Protein Dynamics to Define and Refine Disordered Protein Ensembles

J Phys Chem B. 2022 Mar 10;126(9):1885-1894. doi: 10.1021/acs.jpcb.1c10925. Epub 2022 Feb 25.

Abstract

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 R2 relaxation rates and Lipari-Szabo order parameters (S2 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 Förster resonance energy transfer, and small-angle X-ray scattering.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fluorescence Resonance Energy Transfer
  • Intrinsically Disordered Proteins* / chemistry
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Protein Folding*
  • src Homology Domains

Substances

  • Intrinsically Disordered Proteins