Molecular dynamics simulation of human prion protein including both N-linked oligosaccharides and the GPI anchor

Although glycosylation appears to protect prion protein (PrP(C)) from the conformational transition to the disease-associated scrapie form (PrP(Sc)), available NMR structures are for non-glycosylated PrP(C), only. To investigate the influence of both the two N-linked glycans, Asn181 and Asn197, and of the GPI anchor attached to Ser230, on the structural, dynamical and electrostatic behavior of PrP, we have undertaken molecular dynamics simulations on the C-terminal region of human prion protein HU:PrP(90-230), with and without the three glycans. The simulations used the AMBER94 force field in a periodic box model with explicit water molecules, considering all long-range electrostatic interactions. The results suggest the structured part of the protein, HU:PrP(127-227) is stabilized overall from addition of the glycans, specifically by extensions of Helix-B and Helix-C and reduced flexibility of the linking turn containing Asn197, although some regions such as residues in the turn (165-170) between Strand-B and Helix-B have increased flexibility. The stabilization appears indirect, by reducing the mobility of the surrounding water molecules, and not from specific interactions such as H bonds or ion pairs. The results are consistent with glycosylation at Asn197 having a stabilizing role, while that at Asn181, in a region with already stable secondary structure, having a more functional role, in agreement with literature suggestions. Due to three negatively charged SiaLe(x) groups per N-glycan, the surface electrostatic properties change to a negative electrostatic field covering most of the C-terminal part, including the surface of Helix-B and Helix-C, while the positively charged N-terminal part PrP(90-126) of undefined structure creates a positive potential. The unusual hydrophilic Helix-A (144-152) is not covered by either of these dominant electrostatic fields, and modeling shows it could readily dimerize in anti parallel fashion. In combination with separate simulations of the GPI anchor in a membrane model, the results show the GPI anchor is highly flexible and would maintain the protein at a distance between 9 and 13 A from the membrane surface, with little influence on its structure or orientational freedom.