BIOL368/F14:Chloe Jones Week 7

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  1. Angstrom: (n.) Symbol Å. A unit of length equal to 10−10 metre. It was formerly used to measure wavelengths and intermolecular distances but has now been replaced by the nanometre. 1 Å = 0.1 nanometre. The unit is named after the Swedish pioneer of spectroscopy A. J. Ångstrom Source: Oxford Dictionary of Biology 6ed.
  2. : Symbol for alpha carbon atom.Source: Oxford Dictionary of Biochemistry and Molecular Biology 2ed.
  3. Immunodominant: (adj.) The attribute of a part of an epitope that contributes a disproportionately great portion of the binding energy. Source: Oxford Dictionary of Biochemistry and Molecular Biology
  4. Lattice: The regular arrangement of atoms, ions, or molecules in a crystalline solid.Source: A Dictionary of Physics 6ed.
  5. Mutagenesis: The production of mutations. Source: Oxford Dictionary of Biochemistry and Molecular Biology 2ed.
  6. Optimize/Optimization: (v.) make the best or most effective use of (a situation, opportunity, or resource)Source: New Oxford American Dictionary 3ed.
  7. Recommence: (v.) Begin or cause to begin again.Source: New Oxford American Dictionary 3ed.
  8. Schematic: (adj.) (of a diagram or other representation) symbolic and simplified.Source: Oxford Dictionary of English 3ed.
  9. Superimposed: (v.) Place or lay (one thing) over another, typically so that both are still evidentSource:Oxford Dictionary of English 3ed.
  10. Tenuous: (adj.) Slight; insubstantial; weak; vague.Source: Australian Oxford Dictionary

Structure of a V3-Containing HIV-1 gp120Core

I.HIV-gp20 envelope glycoprotein

A. Spikes on envelope allows for binding of receptors and virus entry.
B. Third variable region (V3)
  1. Immunodominent
  2. Conformational Changes important for coreceptor binding
a.) Spikes on envelope allows for binding of receptors and virus entry.
i.) Conformation change induced by spikes
b.) gp120 binds to CD4 which positions the V3 tip towards the target cell surface
c.) Allow for binding of coreceptor CCR5 or CXCR4 (necessary for viral entry)
i.) Determines which coreceptor appropriate
C. Neutralization in immunization primarily targets V3 region

II. Analysis of HIV-gp20 core with V3 structure

A. Differences observed in core in comparison to what previously was observed f
  1. N –terminus and variable loops
B. V3 around the base maintained structural similarity
  1. prior truncations had no effect on core
C. Large structural difference in X5 antibody
  1. observed in X5 heavy chain, resolution increased
  2. compared free X5 and bound X5
D. Figure 1.An advanced Photon Source generated an image with core gp120, V3 bound distally, CD4 receptor, and X5 antibody (light & heavy chain).Location of the tip of V3 is where the target membrane is located.

III. V3 Sequence and structure

A. V3 comes from outer domain
  1. GP 120 protein has inner and outer domains
a.) Orientation based on spikes
B. Three structural regions: conserved base, flexible stem, β-hairpin tip
  1. Conserved base, essential component of core
  2. Flexible stem, extends away from core
C. Lattice contact of H-bonds in exposed backbone may have effect onV3 tip
D. Figure 2a . Displays the sequence of JR, HXBc2, and three consensus sequences (A,B,C). The upper case letters are denoted by conserved residues and lower case letters are denoted as variable residues. The conserved (Arg-Pro) motif is highlighted yellow, and the conserved (Gly-Pro-Gly-Arg) motif is colored green.
E. Figure 2b . Electron density and B value (atomic mobility) for the V3 region. Higher atomic mobility is located more at the tip (part that touches the host cell membrane) signified by the red color. Blue color indicated lower atomic mobility.
F. Figure 2c . Entire V3 region shown in ball and socket form. Color correlates to atoms: Salmon=carbon, red=oxygen, blue=nitrogen, orange=disulfide bonds. Shows order: base, stem, tip
G. Figure 2d . Zoomed view of V3 region starting at N-terminus. Anti-parallel sheet on outer domain of 120. The conserved (Arg-Pro) motif which is highlighted in yellow (R298) interrupts the 3 residues and then forms side chains, hydrogen bonds to 3 carbonyl oxygen’s and then to Pro299 which initiates the outgoing and returning of V3 strands.
H. Figure 2e .The V3 tip (Ser306 to Gly312), has a confirmation but diminishes in a Gly-Pro-Gly-Arg β turn. After turn density not as defined, carbon atoms of conserved tip colored in green.

IV. Coreceptor binding for gp120

A. Feature important for conreceptor binding: V3 tip and gp120 core around bridging sheet
  1. Both are conserved
  2. V3 Tip
a.) Surprising to see that conserved, but actually similar to core in antibody peptide complexes in previous studies
B. Conserved region for coreceptor binding is separated by 10 to 20 AA
C. Regions that bind gp120: N terminus and second extra cellular loop
  1. May be spatially separated a well
D. How the bonding occurs
  1. N terminus of coreceptor reaches up binds to core and V3 base, V3 tip of gp120 reaches down to 2nd extracellular loop of the coreceptor
a.) Figure 3b . Coreceptor interaction between V3 of gp120 to that of 2nd extracellular loop of CCR5
b.) Figure 3a .A trimetric model orientation of the triggered CD4 gp120 with V3. The conserved (Pro-Gly) V3 tip consisting of 30 Å. positioned towards the host cell membrane.
c.) Evidence of this model
i. binding of CCR5(coreceptor) to gp120 affected by modifications in the core and base of V3
ii. Inhibitors of HIV that bind to 2nd extracellular loop of coreceptor no longer have effect on mutant viruses with V3 truncations
E. Coreceptors CXCR4 or CCR5 primarily support HIV-1 entry
  1. 11/25 rule
a.) 11th or 25th positions has a positive charge than coreceptor CXCR4 will be used, if not use CCR5
b.) positions 11 and 25 within variable stem
i. separated by 17 Å, suggests that recognize different portions of coreceptor
  1. V3 sequences more conserved for CCR5

V. Conformational changes in gp120 due to CD4

A. Binding of CD4 and coreceptor protrudes V3
  1. Conformation of outer domain where V3 originates doesn’t really change

VI. Immuodominance of V3

A. Neutralizing activity directed at V3
  1. antibody-peptide complexes varies in conformation of V3, however Pro-Gly tip conserved.
  2. Figure 4a . Superimposing antibodies on V3 structure with core. Monoclonal antibodies 50.1, 58.2, 59.1, 83.1, and 447-52D bind to conserved V3 tip blocking coreceptor binding.
B. Superimposing conserved tip, limits the V3 peptide binding antibodies access to gp120 core.
  1. Antibodies surround V3
  2. Figure 4b . Two different views of the accessibility of antibodies to V3. Antibodies bind to either the core or V3. V3 engulfed in neutralizing antibodies, proposing a role in immunization.
C. Molecular hook
  1. high surface area, chemically reactive backbone, and conformational flexibility enhance V3 to grab close by neighbors on viral spike
D. Quaternary interactions influence overall neutralization sensitivity
  1. Transfer of neutralization resistance from YU2 to HXBc2
E. Results/Conclusion
  1. V3 projects towards target cell when CD4 binding occurs and when corecetor binding site forms
  2. V3 tip mediates gp41 fusion
  3. Coreceptor interaction and altering quaternary interactions of V3 can aid in HIV avoiding immune system and HIV entry into the cells
  4. V3 plays a major role in the establishment of the HIV virus within the body, from the obtained structure of the V3 region it can be further examined and analyzed towards progression in neutralization.

Journal Club Presentation

Journal Club 2 Presentation

Electronic Lab Notebook

Weekly Assignments

Class Journals

Chloe Jones 03:46, 15 October 2014 (EDT)Chloe Jones