Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Commun Biol. 2021 Feb 23;4(1):243. doi: 10.1038/s42003-021-01759-1.

Abstract

Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Histatins / chemistry
  • Histatins / metabolism
  • Intrinsically Disordered Proteins / chemistry
  • Intrinsically Disordered Proteins / metabolism*
  • Light
  • Molecular Dynamics Simulation*
  • Neutron Diffraction
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Proto-Oncogene Protein c-fli-1 / chemistry
  • Proto-Oncogene Protein c-fli-1 / metabolism
  • Reproducibility of Results
  • Scattering, Small Angle
  • Structure-Activity Relationship

Substances

  • Histatins
  • Intrinsically Disordered Proteins
  • Proto-Oncogene Protein c-fli-1