1. Molecular Dynamics of the Avian Influenza Virus Team Members: Ashvin Srivatsa, Michael Fu, Ellen Chuang, Ravi Sheth Team Leader: Yuan Zhang

2. Contents Influenza Background How Influenza Works Molecular Dynamics Objective Procedure Results Conclusion

3. Influenza Background

4. The Influenza Problem “Flu” Common viral infection of lungs Many different strains which mutate regularly Different levels of virulence Kills roughly half a million people per year

5. Historical Flu Pandemics 1918 Spanish Flu (H1N1) – 500,000 deaths in U.S. 1957 Asian Flu (H2N2) – 69,800 deaths in U.S. 1968 Hong Kong Flu (H3N2) – 33,800 deaths in U.S.

6. Avian Influenza H5N1 Form of Influenza A Virus One of the most virulent strains today, spreads only from birds to humans Similar to human “common flu” Mutates frequently, makes it hard to develop countermeasures If a mutation allows for it to spread from human to human, pandemic would follow

7. How Influenza Works

8. Structure of Bird Flu Virus Protein Coat – Hemagglutinin – bonds virus to cell membrane – Neuraminidase – helps virus reproduce in cell Lipid Membrane RNA

9. Lifecycle of Bird Flu Virus Enters and infects cell Reproduce genetic material Cell lyses, releasing new viruses

10. Fusion Peptide Part of Hemagglutinin protein Binds virus to cell membrane

11. Molecular Dynamics

12. Molecular Dynamics (MD) Involves study of computer simulations that allow molecules and atoms to interact Extremely complex, based on physics laws Must be run on powerful supercomputers

13. MD Software Many different types of software solutions exist We utilized VMD and NAMD – VMD – Visual Molecular Dynamics – NAMD2 – Not (just) Another Molecular Dynamics program

14. A silicon nanopore, rendered with VMD by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign

15. Objective

16. 1.Utilize VMD and NAMD2 to conduct simulations of the influenza fusion peptide being inserted into a lipid membrane on OSC’s supercomputer clusters 2.Determine how various mutations of the fusion peptide affects its ability to penetrate a lipid membrane

17. Procedure

18. 1.Acquire protein structure files (.pdb) – pdb.org 2.Generate lipid membrane, position protein on membrane 3.Solvate (immerse in water) the protein 4.Create batch files that tell supercomputer what to do

19. Procedure (Cont.) 5.Perform an equilibration simulation to equilibrate protein 6.Execute simulation that pulls protein into membrane 7.Produce visualization

21. Results

22. Fusion Peptide Equilibration (H1N1)

23. Fusion Peptide Pulling (H1N1)

24. Fusion Peptide Pulling #2 (H1N1)

25. Next Step: Mutations Random change in genetic material Changes amino acid structure in proteins New strains of influenza arise through random mutations as well as through natural selection

26. Comparison of Amino Sequences Different Strains of the 20 amino acid fusion peptide Mutation Names – based on original amino acid, position, and new amino acid

27. Mutation 1 Mutation at the “head” of the protein Variants G1V, G1S – (Changes to Valine, Serine) Changes way each peptide enters the membrane (Li, Han, Lai, Bushweller, Cafisso, Tamm)

28. G1V(green), G1S (red) mutants, H1N1 (orange)

30. Analysis The H1N1 maintains a straight structure G1V, G1S variants bunch up – reduce efficiency Shows that the Glycine is important amino acid on the “head”

31. Mutation 2 Mutation near bend in peptide W14A / H3N2 Boomerang structure is critical to peptide (Lai, Park, White, Tamm)

32. W14A(green), H1N1 (blue)

34. Analysis W14A bunches up, after going in half way, comes back out H1N1 maintains structure Shows that “boomerang” or bend is essential Also could have contributed the success of the 1918 H1N1 outbreak, compared to H3N2

35. Mutation 3 N12G Affects Boomerang Structure Chosen by team members (not previously attempted)

36. N12G(orange), H1N1 (blue)

38. Analysis N12G bunches up halfway through Does not insert as much as H1N1 Further proves that proper bend is essential

39. Conclusion

40. Conclusions Boomerang structure of the fusion peptide is essential for proper insertion Glycine is essential in the “head” position of the fusion peptide

41. The Bigger Picture The fusion peptide process is a target for drug intervention Influenza mutates quickly Deadly implications if H5N1 mutates to spread from human to human Further research is essential to protect humans from another pandemic

42. Acknowledgements Yuan Zhang (project leader) Barbara Woodall (UNIX) Elaine Pritchard (Organization) Brianna, Daniel (Dorm Supervisors) SI Sponsors Parents VMD (University of Illinois) NAMD2 (University of Illinois) ClustalW (Amino Acid Alignment) OSC (Supercomputing Time)

43. Questions?