Disordered proteins: an interaction "filmed"

How intrinsically disordered proteins can perform a multitude of biological functions without a fixed three-dimensional structure is still a much debated question. Using nuclear magnetic resonance spectroscopy, we have been able to map out the interaction of one such protein with its partner in atomic detail, from its free-state ensemble of conformations via a non-specific encounter complex to the final bound state.

HFSP Long-Term Fellowship holder Robert Schneider and colleagues
authored on Thu, 05 March 2015

Intrinsically disordered proteins (IDPs) challenge the classic structure-function paradigm of structural biology, performing a multitude of functions in diverse biological processes such as signaling and gene transcription despite their lack of a fixed three-dimensional structure. Their importance is further underlined by the fact that they are involved in many human pathologies such as cancer and neurodegenerative disease. However, the mechanistic details of how these proteins interact, as well as the factors that determine their binding specificity are still poorly understood.

Using nuclear magnetic resonance (NMR) spectroscopy, we have been able to characterize the interaction of one such IDP with its binding partner in atomic and kinetic detail. In Sendai virus, a close relative of measles virus, the disordered C-terminal tail of the nucleoprotein (NT) forms a complex with the PX domain of the phosphoprotein. This interaction is essential to initiate genome transcription and replication. NMR data had already shown that NT populates a complex equilibrium of conformations in its free state, comprising states with partial alpha-helical structure. We have used relaxation dispersion measurements on multiple nuclei and at several concentrations of the interacting proteins to learn about the nature of the states involved in the interaction, as well as the kinetics of their formation.

Our results show that, in the course of the binding reaction, one of the conformations of NT already present in its unbound state is stabilized in a dynamic encounter complex on the surface of PX. Using a mutant NT variant, we could demonstrate that electrostatic interactions play an important role in this initial binding phase. In a second binding step, NT locks into its final bound state in a groove between two helices of PX. Strikingly, this part of the binding reaction proceeds at a rate closely corresponding to that of an intrinsic breathing motion of the PX interhelical groove. Thus, formation of the NT-PX complex is regulated by the intrinsic free-state conformational dynamics of both proteins.

Detailed experimental evidence of binding mechanisms employed by disordered proteins is still scarce. Our study thus helps advance our knowledge about the function of these proteins which only recently have been discovered as promising pharmacological targets.

Reference

Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR. Robert Schneider, Damien Maurin, Guillaume Communie, Jaka Kragelj, D. Flemming Hansen, Rob W. H. Ruigrok, Malene Ringkjøbing Jensen, Martin Blackledge. J. Am. Chem. Soc. 137 (3), 1220–1229, 2015. DOI: 10.1021/ja511066q.

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