Simulation of the Structure of Sugar Chains of Glycoproteins


Principal Investigator

Jill E. Gready

John Curtin School of Medical Research


Johannes Zuegg

John Curtin School of Medical Research


x04 - VPP, PC , MDSS

Although the three dimensional structure of many glycoproteins has been determined, the structure of the corresponding oligosaccharide is in most cases unknown, as non-glycosylated forms are usually made for x-ray crystallography studies or the sugar chains are difficult to resolve by solution NMR studies. One example of such a glycoprotein is the prion protein (PrP), which is involved in various diseases like scrapie in sheep, BSE in cows and Creuzfeldt-Jakob diseases in humans, but whose function is still unknown. The prion protein is a glycoprotein with two oligosaccharides bound to two asparagines and additionally one oligosaccharide forming the link between the protein and the cell surface (GPI-anchor). The structure of the prion protein without these sugars has been determined by NMR. Our interest is to find hints for the function of the prion protein by investigating the influence of the oligosaccharides on the conformation of the protein and possible tendencies to move to a different conformation, and by defining a possible orientation of the whole protein with respect to the membrane.  




What are the results to date and the future of the work?

In the first step a homology model of the human prion protein has been made, using the NMR structure of a PrP from Syrian Hamster. In the first molecular dynamics (MD) simulation the structure of the homology model and of the NMR structure turned out be highly dependent on the way the electrostatic interactions are treated in the simulation. Therefore, extensive MD simulations have been carried out on the homology model to identify the optimal simulation parameter in which a stable protein could be achieved. This sensitivity of the prion protein structure to its electrostatic environment may reflect its ability to form two different conformations, one of them associated with the disease state. In the next step, these simulations were extended to the prion protein including the two asparagine-linked oligosaccharides and the GPI-anchor linked to the C-terminal end of the protein. The resulting conformations were then combined with conformations resulting from a MD simulation of only the GPI-anchor linked to a membrane, to model a possible orientation of the whole PrP with respect to the membrane.

Appendix A -



For the next step in analysis of the structure and function of the human prion protein, we intend to extend our model to other parts of the protein, which are flexible disordered in the NMR structure.

What computational techniques are used?

For the molecular dynamics simulations SANDER from the AMBER 5 package has been used on the PC and VPP. The VPP work uses the vectorised version of SANDER optimised under the Fujitsu project.

- Appendix A