMC10872380 DOI: 10.1016/j.biomaterials.2023.122464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/25/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
Abstract
To realize the full potential of emerging nucleic acid therapies, there is a need for effective delivery agents to transport cargo to cells of interest. Protein materials exhibit several unique properties, including biodegradability, biocompatibility, ease of functionalization via recombinant and chemical modifications, among other features, which establish a promising basis for therapeutic nucleic acid delivery systems. In this review, we highlight progress made in the use of non-viral protein-based nanoparticles for nucleic acid delivery in vitro and in vivo, while elaborating on key physicochemical properties that have enabled the use of these materials for nanoparticle formulation and drug delivery. To conclude, we comment on the prospects and unresolved challenges associated with the translation of protein-based nucleic acid delivery systems for therapeutic applications.
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Affiliation(s)
- Feyisayo Eweje
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Harvard and MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA, USA, 02115; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Michelle L Walsh
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Harvard and MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA, USA, 02115
| | - Kiran Ahmad
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Vanessa Ibrahim
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Assma Alrefai
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jiaxuan Chen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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6
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Lebendiker M. Purification and Quality Control of Recombinant Proteins Expressed in Mammalian Cells: A Practical Review. Methods Mol Biol 2024; 2810:329-353. [PMID: 38926289 DOI: 10.1007/978-1-0716-3878-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
In the recent years, there has been a rapid development of new technologies and strategies when it comes to protein purification and quality control (QC), but the basic technologies for these processes go back a long way, with many improvements over the past few decades. The purpose of this chapter is to review these approaches, as well as some other topics such as the advantages and disadvantages of various purification methods for intracellular or extracellular proteins, the most effective and widely used genetically engineered affinity tags, solubility-enhancing tags, and specific proteases for removal of nontarget sequences. Affinity chromatography (AC), like Protein A or G resins for the recovery of antibodies or Fc fusion proteins or immobilized metals for the recovery of histidine-tagged proteins, will be discussed along with other conventional chromatography techniques: ion exchange (IEC), hydrophobic exchange (HEC), mixed mode (MMC), size exclusion (SEC), and ultrafiltration (UF) systems. How to select and combine these different technologies for the purification of any given protein and the minimal criteria for QC characterization of the purity, homogeneity, identity, and integrity of the final product will be presented.
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Affiliation(s)
- Mario Lebendiker
- Protein Expression and Purification Facilities, The Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem, Israel.
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7
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Lyons-Abbott S, Abramov A, Chan CL, Deer JR, Fu G, Hassouneh W, Koch T, Misquith A, O'Neill J, Simon SA, Wolf A, Yeh R, Vernet E. Choice of fusion proteins, expression host, and analytics solves difficult-to-produce protein challenges in discovery research. Biotechnol J 2024; 19:e2300162. [PMID: 37802118 DOI: 10.1002/biot.202300162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
High quality biological reagents are a prerequisite for pharmacological research. Herein a protein production screening approach, including quality assessment methods, for protein-based discovery research is presented. Trends from 2895 expression constructs representing 253 proteins screened in mammalian and bacterial hosts-91% of which are successfully expressed and purified-are discussed. Mammalian expression combined with the use of solubility-promoting fusion proteins is deemed suitable for most targets. Furthermore, cases utilizing stable cell line generation and choice of fusion protein for higher yield and quality of difficult-to-produce proteins (Leucine-rich repeat-containing G-protein coupled receptor 4 (LGR4) and Neurturin) are presented and discussed. In the case of Neurturin, choice of fusion protein impacted the target binding 80-fold. These results highlight the need for exploration of construct designs and careful Quality Control (QC) of difficult-to-produce protein reagents.
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Affiliation(s)
| | - Ariel Abramov
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Chung-Leung Chan
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Jen Running Deer
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Guangsen Fu
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Wafa Hassouneh
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Tyree Koch
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Ayesha Misquith
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Jason O'Neill
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | | | - Anitra Wolf
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Ronald Yeh
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Erik Vernet
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
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8
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Rahiman N, Zamani P, Arabi L, Alavizadeh SH, Nikpoor A, Mashreghi M, Badiee A, Jaafari MR. Novel liposomal glatiramer acetate: Preparation and immunomodulatory evaluation in murine model of multiple sclerosis. Int J Pharm 2023; 648:123620. [PMID: 37981250 DOI: 10.1016/j.ijpharm.2023.123620] [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: 06/12/2023] [Revised: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
The frequent administration rate required for Glatiramer acetate (GA), a first-line therapy for Multiple sclerosis (MS), poses patient compliance issues. Only a small portion of the subcutaneously administered GA is available for phagocytosis by macrophages, as most of it is hydrolyzed at its administration site or excreted renally. To unravel these hurdles, we have prepared liposomal formulations of GA through thin film-hydration method plus extrusion. The clinical and histopathological efficacy of GA-loaded liposomes were assessed in prophylactic and therapeutic manners on murine model of MS (experimental autoimmune encephalomyelitis (EAE)). The selected GA liposomal formulation showed favorable size (275 nm on average), high loading efficiency, and high macrophage localization. Moreover, administration of GA-liposomes in mice robustly suppressed the inflammatory responses and decreased the inflammatory and demyelinated lesion regions in CNS compared to the free GA with subsequent reduction of the EAE clinical score. Our study indicated that liposomal GA could be served as a reliable nanomedicine-based platform to hopefully curb MS-related aberrant autoreactive immune responses with higher efficacy, longer duration of action, fewer administration frequencies, and higher delivery rate to macrophages. This platform has the potential to be introduced as a vaccine for MS after clinical translation and merits further investigations.
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Affiliation(s)
- Niloufar Rahiman
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvin Zamani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Leila Arabi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyedeh Hoda Alavizadeh
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aminreza Nikpoor
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Mashreghi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Badiee
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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9
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Schütz A, Bernhard F, Berrow N, Buyel JF, Ferreira-da-Silva F, Haustraete J, van den Heuvel J, Hoffmann JE, de Marco A, Peleg Y, Suppmann S, Unger T, Vanhoucke M, Witt S, Remans K. A concise guide to choosing suitable gene expression systems for recombinant protein production. STAR Protoc 2023; 4:102572. [PMID: 37917580 PMCID: PMC10643540 DOI: 10.1016/j.xpro.2023.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular protein. By answering four key questions, readers can determine the most suitable gene expression system following a decision scheme. This guide addresses the most commonly used and accessible systems and provides brief descriptions of the main gene expression systems' key characteristics to assist decision making. Additionally, information has been included for selected less frequently used "exotic" gene expression systems.
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Affiliation(s)
- Anja Schütz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform for Protein Production & Characterization, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe-University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Johannes F Buyel
- Univeristy of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria
| | - Frederico Ferreira-da-Silva
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Jurgen Haustraete
- VIB, Center for Inflammation Research & Ugent, Department of Biomedical Molecular Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Joop van den Heuvel
- Helmholtz Centre for Infection Research (HZI), Department of Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sabine Suppmann
- Protein Expression and Purification Core Facility, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tamar Unger
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martine Vanhoucke
- BCCM/GeneCorner Plasmid Collection, Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Gent, Belgium
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Notkestr. 85, 22607 Hamburg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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10
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Pan SQ, Luo P, Chen J, Wu T, Xu B, Chen F, Wu DY, Ren B, Liu GK, Xie J, Xu P, Tian ZQ. Seeing Is Not Necessarily Believing: Is the Surface-Enhanced Raman Spectroscopy Signal Really from the Target? Anal Chem 2023; 95:13346-13352. [PMID: 37611317 DOI: 10.1021/acs.analchem.3c02683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Reagent purity is crucial to experimental research, considering that the ignorance of ultratrace impurities may induce wrong conclusions in either revealing the reaction nature or qualifying the target. Specifically, in the field of surface science, the strong interaction between the impurity and the surface will bring a non-negligible negative effect. Surface-enhanced Raman spectroscopy (SERS) is a highly surface-sensitive technique, providing fingerprint identification and near-single molecule sensitivity. In the SERS analysis of trace chloromethyl diethyl phosphate (DECMP), we figured out that the SERS performance of DECMP is significantly distorted by the trace impurities from DECMP. With the aid of gas chromatography-based techniques, one strongly interfering impurity (2,2-dichloro-N,N-dimethylacetamide), the byproduct during the synthesis of DECMP, was confirmed. Furthermore, the nonignorable interference of impurities on the SERS measurement of NaBr, NaI, or sulfadiazine was also observed. The generality ignited us to refresh and consolidate the guideline for the reliable SERS qualitative analysis, by which the potential misleading brought by ultratrace impurities, especially those strongly adsorbed on Au or Ag surfaces, could be well excluded.
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Affiliation(s)
- Si-Qi Pan
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ping Luo
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jia Chen
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Tairui Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Fushan Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - De-Yin Wu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bin Ren
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Guo-Kun Liu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Pengxiang Xu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhong-Qun Tian
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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11
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Gedeon A, Ayoub N, Brûlé S, Raynal B, Karimova G, Gelin M, Mechaly A, Haouz A, Labesse G, Munier‐Lehmann H. Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases. Protein Sci 2023; 32:e4703. [PMID: 37338125 PMCID: PMC10357500 DOI: 10.1002/pro.4703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inosine 5'-monophosphate (IMP) dehydrogenase (IMPDH) is an ubiquitous enzyme that catalyzes the NAD+ -dependent oxidation of inosine 5'-monophosphate into xanthosine 5'-monophosphate. This enzyme is formed of two distinct domains, a core domain where the catalytic reaction occurs, and a less-conserved Bateman domain. Our previous studies gave rise to the classification of bacterial IMPDHs into two classes, according to their oligomeric and kinetic properties. MgATP is a common effector but cause to different effects when it binds within the Bateman domain: it is either an allosteric activator for Class I IMPDHs or a modulator of the oligomeric state for Class II IMPDHs. To get insight into the role of the Bateman domain in the dissimilar properties of the two classes, deleted variants of the Bateman domain and chimeras issued from the interchange of the Bateman domain between the three selected IMPDHs have been generated and characterized using an integrative structural biology approach. Biochemical, biophysical, structural, and physiological studies of these variants unveil the Bateman domain as being the carrier of the molecular behaviors of both classes.
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Affiliation(s)
- Antoine Gedeon
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Unité de Microbiologie Structurale, CNRS UMR3525ParisFrance
| | - Nour Ayoub
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
| | - Sébastien Brûlé
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Bertrand Raynal
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Gouzel Karimova
- Institut Pasteur, Université Paris Cité, Unité de Biochimie des Interactions Macromoléculaires, CNRS UMR3528ParisFrance
| | - Muriel Gelin
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Gilles Labesse
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Hélène Munier‐Lehmann
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
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12
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Pham PN, Zahradník J, Kolářová L, Schneider B, Fuertes G. Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light. Front Mol Biosci 2023; 10:1214235. [PMID: 37484532 PMCID: PMC10361524 DOI: 10.3389/fmolb.2023.1214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
Human interleukin 24 (IL-24) is a multifunctional cytokine that represents an important target for autoimmune diseases and cancer. Since the biological functions of IL-24 depend on interactions with membrane receptors, on-demand regulation of the affinity between IL-24 and its cognate partners offers exciting possibilities in basic research and may have applications in therapy. As a proof-of-concept, we developed a strategy based on recombinant soluble protein variants and genetic code expansion technology to photocontrol the binding between IL-24 and one of its receptors, IL-20R2. Screening of non-canonical ortho-nitrobenzyl-tyrosine (NBY) residues introduced at several positions in both partners was done by a combination of biophysical and cell signaling assays. We identified one position for installing NBY, tyrosine70 of IL-20R2, which results in clear impairment of heterocomplex assembly in the dark. Irradiation with 365-nm light leads to decaging and reconstitutes the native tyrosine of the receptor that can then associate with IL-24. Photocaged IL-20R2 may be useful for the spatiotemporal control of the JAK/STAT phosphorylation cascade.
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Affiliation(s)
- Phuong Ngoc Pham
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Faculty of Science, Charles University, Prague, Czechia
| | - Jiří Zahradník
- First Faculty of Medicine, BIOCEV Center, Charles University, Prague, Czechia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Gustavo Fuertes
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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13
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England E, Rees DG, Scott IC, Carmen S, Chan DTY, Chaillan Huntington CE, Houslay KF, Erngren T, Penney M, Majithiya JB, Rapley L, Sims DA, Hollins C, Hinchy EC, Strain MD, Kemp BP, Corkill DJ, May RD, Vousden KA, Butler RJ, Mustelin T, Vaughan TJ, Lowe DC, Colley C, Cohen ES. Tozorakimab (MEDI3506): an anti-IL-33 antibody that inhibits IL-33 signalling via ST2 and RAGE/EGFR to reduce inflammation and epithelial dysfunction. Sci Rep 2023; 13:9825. [PMID: 37330528 PMCID: PMC10276851 DOI: 10.1038/s41598-023-36642-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Interleukin (IL)-33 is a broad-acting alarmin cytokine that can drive inflammatory responses following tissue damage or infection and is a promising target for treatment of inflammatory disease. Here, we describe the identification of tozorakimab (MEDI3506), a potent, human anti-IL-33 monoclonal antibody, which can inhibit reduced IL-33 (IL-33red) and oxidized IL-33 (IL-33ox) activities through distinct serum-stimulated 2 (ST2) and receptor for advanced glycation end products/epidermal growth factor receptor (RAGE/EGFR complex) signalling pathways. We hypothesized that a therapeutic antibody would require an affinity higher than that of ST2 for IL-33, with an association rate greater than 107 M-1 s-1, to effectively neutralize IL-33 following rapid release from damaged tissue. An innovative antibody generation campaign identified tozorakimab, an antibody with a femtomolar affinity for IL-33red and a fast association rate (8.5 × 107 M-1 s-1), which was comparable to soluble ST2. Tozorakimab potently inhibited ST2-dependent inflammatory responses driven by IL-33 in primary human cells and in a murine model of lung epithelial injury. Additionally, tozorakimab prevented the oxidation of IL-33 and its activity via the RAGE/EGFR signalling pathway, thus increasing in vitro epithelial cell migration and repair. Tozorakimab is a novel therapeutic agent with a dual mechanism of action that blocks IL-33red and IL-33ox signalling, offering potential to reduce inflammation and epithelial dysfunction in human disease.
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Affiliation(s)
| | - D Gareth Rees
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Ian Christopher Scott
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sara Carmen
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Kirsty F Houslay
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Teodor Erngren
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mark Penney
- Early Oncology DMPK, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jayesh B Majithiya
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Laura Rapley
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dorothy A Sims
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Claire Hollins
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Elizabeth C Hinchy
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Dominic J Corkill
- Bioscience In Vivo, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Richard D May
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - David C Lowe
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | | | - E Suzanne Cohen
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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14
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Beslic D, Tscheuschner G, Renard BY, Weller MG, Muth T. Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly. Brief Bioinform 2023; 24:bbac542. [PMID: 36545804 PMCID: PMC9851299 DOI: 10.1093/bib/bbac542] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody-antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69-99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
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Affiliation(s)
- Denis Beslic
- Robert Koch Institute, MF1, Nordufer 20, 13353 Berlin
| | - Georg Tscheuschner
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin
| | - Bernhard Y Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam
| | - Michael G Weller
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin
| | - Thilo Muth
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin
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15
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Robert C, Kerff F, Bouillenne F, Gavage M, Vandevenne M, Filée P, Matagne A. Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition. J Biol Chem 2023; 299:102892. [PMID: 36642181 PMCID: PMC9929448 DOI: 10.1016/j.jbc.2023.102892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
Bone morphogenetic proteins (BMPs) are secreted cytokines belonging to the transforming growth factor-β superfamily. New therapeutic approaches based on BMP activity, particularly for cartilage and bone repair, have sparked considerable interest; however, a lack of understanding of their interaction pathways and the side effects associated with their use as biopharmaceuticals have dampened initial enthusiasm. Here, we used BMP-2 as a model system to gain further insight into both the relationship between structure and function in BMPs and the principles that govern affinity for their cognate antagonist Noggin. We produced BMP-2 and Noggin as inclusion bodies in Escherichia coli and developed simple and efficient protocols for preparing pure and homogeneous (in terms of size distribution) solutions of the native dimeric forms of the two proteins. The identity and integrity of the proteins were confirmed using mass spectrometry. Additionally, several in vitro cell-based assays, including enzymatic measurements, RT-qPCR, and matrix staining, demonstrated their biological activity during cell chondrogenic and hypertrophic differentiation. Furthermore, we characterized the simple 1:1 noncovalent interaction between the two ligands (KDca. 0.4 nM) using bio-layer interferometry and solved the crystal structure of the complex using X-ray diffraction methods. We identified the residues and binding forces involved in the interaction between the two proteins. Finally, results obtained with the BMP-2 N102D mutant suggest that Noggin is remarkably flexible and able to accommodate major structural changes at the BMP-2 level. Altogether, our findings provide insights into BMP-2 activity and reveal the molecular details of its interaction with Noggin.
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Affiliation(s)
- Charly Robert
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium,Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Frédéric Kerff
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium,Biological Macromolecule Crystallography, University of Liège, Liège, Belgium
| | - Fabrice Bouillenne
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Maxime Gavage
- Analytical Laboratory, CER Groupe, rue du Point du Jour, Marloie, Belgium
| | - Marylène Vandevenne
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium,Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium
| | - Patrice Filée
- Laboratory of immuno-biology, CER Groupe, Novalis Science Park, Aye, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium; Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium.
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16
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Nafaee ZH, Hunyadi-Gulyás É, Gyurcsik B. Temoneira-1 β-lactamase is not a metalloenzyme, but its native metal ion binding sites allow for purification by immobilized metal ion affinity chromatography. Protein Expr Purif 2023; 201:106169. [DOI: 10.1016/j.pep.2022.106169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
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17
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Niebling S, Veith K, Vollmer B, Lizarrondo J, Burastero O, Schiller J, Struve García A, Lewe P, Seuring C, Witt S, García-Alai M. Biophysical Screening Pipeline for Cryo-EM Grid Preparation of Membrane Proteins. Front Mol Biosci 2022; 9:882288. [PMID: 35813810 PMCID: PMC9259969 DOI: 10.3389/fmolb.2022.882288] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Successful sample preparation is the foundation to any structural biology technique. Membrane proteins are of particular interest as these are important targets for drug design, but also notoriously difficult to work with. For electron cryo-microscopy (cryo-EM), the biophysical characterization of sample purity, homogeneity, and integrity as well as biochemical activity is the prerequisite for the preparation of good quality cryo-EM grids as these factors impact the result of the computational reconstruction. Here, we present a quality control pipeline prior to single particle cryo-EM grid preparation using a combination of biophysical techniques to address the integrity, purity, and oligomeric states of membrane proteins and its complexes to enable reproducible conditions for sample vitrification. Differential scanning fluorimetry following the intrinsic protein fluorescence (nDSF) is used for optimizing buffer and detergent conditions, whereas mass photometry and dynamic light scattering are used to assess aggregation behavior, reconstitution efficiency, and oligomerization. The data collected on nDSF and mass photometry instruments can be analyzed with web servers publicly available at spc.embl-hamburg.de. Case studies to optimize conditions prior to cryo-EM sample preparation of membrane proteins present an example quality assessment to corroborate the usefulness of our pipeline.
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Affiliation(s)
- Stephan Niebling
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Benjamin Vollmer
- Centre for Structural Systems Biology (CSSB), Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Osvaldo Burastero
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Janina Schiller
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Angelica Struve García
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - María García-Alai
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- *Correspondence: María García-Alai,
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18
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Remans K, Lebendiker M, Abreu C, Maffei M, Sellathurai S, May MM, Vaněk O, de Marco A. Protein purification strategies must consider downstream applications and individual biological characteristics. Microb Cell Fact 2022; 21:52. [PMID: 35392897 PMCID: PMC8991485 DOI: 10.1186/s12934-022-01778-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins are used as reagents in a broad range of scientific fields. The reliability and reproducibility of experimental data will largely depend on the quality of the (recombinant) proteins and, consequently, these should undergo thorough structural and functional controls. Depending on the downstream application and the biochemical characteristics of the protein, different sets of specific features will need to be checked. RESULTS A number of examples, representative of recurrent issues and previously published strategies, has been reported that illustrate real cases of recombinant protein production in which careful strategy design at the start of the project combined with quality controls throughout the production process was imperative to obtain high-quality samples compatible with the planned downstream applications. Some proteins possess intrinsic properties (e.g., prone to aggregation, rich in cysteines, or a high affinity for nucleic acids) that require certain precautions during the expression and purification process. For other proteins, the downstream application might demand specific conditions, such as for proteins intended for animal use that need to be endotoxin-free. CONCLUSIONS This review has been designed to act as a practical reference list for researchers who wish to produce and evaluate recombinant proteins with certain specific requirements or that need particular care for their preparation and storage.
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Affiliation(s)
- Kim Remans
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mario Lebendiker
- Protein Purification Facility, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Mariano Maffei
- Evvivax Biotech, Via di Castel Romano 100, 00128, Rome, Italy
| | | | - Marina M May
- AiCuris Anti-Infective Cures AG, Friedrich-Ebert-Str. 475, 42117, Wuppertal, Germany
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000, Rožna Dolina-Nova Gorica, Slovenia.
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19
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Cytoplasmic Production of Nanobodies and Nanobody-Based Reagents by Co-Expression of Sulfhydryl Oxidase and DsbC Isomerase. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:145-157. [PMID: 35157272 DOI: 10.1007/978-1-0716-2075-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nanobodies are stable molecules that can often fold correctly even in the absence of the disulfide bond(s) that stabilize their three-dimensional conformation. Nevertheless, some nanobodies require the formation of disulfide bonds, and therefore they are commonly expressed from vectors that promote their secretion into the oxidizing environment of the Escherichia coli periplasm. As an alternative, the bacterial cytoplasm can be an effective compartment for producing correctly folded nanobodies when sulfhydryl oxidase and disulfide-bond isomerase activities are co-expressed from a recombinant vector. The larger volume and wider chaperone/foldase availability of the cytoplasm enable the achievement of high yields of both nanobodies and nanobody-tag fusions, independently of their redox requirements. Among other examples, the protocol described here was used to successfully produce nanobody fusions with fluorescent proteins that do not fold correctly in the periplasm, nanobodies with Fc domains, and nanobodies containing free cysteine tags.
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20
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De March M, Terdoslavich M, Polez S, Guarnaccia C, Poggianella M, Marcello A, Skoko N, de Marco A. Expression, purification and characterization of SARS-CoV-2 spike RBD in ExpiCHO cells. Protein Expr Purif 2022; 194:106071. [PMID: 35172194 PMCID: PMC8841003 DOI: 10.1016/j.pep.2022.106071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/02/2022] [Accepted: 02/11/2022] [Indexed: 11/14/2022]
Abstract
Reliable diagnosis is critical to identify infections of SARS-CoV-2 as well as to evaluate the immune response to virus and vaccines. Consequently, it becomes crucial the isolation of sensitive antibodies to use as immunocapture elements of diagnostic tools. The final bottleneck to achieve these results is the availability of enough antigen of good quality. We have established a robust pipeline for the production of recombinant, functional SARS-CoV-2 Spike receptor binding domain (RBD) at high yield and low cost in culture flasks. RBD was expressed in transiently transfected ExpiCHO cells at 32 °C and 5% CO2 and purified up to 40 mg/L. The progressive protein accumulation in the culture medium was monitored with an immunobinding assay in order to identify the optimal collection time. Successively, a two-step chromatographic protocol enabled its selective purification in the monomeric state. RBD quality assessment was positively evaluated by SDS-PAGE, Western Blotting and Mass Spectrometry, while Bio-Layer Interferometry, flow cytometer and ELISA tests confirmed its functionality. This effective protocol for the RBD production in transient eukaryotic system can be immediately extended to the production of RBD mutants.
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Quality control of purified proteins to improve data quality and reproducibility: results from a large-scale survey. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:453-460. [PMID: 33881595 DOI: 10.1007/s00249-021-01528-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/23/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
As the scientific community strives to make published results more transparent and reliable, it has become obvious that poor data reproducibility can often be attributed to insufficient quality control of experimental reagents. In this context, proteins and peptides reagents require much stricter quality controls than those routinely performed on them in a significant proportion of research laboratories. Members of the ARBRE-MOBIEU and the P4EU networks have combined their expertise to generate guidelines for the evaluation of purified proteins used in life sciences and medical trials. These networks, representing more than 150 laboratories specialized in protein production and/or protein molecular biophysics, have implemented such guidelines in their respective laboratories. Over a one-year period, the network members evaluated the contribution these guidelines made toward obtaining more productive, robust and reproducible research by correlating the applied quality controls to given samples with the reliability and reproducibility of the scientific data obtained using these samples in follow-up experiments. The results indicate that QC guideline implementation facilitates the optimization of the protein purification process and improves the reliability of downstream experiments. It seems, therefore, that investing in protein QC might be advantageous to all the stakeholders in life sciences (researchers, editors, and funding agencies alike), because this practice improves data veracity and minimizes loss of valuable time and resources. In the light of these conclusions, the network members suggest that the implementation of these simple QC guidelines should become minimal reporting practice in the publication of data derived from the use of protein and peptide reagents.
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