1. Introduction to Structural and Molecular Virology Yaroslav Daniel Bodnar University of Illinois at Urbana-Champaign

2. Viruses Highlight Some Big Ideas Structure-Dynamics-Function relationships. A systems perspective: Understanding of complex function by looking at its components. Self-assembly gives rise to complex forms in biological systems. Using a simplified model system to understand a broad range of more complex phenomena.

3. Size Matters: Definition of a Virus

5. A Few Surprises Mutual symbiosis between Polydnaviruses and parasitic wasps. Oncolytic Virotherapy: Seneca Valley Viruses

6. Wendell M. Stanley 1946 Nobel Prize in Chemistry Crystallized Tobacco Mosaic Virus and Systematically Investigated its Biochemistry

7. Structural Biology

8. A Trip Inside of HPV PLAY MOVIE 1 (HPV Density Map)

9. A Trip Inside of HPV

10. What the nucleocapsid and other accessory viral proteins need to do? Protect viral genome: needs to be fully enclosed. Needs to be inert outside the cell and move freely in-search of a new host. Needs to be a dynamic structure:  Change (“activate”) in response to a specific stimulus.  Occurs in a series of “programmed” stages.

11. Icosahedral Helical Symmetry of Viral Capsids

12. Enveloped Viruses

13. Survey of Human Viruses

14. Principles of Viral Capsid Architecture

15. Asymmetric Subunit Each subunit consists of four proteins. Capsid proteins interact by highly specific, flexible non-covalent contacts. Long terminal extensions and loops make each viral capsid unique.

16. The Jelly-Roll Fold

17. Repeat the Asymmetric Subunit to “Tile” the Surface of the Capsid

18. “Quasi-Equivalence” is a Necessary Property of Enclosed Surfaces

19. Triangulation Numbers How many equilateral triangles can fit on one face? The size of each capsid protein must stay approximately the same.  How do you make a larger capsid?...Increase the triangulation number!

20. Play Movie 2 (Harrison; Virus Capsid Dynamics)

21. Formation of New Viruses by Self-Assembly

22. You can make viruses in a test tube! Play Movie 3 (Virus Self-Assembly)

23. The Viral Life Cycle

24. Host Cell Entry By Membrane Fusion

26. Play movie at: http://www.molecularmovies.com/movies/gp41_061 008.html

27. The Viral Life Cycle

28. VIPERdb Exercise 1:(http://viperdb.scripps.edu/) Explore VIPERdb. Be sure to visit viruses of different families and T- numbers. While you surf, write down the T-number, excess surface charge, and average radius of each virus. Some search suggestions include:  Picornaviruses: POLIO: Poliovirus (Type 1; Mahoney strain)‏ POLIO: Poliovirus/Receptor Complex COMMON COLD: Human Rhinovirus 16 COMMON COLD: Human rhinovirus 16 with Receptor  Hepadnaviruses: HEPATITIS: Human Hepatitis B Viral Capsid  Papillomaviruses: HPV (CERVICAL CANCER): Human Papilloma Virus 16 L1 Capsid

29. Did you find a relationship between the T-number and the size of the viruses? Why may this be?  Clue: Most virus capsid proteins are approximately the same size. Did you notice a trend in the charge of virus capsids? Do they tend to be positively or negatively charged? Why does this make sense?  Clue: Remember that virus capsids are essentially “molecular containers.” What do they contain? What is the charge of the contents?

30. VIPERdb Exercise 2 Load 6 to 10 viruses from the same family into STRAP and perform a multi-sequence alignment. Choose one of the viruses from above and list several of the most highly conserved regions. Why do you think that these conserved regions are important? What do you think they do? Use structural information and other information available on VIPERdb to support your answer. Suppose you want to identify regions of your virus that interact with antibodies. How can you use VIPERdb to do this?  Hint: Different strains (or serotypes) of a virus are characterized by which antibodies bind to them. This means that different strains of the same virus will differ in the regions you're interested in.