Computational and experimental reference data: Molecular dynamics of the intrinsically disordered protein COR15A – A force field validation on structure and dynamics

This dataset includes the computational and experimental data for the publication:
"Molecular Dynamics of the Intrinsically Disordered Protein COR15A – A Force Field Validation on Structure and Dynamics".
We provide the simulation trajectory files and the corresponding scripts for system set-up, MD prodcution runs and analysis of results.
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ABSTRACT:
Intrinsically disordered proteins (IDPs) pose a challenge for structural characterization, as experimental methods lack the subnanometer/sub-nanosecond resolution to capture their dynamic conformational ensembles. Molecular dynamics (MD) simulations can, in principle, provide this information, but for the simulation of IDPs dedicated protein and water force fields are needed, as traditional MD models for folded proteins prove inadequate for IDPs. Substantial effort was invested to develop IDP-specific force fields, but their per- formance in describing IDPs that undergo conformational changes—such as those induced by molecular partner binding or changes in solution environment—remains underexplored. In this study, we investigated the ability of 20 MD models to accurately simulate structural and dynamic aspects of COR15A, an IDP just on the verge of folding, with a particular focus on their ability to capture subtle structural differences. We employ a two-step approach: (i) validation of short 200 ns simulations against small-angle X-ray scattering (SAXS) data, and (ii) detailed evaluation of the six best-performing MD models through extended 1.2 μs MD simulations against nuclear magnetic resonance (NMR) data, including a single-point mutant with slightly increased helicity. Only DES-amber and ff99SBws capture helicity differences between wild-type and mutant, but ff99SBws overestimates helicity. Notably, only DES-amber adequately reproduces the COR15A dynamics, as assessed by NMR relaxation times at two different magnetic field strengths. Among the tested force fields, DES-amber emerges as the best MD model for the simulation of COR15A. Its application provides insights into its dynamic conformational landscape, albeit not perfectly reproducing all experimental data. Our study highlights the need for rigorous force field validation for IDPs, and identifies remaining discrepancies in need of fur ther force-field development.

Please cite the following article if you use any of the data/scripts provided here:

Rindfleisch, T., Nencini, R., Ollila, O. S., Walther, D., Miettinen, M. S., & Thalhammer, A. (2025). Molecular Dynamics of the Intrinsically Disordered Protein COR15A─ A Force Field Validation on Structure and Dynamics. Journal of Chemical Theory and Computation, 21(18), 9147–9163.