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Hoppe IJ, Prommegger B, Uhl A, Lohrig U, Huber CG, Brandstetter H. The Fluorescent Enzyme Cascade Detects Low Abundance Protein Modifications Suitable for the Assembly of Functionally Annotated Modificatome Databases. Chembiochem 2022; 23:e202200399. [PMID: 35920326 DOI: 10.1002/cbic.202200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/27/2022] [Indexed: 01/07/2023]
Abstract
Pathophysiological functions of proteins critically depend on both their chemical composition, including post-translational modifications, and their three-dimensional structure, commonly referred to as structure-activity relationship. Current analytical methods, like capillary electrophoresis or mass spectrometry, suffer from limitations, such as the detection of unexpected modifications at low abundance and their insensitivity to conformational changes. Building on previous enzyme-based analytical methods, we here introduce a fluorescence-based enzyme cascade (fEC), which can detect diverse chemical and conformational variations in protein samples and assemble them into digital databases. Together with complementary analytical methods an automated fEC analysis established unique modification-function relationships, which can be expanded to a proteome-wide scale, i. e. a functionally annotated modificatome. The fEC offers diverse applications, including hypersensitive biomarker detection in complex samples.
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Affiliation(s)
- Isabel J Hoppe
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Bernhard Prommegger
- Department of Artificial Intelligence and Human Interfaces, University of Salzburg, Jakob Haringer Str. 2, A-5020, Salzburg, Austria
| | - Andreas Uhl
- Department of Artificial Intelligence and Human Interfaces, University of Salzburg, Jakob Haringer Str. 2, A-5020, Salzburg, Austria
| | - Urs Lohrig
- Technical Development Biosimilars, Global Drug Development, Novartis, Sandoz GmbH, Biochemiestr. 10, A-6250, Kundl, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
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Mills-Goodlet R, Johnson L, Hoppe IJ, Regl C, Geppert M, Schenck M, Huber S, Hauser M, Ferreira F, Hüsing N, Huber CG, Brandstetter H, Duschl A, Himly M. The nanotopography of SiO 2 particles impacts the selectivity and 3D fold of bound allergens. Nanoscale 2021; 13:20508-20520. [PMID: 34854455 PMCID: PMC8675021 DOI: 10.1039/d1nr05958k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
A detailed description of the changes that occur during the formation of protein corona represents a fundamental question in nanoscience, given that it not only impacts the behaviour of nanoparticles but also affects the bound proteins. Relevant questions include whether proteins selectively bind particles, whether a specific orientation is preferred for binding, and whether particle binding leads to a modulation of their 3D fold. For allergens, it is important to answer these questions given that all these effects can modify the allergenic response of atopic individuals. These potential impacts on the bound allergen are closely related to the specific properties of the involved nanoparticles. One important property influencing the formation of protein corona is the nanotopography of the particles. Herein, we studied the effect of nanoparticle porosity on allergen binding using mesoporous and non-porous SiO2 NPs. We investigated (i) the selectivity of allergen binding from a mixture such as crude pollen extract, (ii) whether allergen binding results in a preferred orientation, (iii) the influence of binding on the conformation of the allergen, and (iv) how the binding affects the allergenic response. Nanotopography was found to play a major role in the formation of protein corona, impacting the physicochemical and biological properties of the NP-bound allergen. The porosity of the surface of the SiO2 nanoparticles resulted in a higher binding capacity with pronounced selectivity for (preferentially) binding the major birch pollen allergen Bet v 1. Furthermore, the binding of Bet v 1 to the mesoporous rather than the non-porous SiO2 nanoparticles influenced the 3D fold of the protein, resulting in at least partial unfolding. Consequently, this conformational change influenced the allergenic response, as observed by mediator release assays employing the sera of patients and immune effector cells. For an in-depth understanding of the bio-nano interactions, the properties of the particles need to be considered not only regarding the identity and morphology of the material, but also their nanotopography, given that porosity may greatly influence the structure, and hence the biological behaviour of the bound proteins. Thus, thorough structural investigations upon the formation of protein corona are important when considering immunological outcomes, as particle binding can influence the allergenic response elicited by the bound allergen.
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Affiliation(s)
| | - Litty Johnson
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Isabel J Hoppe
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, Paris Lodron University of Salzburg, Austria
| | - Christof Regl
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Mark Geppert
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Milena Schenck
- Dept. Chemistry and Physics of Materials, Paris Lodron University of Salzburg, Austria
| | - Sara Huber
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Michael Hauser
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Fátima Ferreira
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Nicola Hüsing
- Dept. Chemistry and Physics of Materials, Paris Lodron University of Salzburg, Austria
| | - Christian G Huber
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, Paris Lodron University of Salzburg, Austria
| | - Hans Brandstetter
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, Paris Lodron University of Salzburg, Austria
| | - Albert Duschl
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
| | - Martin Himly
- Dept. Biosciences, Paris Lodron University of Salzburg, Austria.
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