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Dual conformations for the HIV-1 gp120
V3 loop in complexes with different
neutralizing Fabs
Stanfield RL, Cabezas E , Satterthwait
AC , Stura EA, Profy AT and Wilson IA
(1999) Structure 7: 131-142
Alex George
J’aime Moehlman
Amanda Wavrin
Bobek Seddighzadeh
Journal Club Presentation
BIOL 398-01/S10: Bioinformatics
Laboratory
March 9, 2010
Outline
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Background on gp120 protein
Significance of the V3 Loop
Background on antibodies
Introduction to the paper
Results
Discussion
– conformational structures
gp120 Is a Viral Surface
Glycoprotein
• gp120 is a glycoprotein cleaved from
gp160 precursor and remains in noncovalent association with gp40
• gp120 is anchored to the viral membrane
by gp40 where it plays a vital role in the
specificity of the virus
• Binds to CD4 cells and at least one other
coreceptor on the target cell’s surface
– CCR5T-Cells; CXCR4 macrophages
Binding of gp120 to the CD4 Cell
Receptor and Coreceptor
http://www.nature.com/nrd/journal/v2/n7/images/nrd1134-f3.gif
Characteristics of the V3
Loop of HIV-1 gp120
• V3 domain of gp120- is disulfide-linked loop
– Approximately 40 amino acids
– High degree of sequence diversity amongst viral
isolates
• Required for viral entry into the cell
– Membrane fusion
– Interacts with cell surface chemokine receptors on
T cells and macrophages
V3 loop Is an
Immunogenic Site
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Accessibility to V3 loop depends on:
1. Viral isolate type
2. Interaction with CD4
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Causes a conformational change
As a result of gp120-CD4 interaction, the V3
loop becomes susceptible to neutralizing
antibodies and proteases
Conformational variations in
gp120 and the V3 loop can
modulate gp120 function
• La Rosa et al. Study
• The amino acid composition of the loop are
highly conserved in some positions and variable
in others
– E.i. the MN sequence are conserved in 80% of
244 isolates
• This suggests that these amino acid positions
have a key structural and functional role to virus
infectivity
Antibodies Can Help Reveal
Tertiary Conformation of V3 Loop
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Investigation of the neutralizing antibodies
and their complexes with V3 loop reveal:
1. Tertiary conformation of the V3 loop
a) Which can lead to an understanding in co-receptor
usage
2. An understanding of why some antibodies are
viral-specific and others recognize many different
strains
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Antibodies neutralize the virus by preventing
viral-cell membrane fusion
Antibody Fab Fragments 50.1,
59.1 and 58.2
• Antibody Fab fragments:
– Fab 50.1: specific for MN viral strain
– Fab 59.1: strongly neutralize IIIB and weakly
neutralize MN
– Fab 58.2: highly potent and broadly
neutralizing antibody
• Further analysis revealed a double bend around
GRAFY contrary to the study
• Found they could replace the ALA residue in the
double bend with Aib residue to provide a more
rigid scaffold for vaccine or drug design
Introduction to the
Stanfield et al. Paper
• La Rosa study determined conserved
amino acid sequences in the V3 loop
are significant to structure
• Examine antibodies in complex with the
V3 loop to determine the tertiary
conformation
• Attempts to identify why some
antibodies are viral specific while others
recognize many different viral strains
a) The abbreviated amino acid sequences for the V3
peptide RP70, His Loop, Ser Loop and Aib142
b) Detailed view of the His and Ser Loop hydrazone
bond
a)
b)
Results from X-Ray Crystallography of Fab 58.2
in complex with Aib142, His loop and the Ser loop
X-ray structure for the Fab-V3 complexes agreed with the La Rosa
et al. predictions
3-Dimensional views of the
Fab 58.2 complex with:
a) Aib142
b) Histidine Loop
c) Serine Loop
Red sequence= highly
conserved region
Cyan= Light Chain
Purple= Heavy Chain
Comparing the 3D structures of the H1 loops in Fab
Fragments 58.2 (red), N10 (yellow) and AN02 (blue)
Predicted structures from the determination of electron
densities of Aib142 (a,b), the His loop (c) and the Ser loop (d)
Surface Picture of Fab 58.2
indicating acidic (red),
basic (blue) and neutral
(white) regions
a) Indicates the acidic
binding pocket for ArgP322
of Aib 142
b) Stereoview of the
combining site
Summary of the number of Van der Waals interactions
between Fab 58.2 and its bound peptides, Aib142, the
Histidine loop and the Serine loop
Summary of the number of Hydrogen bonds and salt bridge
interactions between Fab 58.2 and its bound peptides, Aib142,
the Histidine loop and the Serine loop
a) The conformations of the V3
loop bound to Fabs 50.1 (yellow),
59.1 (purple) and 58.2 bound to
Aib142 (blue) and His loop
(green)
Figure 6
Summary the turn angles
displayed in Figure 6
Biological Implications
• The V3 loop is involved in virus infectivity.
• There is a high conservation at the tip of the
gp120 V3 loop, surrounded by regions of high
diversity.
• This suggests that structural conservation is
related to biological function.
• Studies have suggested that one or more
amino acid residue alterations within the V3
loop leads to changes in viral tropism.
Further Research
• Unanswered questions provide a
direction for further studies, with intent
of revealing the biological role of the V3
loop.
• This could open up the possibility of
drug design or vaccine development.
References
• Stanfield RL, Cabezas E , Satterthwait
AC, Stura EA, Profy AT and Wilson
IA. (1999) Dual conformations for the
HIV-1 gp120 V3 loop in complexes
with different neutralizing Fabs.
Structure 7: 131-142