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Wohlschlager T, Scheffler K, Forstenlehner IC, Skala W, Senn S, Damoc E, Holzmann J, Huber CG. Native mass spectrometry combined with enzymatic dissection unravels glycoform heterogeneity of biopharmaceuticals. Nat Commun 2018; 9:1713. [PMID: 29712889 PMCID: PMC5928108 DOI: 10.1038/s41467-018-04061-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 03/30/2018] [Indexed: 12/18/2022] Open
Abstract
Robust manufacturing processes resulting in consistent glycosylation are critical for the efficacy and safety of biopharmaceuticals. Information on glycosylation can be obtained by conventional bottom–up methods but is often limited to the glycan or glycopeptide level. Here, we apply high-resolution native mass spectrometry (MS) for the characterization of the therapeutic fusion protein Etanercept to unravel glycoform heterogeneity in conditions of hitherto unmatched mass spectral complexity. Higher spatial resolution at lower charge states, an inherent characteristic of native MS, represents a key component for the successful revelation of glycan heterogeneity. Combined with enzymatic dissection using a set of proteases and glycosidases, assignment of specific glycoforms is achieved by transferring information from subunit to whole protein level. The application of native mass spectrometric analysis of intact Etanercept as a fingerprinting tool for the assessment of batch-to-batch variability is exemplified and may be extended to demonstrate comparability after changes in the biologic manufacturing process. The specific glycosylation patterns of biological drugs often impact the efficacy and safety of the therapeutic product. Here the authors describe a native mass spectrometry approach that allows the resolution of highly complex glycosylation patterns on large proteins, which they apply to the therapeutic Fc-fusion protein Etanercept.
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Affiliation(s)
- Therese Wohlschlager
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Kai Scheffler
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Thermo Fisher Scientific GmbH, Dornierstraße 4, 82110, Germering, Germany
| | - Ines C Forstenlehner
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Technical Development Biosimilars, Global Drug Development, Novartis, Sandoz GmbH, Biochemiestrasse 10, 6250, Kundl, Austria
| | - Wolfgang Skala
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Stefan Senn
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Eugen Damoc
- Thermo Fisher Scientific GmbH, Hanna-Kunath-Strasse 11, 28199, Bremen, Germany
| | - Johann Holzmann
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.,Technical Development Biosimilars, Global Drug Development, Novartis, Sandoz GmbH, Biochemiestrasse 10, 6250, Kundl, Austria
| | - Christian G Huber
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria. .,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
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Skala W, Wohlschlager T, Senn S, Huber GE, Huber CG. MoFi: A Software Tool for Annotating Glycoprotein Mass Spectra by Integrating Hybrid Data from the Intact Protein and Glycopeptide Level. Anal Chem 2018; 90:5728-5736. [DOI: 10.1021/acs.analchem.8b00019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Wolfgang Skala
- Department of Biosciences, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Therese Wohlschlager
- Department of Biosciences, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Stefan Senn
- Department of Biosciences, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Gabriel E. Huber
- Department of Biosciences, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences, Bioanalytical Research Laboratories, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
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Guo S, Skala W, Magdolen V, Briza P, Biniossek ML, Schilling O, Kellermann J, Brandstetter H, Goettig P. A Single Glycan at the 99-Loop of Human Kallikrein-related Peptidase 2 Regulates Activation and Enzymatic Activity. J Biol Chem 2015; 291:593-604. [PMID: 26582203 PMCID: PMC4705380 DOI: 10.1074/jbc.m115.691097] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 01/20/2023] Open
Abstract
Human kallikrein-related peptidase 2 (KLK2) is a key serine protease in semen liquefaction and prostate cancer together with KLK3/prostate-specific antigen. In order to decipher the function of its potential N-glycosylation site, we produced pro-KLK2 in Leishmania tarentolae cells and compared it with its non-glycosylated counterpart from Escherichia coli expression. Mass spectrometry revealed that Asn-95 carries a core glycan, consisting of two GlcNAc and three hexoses. Autocatalytic activation was retarded in glyco-pro-KLK2, whereas the activated glyco-form exhibited an increased proteolytic resistance. The specificity patterns obtained by the PICS (proteomic identification of protease cleavage sites) method are similar for both KLK2 variants, with a major preference for P1-Arg. However, glycosylation changes the enzymatic activity of KLK2 in a drastically substrate-dependent manner. Although glyco-KLK2 has a considerably lower catalytic efficiency than glycan-free KLK2 toward peptidic substrates with P2-Phe, the situation was reverted toward protein substrates, such as glyco-pro-KLK2 itself. These findings can be rationalized by the glycan-carrying 99-loop that prefers to cover the active site like a lid. By contrast, the non-glycosylated 99-loop seems to favor a wide open conformation, which mostly increases the apparent affinity for the substrates (i.e. by a reduction of Km). Also, the cleavage pattern and kinetics in autolytic inactivation of both KLK2 variants can be explained by a shift of the target sites due to the presence of the glycan. These striking effects of glycosylation pave the way to a deeper understanding of kallikrein-related peptidase biology and pathology.
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Affiliation(s)
- Shihui Guo
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Wolfgang Skala
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Viktor Magdolen
- the Klinische Forschergruppe der Frauenklinik, Klinikum Rechts der Isar der TU München, 81675 Munich, Germany
| | - Peter Briza
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | | | - Oliver Schilling
- the Institute of Molecular Medicine and Cell Research and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany, the German Cancer Consortium (DKTK), 69120 Heidelberg, Germany, the German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, and
| | - Josef Kellermann
- the Max-Planck-Institute for Biochemistry, 82152 Martinsried, Germany
| | - Hans Brandstetter
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Peter Goettig
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria,
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Skala W, Utzschneider DT, Magdolen V, Debela M, Guo S, Craik CS, Brandstetter H, Goettig P. Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity. J Biol Chem 2014; 289:34267-83. [PMID: 25326387 PMCID: PMC4256358 DOI: 10.1074/jbc.m114.598201] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the “classical” KLKs 1–3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn2+ concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn2+, which located the Zn2+ binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation.
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Affiliation(s)
- Wolfgang Skala
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Daniel T Utzschneider
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, D-81675 Munich, Germany
| | - Viktor Magdolen
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, D-81675 Munich, Germany
| | - Mekdes Debela
- Max-Planck-Institut for Biochemistry, Proteinase Research Group, D-82152 Martinsried, Germany, and
| | - Shihui Guo
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Hans Brandstetter
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Peter Goettig
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria,
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Guo S, Skala W, Magdolen V, Brandstetter H, Goettig P. Sweetened kallikrein-related peptidases (KLKs): glycan trees as potential regulators of activation and activity. Biol Chem 2014; 395:959-76. [PMID: 25153382 DOI: 10.1515/hsz-2014-0140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/29/2014] [Indexed: 02/15/2024]
Abstract
Most kallikrein-related peptidases (KLKs) are N-glycosylated with N-acetylglucosamine2-mannose9 units at Asn-Xaa-Ser/Thr sequons during protein synthesis and translocation into the endoplasmic reticulum. These N-glycans are modified in the Golgi machinery, where additional O-glycosylation at Ser and Thr takes place, before exocytotic release of the KLKs into the extracellular space. Sequons are present in all 15 members of the KLKs and comparative studies for KLKs from natural and recombinant sources elucidated some aspects of glycosylation. Although glycosylation of mammalian KLKs 1, 3, 4, 6, and 8 has been analyzed in great detail, e.g., by crystal structures, the respective function remains largely unclear. In some cases, altered enzymatic activity was observed for KLKs upon glycosylation. Remarkably, for KLK3/PSA, changes in the glycosylation pattern were observed in samples of benign prostatic hyperplasia and prostate cancer with respect to healthy individuals. Potential functions of KLK glycosylation in structural stabilization, protection against degradation, and activity modulation of substrate specificity can be deduced from a comparison with other glycosylated proteins and their regulation. According to the new concept of protein sectors, glycosylation distant from the active site might significantly influence the activity of proteases. Novel pharmacological approaches can exploit engineered glycans in the therapeutical context.
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Skala W, Goettig P, Brandstetter H. Do-it-yourself histidine-tagged bovine enterokinase: a handy member of the protein engineer's toolbox. J Biotechnol 2013; 168:421-5. [PMID: 24184090 PMCID: PMC3863954 DOI: 10.1016/j.jbiotec.2013.10.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/08/2013] [Accepted: 10/14/2013] [Indexed: 11/21/2022]
Abstract
Enterokinase, a two-chain duodenal serine protease, activates trypsinogen by removing its N-terminal propeptide. Due to a clean cut after the non-primed site recognition sequence, the enterokinase light chain is frequently employed in biotechnology to separate N-terminal affinity tags from target proteins with authentic N-termini. In order to obtain large quantities of this protease, we adapted an in vitro folding protocol for a pentahistidine-tagged triple mutant of the bovine enterokinase light chain. The purified, highly active enzyme successfully processed recombinant target proteins, while the pentahistidine-tag facilitated post-cleavage removal. Hence, we conclude that producing enterokinase in one's own laboratory is an efficient alternative to the commercial enzyme.
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Affiliation(s)
| | | | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstraße 11, 5020 Salzburg, Austria
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