期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 126, 期 9, 页码 1885-1894出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.1c10925
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资金
- National Institute of Health [5R01GM12762704]
- Natural Sciences and Engineering Research Council of Canada
This article introduces a computational framework for generating dynamic disordered ensembles consistent with NMR-derived dynamics parameters. The approach is validated using the unfolded state of the drkN SH3 domain, and the results show that the dynamic ensembles have better agreement with a wide range of experimental validation data.
Intrinsically disordered proteins and unfolded proteins have fluctuating conformational ensembles that are fundamental to their biological function and impact protein folding, stability, and misfolding. Despite the importance of protein dynamics and conformational sampling, time-dependent data types are not fully exploited when defining and refining disordered protein ensembles. Here we introduce a computational framework using an elastic network model and normal-mode displacements to generate a dynamic disordered ensemble consistent with NMR-derived dynamics parameters, including transverse R-2 relaxation rates and Lipari-Szabo order parameters (S-2 values). We illustrate our approach using the unfolded state of the drkN SH3 domain to show that the dynamical ensembles give better agreement than a static ensemble for a wide range of experimental validation data including NMR chemical shifts, J-couplings, nuclear Overhauser effects, paramagnetic relaxation enhancements, residual dipolar couplings, hydrodynamic radii, single-molecule fluorescence Forster resonance energy transfer, and small-angle X-ray scattering.
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