1. Chapter 3 - Genomes Use chapter as reference.

2. Chapter 4 - Virus Structure

4. How are genomes protected? 1) 2) 3)

5. Chapter 4 - Virus Structure Why look at structure of viruses?? –Models for protein-protein & protein-NA complexes –Receptor binding sites might be drug targets (rhinovirus) –Antigenic sites on virion –Neutralizing vs non-neutralizing Abs –Escape mutants –?? why few serotypes of poliovirus, but many for rhinovirus –Uncoating and assembly could be targets for therapeutics –Often final assembly includes proteolytic processing –?? why poliovirus is acid stable, but rhinovirus is not

6. Assume basic knowledge of protein structure Box 4.1

7. Chapter 4 - Virus Structure Basically: nucleic acid + protein capsid for protection (+ extras) –Self assembling structures (often) –Built out of repeating units - economy and assembly Coding triplet = 1000 Daltons; 1 amino acid = 100 Daltons MW Therefore DNA or RNA cannot encode single protein to act as protein coat. –Advantages of subunits: –minimal genetic info, –less wastage in building a functional particle smaller units discarded if faults in translation or folding of protein –stable virus stucture Repeated patterns of subunits leads to maximum stability Self-assembly because of minimum free energy in system

8. Chapter 4 - Virus Structure But: –Use of subunits leads to limited virus architecture –Proteins may have some regular structure -  helix;  sheet But tertiary structure of proteins is not symmetrical –Since the subunits not symmetrical, need to: arrange subunits symmetrically with maximum bonding

9. Chapter 4 - Virus Structure Most viruses use 1 of 2 structural principles - rod-like - thread like appearance, helical structure - isometric- roughly spherical NB helical nucleocapsid can be surrounded by spherical outer shell

10. Rod-like viruses Arrange protein subunits in circle to form a “cylinder” with space for genome Actually, it’s helical Why not cylinder rather than helical??

11. Rod 18 x 300 nm 17.5 kDa subunit Units per turn (u ) for TMV = 16 1/3 Axial rise per unit (p ) for TMV = 0.14 nm Pitch of the helix ( P = u x p ) 2.3 nm Can build TMV virion in the absence of RNA TF protein specifies structure

12. How is this assembled?

14. TMV Assembly of subunits around RNA must be orderly Subunits must have more affinity for each other that for RNA - pre-assemble small sections Unique origin of assembly~ 800 nucleotides from 3' end - growth towards 5' end rapid+ double disks - growth towards 5' end rapid+ monomers or sm. aggregates RNA passes through axial channel, each subunit has 3 basic amino acids, binds 3 nucleotide phosphates

15. TMV Disassembly: For TMV, is co-translational As RNA translated from 5' end, protein coat subunits removed Mass of coat protein = 14.5 kDa Mass of ribosome = > 1000 kDa

16. ICOSAHEDRAL VIRUSES Originally discovered by comparing EM shadowed viruses with various models. For self assembly need to have simple rules. How to divide surface of sphere into regular units…. Caspar and Klug. Simplest and most common shape for virions shows icosahedral symmetry - must have 2, 3 and 5 fold symmetries - most efficient biological container is a geodesic dome design

17. link to ICOSAHEDRON structure

18. link to Principles of Virus Architecture

19. Icosahedron = 20 equilateral triangular facets, 12 vertices (pentamers)

20. Icosahedron In simplest form: - each facet has 3 identical protein subunits b/c needs 3-fold symmetry

21. Icosahedron Larger viruses use more subunits rather than larger proteins. If use multiples of 60 subunits, but not all positions are the same… b/c this introduces hexamers between pentamer vertices Get: quasi-equivalence if single type of protein used Get: PseudoT3 if multiple proteins used

22. PSEUDO-T3 symmetry (a, b and c are different)

24. Triangulation number = square of the distance between pentamer vertices - reflects number of triangles mapped onto sphere For: T = 1 x 20 triangular facets x 3 subunits = 60 T = 3.......................................... = 180 T = 4.......................................... = 240 Only for T=1, with 60 identical subunits, is each subunit in equivalent position

29. Loops and tails…

31. Assembly - from pre-assembled units "Genes" for protomer subunits are contiguous in genome - translation, cleavage, assembly of basic unit = 1 process To assemble into pentamers and hexamers - requires different bonding preferences - non-covalent bonding, easier to reject mistakes Pentamers / hexamers + RNA seeds assemble of complete capsids Final cleavage of VP0 gives VP2 + VP4 as assembled - ?? locks in place for stability - ?? primes for release of RNA

32. These are WRONG!!!!! Bonus Q.

33. Some bigger viruses:

34. Some variability:

35. Link to: virology.wisc.edu/virusworld/