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Koy C, Röwer C, Thiesen HJ, Neamtu A, Glocker MO. Intact Transition Epitope Mapping-Force Interferences by Variable Extensions (ITEM-FIVE). Biomolecules 2024; 14:454. [PMID: 38672470 PMCID: PMC11048379 DOI: 10.3390/biom14040454] [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: 02/28/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Investigations on binding strength differences of non-covalent protein complex components were performed by mass spectrometry. T4 fibritin foldon (T4Ff) is a well-studied miniprotein, which together with its biotinylated version served as model system to represent a compactly folded protein to which an Intrinsically Disordered Region (IDR) was attached. The apparent enthalpies of the gas phase dissociation reactions of the homo-trimeric foldon F-F-F and of the homo-trimeric triply biotinylated foldon bF-bF-bF have been determined to be rather similar (3.32 kJ/mol and 3.85 kJ/mol) but quite distinct from those of the singly and doubly biotinylated hetero-trimers F-F-bF and F-bF-bF (1.86 kJ/mol and 1.08 kJ/mol). Molecular dynamics simulations suggest that the ground states of the (biotinylated) T4Ff trimers are highly symmetric and well comparable to each other, indicating that the energy levels of all four (biotinylated) T4Ff trimer ground states are nearly indistinguishable. The experimentally determined differences and/or similarities in enthalpies of the complex dissociation reactions are explained by entropic spring effects, which are noticeable in the T4Ff hetero-trimers but not in the T4Ff homo-trimers. A lowering of the transition state energy levels of the T4Ff hetero-trimers seems likely because the biotin moieties, mimicking intrinsically disordered regions (IDRs), induced asymmetries in the transition states of the biotinylated T4Ff hetero-trimers. This transition state energy level lowering effect is absent in the T4Ff homo-trimer, as well as in the triply biotinylated T4Ff homo-trimer. In the latter, the IDR-associated entropic spring effects on complex stability cancel each other out. ITEM-FIVE enabled semi-quantitative determination of energy differences of complex dissociation reactions, whose differences were modulated by IDRs attached to compactly folded proteins.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
| | - Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
| | - Hans-Jürgen Thiesen
- Institute for Immunology, Medical Faculty, University of Rostock, Schillingallee 70, 18057 Rostock, Germany;
| | - Andrei Neamtu
- Department of Physiology, “Gr. T. Popa” University of Medicine and Pharmacy, Str. Universitatii nr. 16, 700115 Iasi, Romania
- TRANSCEND Centre, Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2–4, 700483 Iasi, Romania
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
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Röwer C, Olaleye OO, Bischoff R, Glocker MO. Mass Spectrometric ITEM-ONE and ITEM-TWO Analyses Confirm and Refine an Assembled Epitope of an Anti-Pertuzumab Affimer. Biomolecules 2023; 14:24. [PMID: 38254624 PMCID: PMC10813730 DOI: 10.3390/biom14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Intact Transition Epitope Mapping-One-step Non-covalent force Exploitation (ITEM-ONE) analysis reveals an assembled epitope on the surface of Pertuzumab, which is recognized by the anti-Pertuzumab affimer 00557_709097. It encompasses amino acid residues NSGGSIYNQRFKGR, which are part of CDR2, as well as residues FTLSVDR, which are located on the variable region of Pertuzumab's heavy chain and together form a surface area of 1381.46 Å2. Despite not being part of Pertuzumab's CDR2, the partial sequence FTLSVDR marks a unique proteotypic Pertuzumab peptide. Binding between intact Pertuzumab and the anti-Pertuzumab affimer was further investigated using the Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) approach. Quantitative analysis of the complex dissociation reaction in the gas phase afforded a quasi-equilibrium constant (KD m0g#) of 3.07 × 10-12. The experimentally determined apparent enthalpy (ΔHm0g#) and apparent free energy (ΔGm0g#) of the complex dissociation reaction indicate that the opposite reaction-complex formation-is spontaneous at room temperature. Due to strong binding to Pertuzumab and because of recognizing Pertuzumab's unique partial amino acid sequences, the anti-Pertuzumab affimer 00557_709097 is considered excellently suitable for implementation in Pertuzumab quantitation assays as well as for the accurate therapeutic drug monitoring of Pertuzumab in biological fluids.
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
| | - Oladapo O. Olaleye
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
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Billinger K, Okai CA, Russ M, Koy C, Röwer C, Opuni KFM, Illges H, Pecks U, Glocker MO. Dried serum spots on pre-punched filter paper discs are ready-to-use storage and shipping devices for blood-borne antigens and antibodies. J Immunol Methods 2023; 519:113519. [PMID: 37419022 DOI: 10.1016/j.jim.2023.113519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
Dried serum spots that are well prepared can be attractive alternatives to frozen serum samples for shelving specimens in a medical or research center's biobank and mailing freshly prepared serum to specialized laboratories. During the pre-analytical phase, complications can arise which are often challenging to identify or are entirely overlooked. These complications can lead to reproducibility issues, which can be avoided in serum protein analysis by implementing optimized storage and transfer procedures. With a method that ensures accurate loading of filter paper discs with donor or patient serum, a gap in dried serum spot preparation and subsequent serum analysis shall be filled. Pre-punched filter paper discs with a 3 mm diameter are loaded within seconds in a highly reproducible fashion (approximately 10% standard deviation) when fully submerged in 10 μl of serum, named the "Submerge and Dry" protocol. Such prepared dried serum spots can store several hundred micrograms of proteins and other serum components. Serum-borne antigens and antibodies are reproducibly released in 20 μl elution buffer in high yields (approximately 90%). Dried serum spot-stored and eluted antigens kept their epitopes and antibodies their antigen binding abilities as was assessed by SDS-PAGE, 2D gel electrophoresis-based proteomics, and Western blot analysis, suggesting pre-punched filter paper discs as handy solution for serological tests.
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Affiliation(s)
- Kira Billinger
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Charles A Okai
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Manuela Russ
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Kwabena F M Opuni
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, P. O. Box LG43, Legon, Ghana
| | - Harald Illges
- Department of Applied Natural Sciences, Immunology and Cell Biology, Institute of Functional Gene Analytics, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359 Rheinbach, Germany
| | - Ulrich Pecks
- Department of Obstetrics and Gynecology, Medical Faculty, University of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany.
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Lupu LM, Wiegand P, Holdschick D, Mihoc D, Maeser S, Rawer S, Völklein F, Malek E, Barka F, Knauer S, Uth C, Hennermann J, Kleinekofort W, Hahn A, Barka G, Przybylski M. Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination. Int J Mol Sci 2021; 22:12832. [PMID: 34884636 PMCID: PMC8657952 DOI: 10.3390/ijms222312832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (KD) of a protein-antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled ("conformational") antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA-aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.
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Affiliation(s)
- Loredana-Mirela Lupu
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Pascal Wiegand
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Daria Holdschick
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Delia Mihoc
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stefan Maeser
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stephan Rawer
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Friedemann Völklein
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Ebrahim Malek
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Frederik Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Sascha Knauer
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Christina Uth
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Julia Hennermann
- Department of Pediatrics, Universitätsmedizin Mainz, 55130 Mainz, Germany;
| | - Wolfgang Kleinekofort
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, Feulgenstraße 10-12, 35389 Giessen, Germany;
| | - Günes Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Michael Przybylski
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
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Danquah BD, Röwer C, Opuni KM, El-Kased R, Frommholz D, Illges H, Koy C, Glocker MO. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE). Mol Cell Proteomics 2019; 18:1543-1555. [PMID: 31147491 PMCID: PMC6683010 DOI: 10.1074/mcp.ra119.001429] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
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Affiliation(s)
- Bright D Danquah
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Reham El-Kased
- ¶Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - David Frommholz
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany
| | - Harald Illges
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany;; **University of Applied Sciences Bonn-Rhein-Sieg, Institute for Functional Gene Analytics, Rheinbach, Germany
| | - Cornelia Koy
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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Ion L, Petre BA. Immuno-Affinity Mass Spectrometry: A Novel Approaches with Biomedical Relevance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:377-388. [DOI: 10.1007/978-3-030-15950-4_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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El-Kased RF. Immuno-analytical approach and its application for cardiac disease marker detection. J Immunoassay Immunochem 2018; 39:538-550. [PMID: 30212265 DOI: 10.1080/15321819.2018.1518241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cardiac troponin-I is a promising diagnostic marker for cardiovascular diseases. Troponin-I immunoassays rely on monoclonal antibodies, while polyclonal antibodies, cheaper to manufacture, are uncommonly used. The current study established an immuno-analytical assay using a polyclonal antibody capable of mapping troponin-I antigenic determinant. Proteolytic digestion of troponin-I was performed. Antigenic determinant was assigned by separation of fragments using gel electrophoresis followed by Western blot and high-performance liquid chromatography followed by dot blot. The antigenic determinant region appeared within amino acid sequence 30-90. This robust procedure is suitable for early prognosis of diseases, stratification of patients, and possibly individualized therapy.
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Affiliation(s)
- Reham F El-Kased
- a Microbiology and Immunology, Faculty of Pharmacy , The British University in Egypt (BUE) , Cairo , Egypt
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8
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Opuni KFM, Al-Majdoub M, Yefremova Y, El-Kased RF, Koy C, Glocker MO. Mass spectrometric epitope mapping. MASS SPECTROMETRY REVIEWS 2018; 37:229-241. [PMID: 27403762 DOI: 10.1002/mas.21516] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies. While up to now monoclonal antibodies have been mostly used in epitope mapping experiments, the applicability of polyclonal antibodies has been proven. The antibody's resistance towards enzymatic proteolysis has been of key importance for the two mostly applied methods: epitope excision and epitope extraction. Sample consumption has dropped to low pmol amounts on both, the antigen and the antibody. While adequate in-solution sample handling has been most important for successful epitope mapping, mass spectrometric analysis has been found the most suitable read-out method from early on. The rapidity by which mass spectrometric epitope mapping nowadays is executed outperforms all alternative methods. Thus, it can be asserted that mass spectrometric epitope mapping has reached a state of maturity, which allows it to be used in any mass spectrometry laboratory. After 25 years of constant and steady improvements, its application to clinical samples, for example, for patient characterization and stratification, is anticipated in the near future. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:229-241, 2018.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Mahmoud Al-Majdoub
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Reham F El-Kased
- Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
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Yefremova Y, Opuni KFM, Danquah BD, Thiesen HJ, Glocker MO. Intact Transition Epitope Mapping (ITEM). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1612-1622. [PMID: 28616748 DOI: 10.1007/s13361-017-1654-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
Intact transition epitope mapping (ITEM) enables rapid and accurate determination of protein antigen-derived epitopes by either epitope extraction or epitope excision. Upon formation of the antigen peptide-containing immune complex in solution, the entire mixture is electrosprayed to translate all constituents as protonated ions into the gas phase. There, ions from antibody-peptide complexes are separated from unbound peptide ions according to their masses, charges, and shapes either by ion mobility drift or by quadrupole ion filtering. Subsequently, immune complexes are dissociated by collision induced fragmentation and the ion signals of the "complex-released peptides," which in effect are the epitope peptides, are recorded in the time-of-flight analyzer of the mass spectrometer. Mixing of an antibody solution with a solution in which antigens or antigen-derived peptides are dissolved is, together with antigen proteolysis, the only required in-solution handling step. Simplicity of sample handling and speed of analysis together with very low sample consumption makes ITEM faster and easier to perform than other experimental epitope mapping methods. Graphical Abstract ᅟ.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Kwabena F M Opuni
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Hans-Juergen Thiesen
- Institute of Immunology, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany.
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IgG anti-tTG responses in different autoimmune conditions differ in their epitope targets and subclass usage. Mol Immunol 2015; 67:369-76. [DOI: 10.1016/j.molimm.2015.06.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/18/2015] [Accepted: 06/24/2015] [Indexed: 02/07/2023]
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11
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Yefremova Y, Al-Majdoub M, Opuni KF, Koy C, Cui W, Yan Y, Gross M, Glocker MO. "De-novo" amino acid sequence elucidation of protein G'e by combined "top-down" and "bottom-up" mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:482-492. [PMID: 25560987 PMCID: PMC6130978 DOI: 10.1007/s13361-014-1053-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 11/20/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Mass spectrometric de-novo sequencing was applied to review the amino acid sequence of a commercially available recombinant protein G´ with great scientific and economic importance. Substantial deviations to the published amino acid sequence (Uniprot Q54181) were found by the presence of 46 additional amino acids at the N-terminus, including a so-called "His-tag" as well as an N-terminal partial α-N-gluconoylation and α-N-phosphogluconoylation, respectively. The unexpected amino acid sequence of the commercial protein G' comprised 241 amino acids and resulted in a molecular mass of 25,998.9 ± 0.2 Da for the unmodified protein. Due to the higher mass that is caused by its extended amino acid sequence compared with the original protein G' (185 amino acids), we named this protein "protein G'e." By means of mass spectrometric peptide mapping, the suggested amino acid sequence, as well as the N-terminal partial α-N-gluconoylations, was confirmed with 100% sequence coverage. After the protein G'e sequence was determined, we were able to determine the expression vector pET-28b from Novagen with the Xho I restriction enzyme cleavage site as the best option that was used for cloning and expressing the recombinant protein G'e in E. coli. A dissociation constant (K(d)) value of 9.4 nM for protein G'e was determined thermophoretically, showing that the N-terminal flanking sequence extension did not cause significant changes in the binding affinity to immunoglobulins.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | | | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Weidong Cui
- Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yuetian Yan
- Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Gross
- Washington University in St. Louis, St. Louis, Missouri, USA
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12
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Al-Majdoub M, Opuni KFM, Koy C, Glocker MO. Facile Fabrication and Instant Application of Miniaturized Antibody-Decorated Affinity Columns for Higher-Order Structure and Functional Characterization of TRIM21 Epitope Peptides. Anal Chem 2013; 85:10479-87. [DOI: 10.1021/ac402559m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M. Al-Majdoub
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - K. F. M. Opuni
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - C. Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - M. O. Glocker
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
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13
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Al-Majdoub M, Koy C, Lorenz P, Thiesen HJ, Glocker MO. Mass spectrometric and peptide chip characterization of an assembled epitope: analysis of a polyclonal antibody model serum directed against the Sjøgren/systemic lupus erythematosus autoantigen TRIM21. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:651-659. [PMID: 23722955 DOI: 10.1002/jms.3208] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 03/19/2013] [Accepted: 03/24/2013] [Indexed: 06/02/2023]
Abstract
We demonstrate the development of a mass spectrometry-based epitope-mapping procedure in combination with Western blot analysis that works also with antigens that are insoluble in nondenaturing buffers consuming minute amounts of antigen (approximately 200 pmol) and antibody (approximately 15 pmol), respectively. A polyclonal anti-TRIM21 rabbit antibody serum is applied as a model serum for future patient analyses to set up the system. The major epitope that is recognized by the anti-TRIM21 serum spans the central TRIM21 region LQ-ELEKDEREQLRILGE-KE, showing that immunization with a 139-amino acid residue long peptide resulted in a 'monospecific' polyclonal antibody repertoire. Protein structure investigations, secondary structure predictions, and surface area calculations revealed that the best matching partial sequence to fulfill all primary and secondary structure requirements was the four amino acid spanning motif 'L-E-Q-L', which is present in both the sequential and the α-helical peptide conformation. Peptide chip analyses confirmed the mass spectrometric results and showed that the peptide chip platform is an appropriate method for displaying secondary structure-relying epitope conformations. As the same secondary structures are present in vivo, patient antibody screening, e.g., to identify subgroups of patients according to distinct epitope antibody reactivities, is feasible.
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Affiliation(s)
- M Al-Majdoub
- Proteome Center Rostock, University of Rostock, Rostock, Germany
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14
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Kubrycht J, Sigler K, Souček P. Virtual interactomics of proteins from biochemical standpoint. Mol Biol Int 2012; 2012:976385. [PMID: 22928109 PMCID: PMC3423939 DOI: 10.1155/2012/976385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/18/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022] Open
Abstract
Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.
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Affiliation(s)
- Jaroslav Kubrycht
- Department of Physiology, Second Medical School, Charles University, 150 00 Prague, Czech Republic
| | - Karel Sigler
- Laboratory of Cell Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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15
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Linnebacher M, Lorenz P, Koy C, Jahnke A, Born N, Steinbeck F, Wollbold J, Latzkow T, Thiesen HJ, Glocker MO. Clonality characterization of natural epitope-specific antibodies against the tumor-related antigen topoisomerase IIa by peptide chip and proteome analysis: a pilot study with colorectal carcinoma patient samples. Anal Bioanal Chem 2012; 403:227-38. [PMID: 22349330 DOI: 10.1007/s00216-012-5781-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 01/16/2012] [Accepted: 01/23/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Medical Faculty, University of Rostock, Rostock, Germany
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16
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Wei J, Gu Y, Yang J, Yang Y, Wang S, Cui S, Zhu X. Identification and characterization of protective epitope of Trichinella spiralis paramyosin. Vaccine 2011; 29:3162-8. [PMID: 21382481 DOI: 10.1016/j.vaccine.2011.02.072] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 02/10/2011] [Accepted: 02/15/2011] [Indexed: 11/16/2022]
Abstract
Trichinella spiralis paramyosin (Ts-Pmy) is a protective antigen that induces partial immunity against T. spiralis infection in mice. To identify protective epitope of Ts-Pmy, a monoclonal antibody (mAb) 7E2 against the recombinant protein was generated, which partially protected against T. spiralis infection following passive transfer. The mAb was used to screen a random phage-displayed peptide library. Ten positive clones were identified, most of which matched amino acids 88-107 or 108-127 of Ts-Pmy. Expression of overlapping fragments of Ts-Pmy in E. coli confirmed that region 88-107 was specifically recognized by 7E2. A peptide based on this epitope region (YX1) was synthesized and shown to compete with native Ts-Pmy for binding to 7E2. Mice immunized with KLH-conjugated YX1 were protected against T. spiralis larval challenge. The identification of a protective epitope within Ts-Pmy highlights the possibility of developing a subunit vaccine against T. spiralis infection.
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Affiliation(s)
- Junfei Wei
- Department of Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China
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17
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El Khoury G, Laurenceau E, Chevolot Y, Souteyrand E, Cloarec JP. A generic surface chemistry for peptide microarrays implementation: Application to the detection of anti-H3 antibody. Biosens Bioelectron 2010; 26:1320-5. [DOI: 10.1016/j.bios.2010.07.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 07/02/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
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18
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El-Kased RF, Koy C, Lorenz P, Drynda S, Guthke R, Qian Z, Koczan D, Li Y, Kekow J, Thiesen HJ, Glocker MO. Mass spectrometric and peptide chip epitope analysis on the RA33 autoantigen with sera from rheumatoid arthritis patients. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:443-451. [PMID: 20530829 DOI: 10.1255/ejms.1046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
As the potential of epitope chips for routine application in diagnostics relies on the careful selection of peptides, reliable epitope mapping results are of utmost interest to the medical community. Mass spectrometric epitope mapping in combination with peptide chip analysis showed that autoantibodies from patients who suffered from rheumatoid arthritis (RA) were directed against distinct surface structures on the full-length human autoantigen RA33 as well as against partial sequences. Using the combined mass spectrometric epitope extraction and peptide chip analysis approach, four sequence motifs on RA33 emerged as immuno-positive, showing that epitopes were not randomly distributed on the entire RA33 amino acid sequence. A sequential epitope motif ((245)GYGGG(249)) was determined on the C-terminal part of RA33 which matched with the Western blot patient screening results using the full-length protein and, thus, was regarded as a disease-associated epitope. Other epitope motifs were found on N-terminal partial sequences ((59)RSRGFGF(65), (111)KKLFVG(116)) and again on the C-terminal part ((266)NQQPSNYG(273)) of RA33. As recognition of these latter three motifs was also recorded by peptide chip analysis using control samples which were negative in the Western blot screening, these latter motifs were regarded as "cryptic epitopes". Knowledge of disease-associated epitopes is crucial for improving the design of a customized epitope peptide chip for RA and mass spectrometric epitope mapping pivotally assisted with selecting the most informative peptide(s) to be used for future diagnostic purposes.
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Affiliation(s)
- R F El-Kased
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Germany
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