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Article Dans Une Revue Scientific Reports Année : 2019

Experimental protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement

Résumé

Protein dynamics covers multiple spatiotemporal scale processes, among which slow motions, not much understood even though they are underlying protein folding and protein functions. protein slow motions are associated with structural heterogeneity, short-lived and poorly populated conformations, hard to detect individually. In addition, they involve collective motions of many atoms, not easily tracked by simulation and experimental devices. Here we propose a biophysical approach, coupling geometrical nanoconfinement and broadband dielectric spectroscopy (BDS), which distinguishes protein conformations by their respective molecular dynamics. In particular, protein-unfolding intermediates, usually poorly populated in macroscopic solutions are detected. The protein dynamics is observed under unusual conditions (sample nanoconfinement and dehydration) highlighting the robustness of protein structure and protein dynamics to a variety of conditions consistent with protein sustainability. the protein dielectric signals evolve with the temperature of thermal treatments indicating sensitivity to atomic and molecular interaction changes triggered by the protein thermal unfolding. As dipole fluctuations depend on both collective large-scale motions and local motions, the approach offers a prospect to track in-depth unfolding events. Proteins produce biological activities in living organisms thanks to their 3D-structure and the associated dynamics. The 3D structure relies on chemical interactions between atoms of the amino acids that compose a protein. The molecular dynamics is based on molecular fluctuations, which produce motions from a local scale (amino acid side chain fluctuations) to a larger scale (structural relaxation) to respond to the protein folding and the protein function 1-3. Accordingly, proteins dynamics covers several orders of magnitude of spatiotemporal motions from femtosecond to second for molecular fluctuations from Angströms to nanometers. Basically, fast motions (femtosecond to nanosecond) concern local atomic motions (vibration, side chain motions) while slow motions concern the collective motions of many atoms within larger size areas such as secondary and tertiary structural elements (microsecond to millisecond) up to domains (millisecond to second) 3. To track protein dynamics, several experimental and theoretical approaches are required. Ultra resolution X-ray crystallography and x-ray laser have been successfully applied on few cases to monitor time-resolution of conformational motions 4-7. Ultra fast NMR, femtosecond simulated Raman spectroscopy and ultra fast transient Infra Red spectroscopy are measuring atomic motions from femtosecond to nanosecond 8-13. Slower motions above nanosecond are monitored by low spatial resolution techniques such as AFM and fluorescence spectros-copy (FRET) where the molecular dynamics are inaccessible 14-16. Theoretical approaches such as molecular dynamics (MD) simulations have atomic resolution and cover motions up to millisecond now thanks to ANTON super computer 1. But MD simulation at high resolution is limited in terms of size and it remains hard to assess motions above microsecond range 17,18. Network models are also useful to study protein dynamics 19-22. Most successful approaches are integrative, combining experimental and multiple theoretical approaches in order to cover more length and time scale motions of protein structure dynamics 23-25. They are particularly successful in monitoring the slow motions involved in protein assembly and pore-formation 26-32 .
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hal-02404528 , version 1 (11-12-2019)

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Laëtitia Bourgeat, Anatoli Serghei, Claire Lesieur. Experimental protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement. Scientific Reports, 2019, 9, pp.17988 (2019). ⟨10.1038/s41598-019-54562-8⟩. ⟨hal-02404528⟩
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