Characterising Intrinsically Disordered Proteins Using NMR Spectroscopy and MD Simulations

Abstract

Intrinsically disordered proteins and regions comprise about 30% of the human proteome. These functionally important and dynamic biomolecules are generally not amenable to standard techniques of structural biology, including X-ray crystallography and cryogenic electron microscopy (cryo-EM) due to their extreme structural heterogeneity. Nuclear magnetic resonance (NMR) spectroscopy is particularly well-suited to experimentally characterise disordered proteins in solution, revealing insights into the structural and dynamic properties of these biomolecules, their interactions, and functional mechanisms. Nevertheless, NMR experiments report on time and ensemble averages, preventing full characterisations of the diverse structures adopted by disordered proteins. Molecular dynamics (MD) simulations are highly complementary to NMR measurements and have the potential to fully characterise the structural ensembles of disordered proteins. Nevertheless, simulations suffer from limitations such as force field inaccuracies and poor convergence. In this chapter, we highlight recent advancements made in NMR and MD, with particular emphasis on NMR techniques to quantify conformational exchange and integrative MD simulations, respectively, which have revealed important mechanistic details on the structural ensembles of disordered proteins and their interactions.