Human Immunodeficiency Virus Flashcards
HIV - basic information
- reverse RNA
- enveloped
- 9.7 kb
- Genus: Lenti (“slow”)
Retroviridae
Exogenic: viral genome holds all information needed for the complete sequence of events connected to infection. Genome may also contain so-called oncogenes.
Endogenous: viral genome lacks essential information for performing a complete and productive infection cycle (oncogenes sometimes compensate the lack).
Another infection with a helper retrovirus is needed in order to balance the deficit.
Transposons
Transposable genetic elements – sequences that can move from one position in the genome to another: simple- and retro-transposons (transcription / reverse transcription / integration)
Responsible for most of the observed mutations and genetic rearrangements (deletions, duplications and translocations)
Control their own transposition function: cis-acting (same nucleic acid molecule affected) or trans-acting (all nucleic acid molecules in the cell)
HIV proteins
gp120 -> external -> glycosylated trimer
gp41 -> membrane -> glcosylated trimer
p17 -> matrix -> myristylated phosphorylated
p24 -> capsid -> hexameter and pentamer
p7 -> nucleocapsid -> zinc-finger motive
p6 -> link
p51/66 -> D/RNA-dep. polymerase RNAseH -> dimer
p9 (p10) -> protease -> dimer
p38 -> integrase; ligase endonuclease -> tetramer
p9/14 (Tat) -> transcriptional transactivator -> phosphorylated
p19 (Rev) -> posttranscriptional transactivator -> phosphorylated
p23 (Vif) -> infectivity factor cysteinprotease?
p11/15 (Vpr) -> associated protein R, transactivator
p14/16 (Vpu HIV-1) -> viral protein U -> phosphorylated
p25/27 (Nef) -> non evident function (G-protein like?) -> mysristylated
p13/16 (Vpx HIV-2) -> viral protein X
Biological active are often oligomers!
Infection: receptors
Primary receptor:
helper T-cell differentiation antigen, CD4 receptor
Accessory factors:
alpha-chemokine receptors CCR5 (macrophage, mono- cytes and dendritic cells) and/or CXCR4 (helper T4)
alpha-Chemokine receptors are of the 7-TM type (e.g. GPCR receptors)
Mutant allele of CCR5 with 32 base pair deletion frequent among Europeans i.e. Caucasians: homozygous people are resistant to infection because CCR5 does not end up on cell surface!
CD4
Fibronectin type III domain with beta-sandwich fold closely related to immunoglobulin fold
Two domains of CD4: gp120 binds to C’C’’ beta-hairpin
CD4 binding to gp120 changes the position of several loops to expose the chemokine receptor binding site (17b is a mimic for CCR5)
A model for HIV entry is shown, with the steps prevented by different entry inhibitors
1) Native trimer
2) CD4 Binding / T20 binding site exposure (Pro 542, BMS 806, TNX 355)
3) CoR Binding / Fusion peptide insertion? (SCH-C, SCH-D, AMD3100, AMD070, PRO-140, UK-427, 857)
4) 6-Helix Bundle Formation / Membrane fusion (T20 (Enfuvirtide), T1249)
T20: synthetic 36 amino acid peptide homologous to the C-terminal region of HR2
Capsid structure of HIV-1
-> Eular’s polyhedron theorem
HIV-1 capsid remains intact (initially) in cytosol:
- Prematurely uncoating trigger innate immune sensing: Capsid stability and virion infectivity appear to be optimally balanced
- Reverse transcription occurs within the HIV-1 virion; ATP and dNTP enter via pores
- interacts with microtubu- les and is actively transpor- ted to the vicinity of cell nucleus
216 Hexamers and 12 Pentamers (at locations of sharp curvature change)
Reverse transcriptase
- Heterodimer of P66+P51
- P66 with RNaseH domain
- RNAseH: non- sequence-specific endonuclease for cleavage of RNA in RNA/DNA hybrid substrate
- Strand swapping?
Peculiarities of reverse transcription*
- Cellular t-RNALys3 molecule functions as primer
- (+)sense ssRNA molecule(s) is/are converted into (one or two?) dsDNA:
- does not work accurately in vitro without capsid
- does not work if DIS is mutated - Discontinuous reverse transcription with strand swapping (at least once)
- Error prone process; no proof-reading like DNA- dependent DNA-Pol. (rapid genetic variations!)
- Big advantage for genome recombination, drug resistance, and repair!
- Only virus that is truly diploid (capsid content)
NRTIs
Note that the nucleoside analogues all lack a 3’-OH, a prerequisite for their ability to halt polymerization
2 bp lost at end of each LTR upon integration!
Initial stable synaptic complex
1) 3’ processing
Cleaved synaptic complex
2) Chromosome binding
Target capture complex
3) Strand transfer
Strand transfer complex
4) DNA polymerase
5) 5’ flap removal
6) DNA ligase
7) Stable provirus
Nef
Nef (negative factor / non evident function, 25-27 kD), N-terminal myristylation, phosphorylation by Protein kinase C. Nef can be processed to two part by the viral proteinase.
Nef induces a signal cascade thereby increasing the expression of NF-kB, AP- 1 and NF-AT. This in turn stimulates infected T-cells.
MHC-class-1 and -2 antigens are reducedFreduced recognition of infected cells by cytotoxic T-lymphocytes.
Infected persons carrying Nef mutations develop the disease very slowly. Nef is produced in an early stage of infection and plays a decisive role in the onset of events (Nef binds to AP-1).
Tat
Tat (trans-activator of transcription) binds to Tar (transactivation-response) element: 100-fold increase of transcription by LTR promotor. Two exon product, 86-104 a.a., 9-14 kD. Is released into the blood and can act directly as a toxin producing cell death via apoptosis in uninfected “bystander” T cells.
TAR element with Tat and TRP (TAR-RNA binding protein) binding sites. Tat prevents breakdown of viral mRNAs in nucleus. TRP perturbs mRNA synthesis. Delicate equilibrium regulates mRNA synthesis.
Formation and structure of the Cyclin T1-Tat-TAR RNA complex from equine infectious anemia virus EIAV
Tat interacts with Cyclin T1 of the positive transcription-elongation factor P-TEFb to recruit the transactivation-response TAR RNA.
Tat hijacks the host cell’s RNA pol II through interaction with the positive transcription elongation factor,
P-TEFb: The crystal structure of the Tat-P-TEFb complex containing HIV-1 Tat, human Cdk9, and human cyclin T1 (i.e. CCNT1).
