1HJM native conformation
The right hand side depicts the navtive conformations of the C-terminal domain of human prion (PDB code 1hjm). Highlighted in blue is the segment (residues 197-207) found to be most deeply buried in fibers of recombinant PrP32. It i reasonable to assume that in order to be buried in the fibril a significant conformational change involving this segemtn needs to occur. Using the MRR procedure developed in the Wodak group it is possible to selectively explore PrP conformations displaying largest conformational changes in this segment, yielding the conformational ensemble shown on the left hand side. A very similar procedure is applied to map the conformational variability of specific PrP petide epitopes.
Misfolded of molten globule conformation in ensemble of dissimilar replicas
The neurodegenerative prion diseases are believed to result from a self-perpetuating conversion of the prion protein (PrP) from the normal cellular form (PrPc) to the infectious disease causing isoform (PrPsc). This conversion is triggered by the presence of PrPsc but its molecular mechanism is unknown. PrP contains a large intrinsically disordered N-terminal region followed by a folded C-terminal domain. The process of PrP conversion is believed to proceed through a partially unfolded form of the globular C-terminal domain, leading to the formation of small toxic oligomers, which then progress to yield the final fibrillar amyloids.
In close collaboration with colleagues experts in NMR spectroscopy (Dr. J. Forman-Kay, at Sickkids, and Dr. L. Kay at the University of Toronto) and biophysical methods (A.Chakrabartty, Princess Margaret Hospital) we are using molecular simulations and modelling methods to translate experimental data on prion monomers and oligomers into detailed atomic descriptions. We are furthermore working on extending the scope of the experimental investigations by deriving alternative candidate models and new hypotheses that can be tested experimentally. In particular we are characterizing at the atomic level the structural and dynamic properties of transiently populated (intermediate) forms of the C-terminal domain of PrP known to be involved in the conversion. We are also investigating conformational states of the C-terminal region of the PrP protein associated with differential exposure of specific epitopes, in order to provide clues on regions of the protein undergoing conformational transitions leading to aggregation. Information gained from our simulations and the experimental studies will be used to build atomic models of prion oligomers and higher aggregates, believed to mimic the in-vivo infectious and fibrillar forms of the protein.
Group members:
Anatoly Malevanets (PhD)
Steve MacKinnon (Graduate Student)
Funding sources:
PrioNet Canada, CIHR and Sickkids
