Abstract
Many proteins perform essential biological functions by means of regions that lacking specific organized structure exist as an ensemble of interconverting transient conformers. The characterization of such regions, including the description of their structural propensities, number of conformations and relative populations can provide useful insights. Prion diseases result from the conversion of a normal glycoprotein into a misfolded pathogenic isoform. The structures of mammal and chicken prion proteins show a similar fold with a globular domain and a flexible N-terminal portion that contains different repeated regions: octarepeats (PHGGGWGQ) in mammals and hexarepeats (PHNPGY) in chickens. The higher number of prolines in the hexarepeat region suggests that this region may retain a significant amount of residual secondary structure. Here, we report the CD, NMR and MD characterization of a peptide (2-HexaPY) composed of two hexarepeats. We combine experimental NMR data and MD to investigate at atomic level its ensemble-averaged structural properties, demonstrating how each residue of both repeats has a different quantified PPII propensity that shows a periodicity along the sequence. This feature explains the absence of cooperativity to stabilize a PPII conformation. Nonetheless, such residual structure can play a role in nucleating local structural transitions as well as modulating intra-molecular or inter-molecular interactions.
Highlights
Many proteins perform crucial functions by means of disordered regions
The CD spectrum of 2-HexaPY in aqueous solutions at acidic pH is characterized by a strong negative minimum at 205 nm and a weaker positive band centered at 230 nm (Figure 1A)
The spectrum shape is similar to that previously reported for the tetrahexarepeat [10] and suggests the presence of a polyproII (PPII) helix conformation
Summary
Many proteins perform crucial functions by means of disordered regions. Structural disorder under physiological conditions offers a variety of functional advantages: flexibility of interaction with different partners, specific but low-affinity binding, and fine modulation by post-translational modifications. The higher amount of glycine in the human protein is in agreement with the flexible and disordered structure of the N-terminal domain, while the increased content of prolines suggests the presence of a preferred structured conformation of this domain in the avian species [3]. Further studies on the tetraHexaPY (PHNPGY) conformation, at different pH values [10], have shown for this peptide a periodic-like shape that reflects the periodicity in the primary structure and with it the differences with the flexible and disordered structure of the human N-terminal domain. Our data strongly support that, despite the reported high flexibility of the hexarepeat region, the 2-HexaPY is not completely random coil in solution but rather shows a residuebased (per residue) quantified propensity to poly-L-proline II conformation. Our findings are in agreement with the reported CD behaviour of tetraHexaPY [10] offering valuable hints on PPII conformation propensity of the full hexarepeat region of the chicken prion protein
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