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Abstract
Membrane proteins are responsible for a large variety of tasks in organisms and of particular interesting as drug targets. At the same time, they are notoriously difficult to work with and require a thorough characterization before proceeding with structural studies. Here, we present a biophysical pipeline to characterize membrane proteins focusing on the optimization of stability, aggregation behavior, and homogeneity. The pipeline shown here is built on three biophysical techniques: differential scanning fluorimetry using native protein fluorescence (nano differential scanning fluorimetry), dynamic light scattering, and mass photometry. For each of these techniques, we provide detailed protocols for performing experiments and data analysis.
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Affiliation(s)
- Stephan Niebling
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Osvaldo Burastero
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - María García-Alai
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
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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: 8] [Impact Index Per Article: 4.0] [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: 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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3
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Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG. Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. J Biol Chem 2021; 297:101175. [PMID: 34499924 PMCID: PMC8421091 DOI: 10.1016/j.jbc.2021.101175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/08/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 01/22/2023] Open
Abstract
The spike protein is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the human angiotensin-converting enzyme 2 receptor, a critical step in infection, and is the preferential target for spike-neutralizing antibodies. Posttranslational modifications of the spike receptor-binding motif have been shown to modulate viral infectivity and host immune response, but these modifications are still being explored. Here we studied asparagine deamidation of the spike protein, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, which affect both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike protein. Asparagine residues 481 and 501 in the receptor-binding motif deamidate with a half-life of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed at 4 °C, indicating a strong dependence of spike protein molecular aging on environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the human angiotensin-converting enzyme 2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion illustrating how deamidation of the spike receptor-binding motif could lead to the accumulation on the virion surface of a nonnegligible chemically diverse spike population in a timescale of days. Our findings provide a potential mechanism for molecular aging of the spike protein with significant consequences for understanding virus infectivity and vaccine development.
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Affiliation(s)
- Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Lucas A Defelipe
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lucio Aliperti
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Christian Löw
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María García-Alai
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Ignacio E Sánchez
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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