Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

J Chem Theory Comput. 2022 Oct 11;18(10):6310-6323. doi: 10.1021/acs.jctc.2c00328. Epub 2022 Sep 9.

Abstract

For intrinsically disordered proteins (IDPs), a pressing question is how sequence codes for function. Dynamics serves as a crucial link, reminiscent of the role of structure in sequence-function relations of structured proteins. To define general rules governing sequence-dependent backbone dynamics, we carried out long molecular dynamics simulations of eight IDPs. Blocks of residues exhibiting large amplitudes in slow dynamics are rigidified by local inter-residue interactions or secondary structures. A long region or an entire IDP can be slowed down by long-range contacts or secondary-structure packing. On the other hand, glycines promote fast dynamics and either demarcate rigid blocks or facilitate multiple modes of local and long-range inter-residue interactions. The sequence-dependent backbone dynamics endows IDPs with versatile response to binding partners, with some blocks recalcitrant while others readily adapting to intermolecular interactions.

MeSH terms

  • Intrinsically Disordered Proteins* / chemistry
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Protein Structure, Secondary

Substances

  • Intrinsically Disordered Proteins