Integrating multiple experimental data to determine conformational ensembles of an intrinsically disordered protein
| Autor: | Gregory-Neal W. Gomes, Julie D. Forman-Kay, Mickael Krzeminski, Ashley Namini, Claudiu C. Gradinaru, Teresa Head-Gordon, Tanja Mittag, Erik W. Martin |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Physics
0303 health sciences Quantitative Biology::Biomolecules Small-angle X-ray scattering Experimental data 010402 general chemistry Intrinsically disordered proteins 01 natural sciences 0104 chemical sciences Characterization (materials science) 03 medical and health sciences Förster resonance energy transfer Statistical physics Degree of confidence Conformational ensembles 030304 developmental biology |
| DOI: | 10.1101/2020.02.05.935890 |
| Popis: | Intrinsically disordered proteins (IDPs) have fluctuating heterogeneous conformations, which makes structural characterization challenging. Although challenging, characterizing the conformational ensembles of IDPs is of great interest, since their conformational ensembles are the link between their sequences and functions. An accurate description of IDP conformational ensembles depends crucially on the amount and quality of the experimental data used in their calculations. We used integrative modelling to understand and implement conformational restraints imposed by the most common structural techniques for IDPs: Nuclear Magnetic Resonance (NMR) spectroscopy, Small-angle X-ray Scattering (SAXS), and single-molecule Forster Resonance Energy Transfer (smFRET). Agreement with such a diverse set of experimental data suggests that details of the generated ensembles can be examined with a high degree of confidence. Using the disordered N-terminal region of the Sic1 protein as a test case, we examined relationships between average global polymeric descriptions and higher-moments of their distributions. To resolve apparent discrepancies between smFRET and SAXS inferences, we integrated SAXS data with non-smFRET (NMR) data and reserved the smFRET data as an independent validation. Consistency with smFRET, which was not guaranteed a priori, indicates that, globally, the perturbative effects of NMR or smFRET labels on the Sic1 ensemble are minimal. Analysis of the integrative ensembles revealed distinguishing features of Sic1, such as overall compactness and large end-to-end distance fluctuations, which are consistent with biophysical models of Sic1’s ultrasensitive binding to its partner Cdc4. Our results underscore the importance of integrative modelling in calculating and drawing conclusions from IDP conformational ensembles. |
| Databáze: | OpenAIRE |
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