Structural stability of chromophore-grafted Ubiquitin mutants in vacuum
Structural biology is witnessing a transformative era with gas-phase techniques such as native mass spectrometry (MS), ion mobility, and single-particle imaging (SPI) emerging as critical tools for studying biomolecular assemblies like protein capsids in their native states. SPI with X-ray free-electron lasers has the potential to allow for capturing atomic-resolution structures of proteins without crystallization. However, determining particle orientation during exposure remains a major challenge, compounded by the heterogeneity of the protein complexes. Gas-phase Förster resonance energy transfer (FRET) offers a promising solution to assess alignment-induced structural perturbations, providing insights into the stability of the tertiary structure under various activation methods. This study employs molecular dynamics (MD) simulations to explore chromophore integration's effect on ubiquitin's structure and alignment properties in vacuum. Ubiquitin serves as an ideal model due to its small size, well-characterized properties, and computational simplicity. By investigating chromophore placement, we identified optimal sites for monitoring gas-phase denaturation and unfolding processes, advancing SPI applications and a broader understanding of protein stability in the gas phase.
Authors
- Thomas Mandl (ORCID: https://orcid.org/0000-0002-8398-9699)
- Charlotte Uetrecht (ORCID: https://orcid.org/0000-0002-1991-7922)
- Jocky C. K. Kung (ORCID: https://orcid.org/0000-0002-1943-4832)
- Steven Daly (ORCID: https://orcid.org/0000-0002-3268-8247)
- Carl Caleman (ORCID: https://orcid.org/0000-0003-2638-1940)
- Emiliano De Santis (ORCID: https://orcid.org/0000-0001-5029-7429)
- Luke MacAleese (ORCID: https://orcid.org/0000-0001-8821-6049)
- Khôn Huynh (ORCID: https://orcid.org/0000-0001-5630-0369)
- Erik G. Marklund (ORCID: https://orcid.org/0000-0002-9804-5009)
- Lorenza A. D'Alessandro (ORCID: https://orcid.org/0009-0003-5786-6833)
Institutions
- Université Claude Bernard Lyon 1 (FR)
- University of Rome Tor Vergata (IT)
- University of Applied Sciences Technikum Wien (AT)
- Uppsala University (SE)
- Vietnam National University Ho Chi Minh City (VN)
- Centre National de la Recherche Scientifique (FR)
- Leibniz Institute of Virology (LIV) (DE)
- Universität Hamburg (DE)
- Deutsches Elektronen-Synchrotron DESY (DE)
- Institut Lumière Matière (FR)
- Center for Free-Electron Laser Science (DE)
- Centre for Structural Systems Biology (DE)
- University of Lübeck (DE)
Publication Details
- Journal
- Physical Chemistry Chemical Physics
- Published
- 2025-01-01
- DOI
- https://doi.org/10.1039/d5cp01297j
- Primary Topic
- DNA and Nucleic Acid Chemistry
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Bundesministerium für Bildung und Forschung
- Vetenskapsrådet
- Röntgen-Ångström Cluster
- Deutsches Elektronen-Synchrotron