Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV N TAIL through Enhanced Sampling Simulations - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Journal of Physical Chemistry B Année : 2017

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV N TAIL through Enhanced Sampling Simulations

Résumé

Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev NTAIL, a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics. To validate our simulation strategy, we compared the predicted NMR properties against available experimental data. Our simulations reveal a rough free-energy surface comprising multiple local minima, which are separated by low energy barriers. Moreover, we identified interconversion rates between the main kinetic states, which lie in the sub-μs time scales, as suggested in previous works for Sev NTAIL. Therefore, the emerging picture is in agreement with the atomic-level properties possessed by the free IDP in solution. By providing both a thermodynamic and kinetic characterization of this IDP test case, our study demonstrates how computational methods can be effective tools for studying this challenging class of proteins.
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Dates et versions

hal-04538333 , version 1 (09-04-2024)

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Mattia Bernetti, Matteo Masetti, Fabio Pietrucci, Martin Blackledge, Malene Ringkjobing Jensen, et al.. Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV N TAIL through Enhanced Sampling Simulations. Journal of Physical Chemistry B, 2017, 121 (41), pp.9572-9582. ⟨10.1021/acs.jpcb.7b08925⟩. ⟨hal-04538333⟩
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