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Specifying conformational heterogeneity of multi-domain proteins at atomic resolution

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2023

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Structure. Elsevier. 2023, 31(10), pp. 1259-1274.e10. ISSN 0969-2126. eISSN 1878-4186. Available under: doi: 10.1016/j.str.2023.07.008

Zusammenfassung

The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.

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540 Chemie

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click chemistry, conformational ensembles, conformational heterogeneity, MD simulations, multi-domain proteins, NMR spectroscopy, paramagnetic relaxation enhancement, spin relaxation, protein dynamics, ubiquitin chains

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ISO 690SCHNEIDER, Tobias, Kevin SAWADE, Frederic BERNER, Christine PETER, Michael KOVERMANN, 2023. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. In: Structure. Elsevier. 2023, 31(10), pp. 1259-1274.e10. ISSN 0969-2126. eISSN 1878-4186. Available under: doi: 10.1016/j.str.2023.07.008
BibTex
@article{Schneider2023-10Speci-67597,
  year={2023},
  doi={10.1016/j.str.2023.07.008},
  title={Specifying conformational heterogeneity of multi-domain proteins at atomic resolution},
  number={10},
  volume={31},
  issn={0969-2126},
  journal={Structure},
  pages={1259--1274.e10},
  author={Schneider, Tobias and Sawade, Kevin and Berner, Frederic and Peter, Christine and Kovermann, Michael}
}
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