Project Prion: Evolution and Structural Connections

1. Project Prion:Evolution and Structural Connections MDG5101 Group 2

2. Historical Background The earliest record dates from several centuries ago, when scrapie was first observed in sheep In 1972, Tikvah Alper was the first to suggest the agent of scrapie might replicate without nucleic acid And in 1982, Stanley Prusiner coined the term prion (‘pree-on’)

3. What is prion? • A prion has been defined as "small proteinaceous infectious particles which resist inactivation by procedures that modify nucleic acids". ------ Prion Diseases: Just as nucleic acids can carry out enzymatic reactions, proteins can be genes.   Reed Wickner. Microbiology @ Leicester: Virology: Prions

4. Prion conformations http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Prions.html

5. Classification

6. Spongiform Encephalopathies

7. Figure 1. Molecular models of the structures of PrPc(left) and PrPsc(right). Usefulness of Bioinformatics Prion diseases, e.g. CJD, can take on different forms due to specific mutations in the primary amino acid sequence • Protein functions dependent on Tertiary or Quaternary Structure • Mutations can lead to a change in 3D structure  could change protein function

8. Usefulness of Bioinformatics Various 3D protein visualization tools available RasMol, CHIME, MAGE, DeepView, etc Used to predict 3D structures of proteins Enable us to compare structures of various mutated forms of human PrP Allows us to visualize the change in protein structures caused by different mutations

9. Our Bioinformatics Approach • Searching • Visualising • Validating • Predicting

10. Searching

11. Searching

12. Searching for Structures • Most commonly used protein databases • RCSB PDB • NCBI Entrez Structure • Search query : human prion

13. Visualizing • RasMol • DeepView • CN3D • Features Vs Learning Curve

14. Visualizing Human PrPc RasMol DeepView CN3D

15. Validating • Make point mutations, using DeepView, on the human PrPc • But how accurate will our model be in simulating mutation and predicting its effects?

16. Validating Variants of PrP found in Creutzfeldt-Jakob Disease (CJD)

17. Wild type human PrP E200K variant of PrP Validating Solution Structure of the E200K Variant of Human PrP (NMR spectroscopy) • The only major consequence of the mutation is the change of surface electrostatic potential. (red -, blue +) Backbone tertiary structure is nearly identical. • This change may disturb the interaction of PrP with auxiliary proteins/chaperones or cellular membranes. • This may cause a spontaneous PrPc to PrPsc conversion in the E200K form of hereditary prion disease. Zhang Y, et al.J. Biol. Chem. 275:33650-33654(2000).

18. Validating Backbone Structure E200K

19. Validating Electrostatic Potential red - blue + E200K

20. Exception • Variant V203I created • No difference in electrostatic potential distribution after mutation • Mutation may cause change in H-bond distribution

21. Exception (Electrostatic Potential) red - blue + V203I

22. H-bonds Exception (H-bonds) E200K

23. Predicting • Does point mutation(s) really affect conformation of the prion? • Key factors for protein folding • H-bonds • Surface Electrostatic Potential

24. H-bonds Predicting backbone structure and H-bond distribution E200K E196K V203I E211Q

25. Predicting surface electrostatic potential distribution red - blue + E200K E196K V203I E211Q

26. Predicting CJD PrPc Model • How will the CJD PrPc protein structure look like after mutations?

27. H-bonds CJD PrPc Model (Backbone structure and H-bonds)

28. CJD PrPc Model(Electrostatic Potential) red - blue +

29. Conclusion • Mutations can lead to changes in distributions in H-bonds and electrostatic potential • Changes may increase the PrPc’s susceptibility to conformational change towards PrPsc • Bioinformatics is definitely a useful and essential tool for visualising, predicting and understanding protein structures

30. Thanks For Your Attention!