Cryptic disorder: an order-disorder transformation regulates the function of nucleophosmin

It is now well appreciated that disordered proteins and domains are prevalent in eukaryotic proteomes and that disorder is critically linked with their regulation and functionality. However, our recent observations with the multi-domain protein, nucleophosmin (Npm), suggest that the biological palette of disorder is more diverse than currently understood. The N-terminal oligomerization domain of Npm (Npm-N) can be transformed from a folded, pentameric structure to a monomeric, disordered state through changes in solution ionic strength and, importantly, through physiologically relevant post-translational modifications. Thus, it appears that Npm has been evolutionarily tuned to exist in equilibrium between disordered and ordered states. Results from us and others suggest that the function of Npm is regulated through shifts in this equilibrium via post-translational modifications. Interestingly, this polymorphic behavior is not detected using standard secondary structure and disorder prediction algorithms, which show Npm-N to be folded into β-strands, consistent with the structure of the pentameric form. We have used a combination of computational tools, including structure-based analysis, sequence analysis algorithms (NetPhos 1.0, SCRATCH, KinasePhos, GPS2.1, PONDR) and molecular mechanics energy calculations, to test the hypothesis that the polymorphic behavior of Npm-N can be understood on structural and energetic grounds. This computational strategy has resulted in the identification of unfavorable energetic "hot-spots" within the Npm-N structure which coincide with experimentally observed sites of post-translational modification. Based on these observations, we propose that Npm-N has evolved energetic switches within its structure to enable transformation to a disordered state through phosphorylation. We further propose that the transformation process is triggered by sequential phosphorylation of solvent exposed hot-spots followed by exposure and modification of additional but initially buried sites to completely shift the equilibrium to the disordered state. This regulated, shifting equilibrium is associated with control of Npm localization within the nucleolus, nucleoplasm and cytoplasm, and with its role in regulation of centrosome duplication through interactions with Crm1-Ran. More broadly, we present a general computational strategy to identify transformational hot-spots within proteins and to test the hypothesis that other proteins currently understood to be folded participate in functionally-relevant order-disorder equilibria as we have observed for Npm. The identification of such polymorphic proteins would broaden the palette of protein disorder utilized in biological systems.