Viruses

1. Viruses

4. HIV buds out of cells.

7. Figure 5.11 HIV + CD4 CD4 yellow= contacts with HIV

8. The process begins with interactions between the trimeric envelope complex--a cluster of proteins on HIV's outercoat, sometimes referred to as the gp160 spike--and both CD4 and a chemokine receptor (either CCR5 or CCR4) on the cell surface. This complex is made up of three transmembrane glycoproteins (gp41), which anchor the cluster to the virus, and three extracellular glycoproteins (gp120), which contain the binding domains for both CD4 and the chemokine receptors.

9. The first step in fusion involves the high-affinity attachment of the CD4 binding domains of gp120 to the N-terminal membrane-distal domains of CD4. CD4 attachment inhibitors (e.g., PRO 542) act here

10. Once gp120 is bound with the CD4 protein, the envelope complex undergoes a structural change, bringing the chemokine binding domains of gp120 into proximity with the chemokine receptor, allowing for a more stable two-pronged attachment. Antagonists of CCR5 (e.g., SCH-C) and CXCR4 act here. If the virus latches on to both CD4 and the chemokine receptor, additional conformational changes allow for the N-terminal fusion peptide of gp41 to enter the CD4+ cell membrane.

11. Two heptad repeat sequences--HR1 (blue) and HR2 (orange)--of gp41 interact, resulting in collapse of the extracellular portion of gp41 to form a hairpin, which is sometimes referred to as a coiled-coil bundle. The fusion inhibitors T-20 and T-1249 act here by mimicking HR2, resulting in a botched formation of the hairpin. In the absence of an inhibitor, the hairpin structure brings the virus and cell membrane close together, allowing fusion of the membranes and subsequent entry of viral RNA.

12. Uncoating

13. Figure 5.29 HIV uncoating and cyclophilin A A chaperone destabilizes capsid

16. Reverse Transcription and Integration

17. Devise a replication strategy for HIV Components: template (+) ss RNA Enzyme: Reverse transcriptase (in capsid) Like most polymerase, it only works in a 5’-3’ direction Location: cytoplasm Mission: produce ds DNA complementary to full length gRNA

20. Figure 7.2 Primer binding

21. Fig. 7.3 Replication

23. Figure 7.5 Recombinaton Models

24. Figure 7.6 RTs from Avian Sarcoma/Leukosis Virus Murine leukemia Virus and HIV

25. Figure 7.7 Mutational Intermediates

26. Figure 7.8 Conserved Residues in HIV-1 RTase Purple indicates homologies with other RTases

27. Figures 7.10 and 7.12

28. Figure 7.11 RTase Mechanism

29. Figure 7.14 Integration

30. Figure 7.15

31. Figure 7.17 Integrase Domain Structure

32. Figure 7.20 Tetramer Model

40. Negative-Strand RNA Viruses: • Viruses with negative-sense RNA genomes are a little more diverse than positive-stranded viruses. Possibly because of the difficulties of expression, they tend to have larger genomes encoding more genetic information. Because of this, segmentation is a common though not universal feature of such viruses.

41. Negative-sense RNA genomes are not infectious as purified RNA. Virus particles all contain a virus-specific polymerase. The first event when the virus genome enters the cell is that the (-)sense genome is copied by the polymerase, forming either (+)sense transcripts which are used directly as mRNA, or a double-stranded molecule known either as the replicative intermediate (RI) or replicative form (RF), which serves as a template for further rounds of mRNA synthesis.

43. Figure 5.10

44. Figure 5.14 Influenza + receptor--sialic acid Different strains prefer different oligos

45. Flu Viral Uptake

46. Figure 5.20 Flu entry

47. Fig. A-8 Orthomyxoviruses (like Flu)

48. Figure A-9 Flu Life Cycle

49. Figure 5-21 HA changes

50. Figure 5-22