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

Although glycosylation appears to protect prion protein (PrPC) from the conformational transition to the disease-associated scrapie form (PrPSc), available NMR structures are for non-glycosylated PrPC, 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 HuPrP(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, HuPrP(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 membrane model, the results show the GPI anchor is highly flexible and would maintain the protein at a distance between 9 and 13 Angstrom from the membrane surface, with little influence on its structure or orientational freedom.