Transcript Title of Project

More Frequent Nonconservative Amino Acid
Substitutions in the gp120 V3 Region in Patients with
Rapid CD4+ T Cell Decline Versus Patients with
High CD4+ T Cell Variability
Kevin Paiz-Ramirez
Janelle N. Ruiz
Biology 398.01
Department of Biology
Loyola Marymount University
March 20, 2010
Outline
I.
Entry of HIV-1 involves binding of gp120 to CD4
receptor and co-receptors
Are there structural differences in V3 region of
HIV-1 gp120 between participants with rapid
CD4+ T cell decline versus patients with high
CD4+ T Cell variability?
Results: comparing our groups
II.
III.
I.
II.
III.
IV.
Diversity and divergence of gp120 V3 region amino acid
sequences is higher in linear progresors versus high
variability subjects
There are differences in secondary structure predictions
between the two groups
Amino acid changes take place on the surface of gp120
and near the co-receptor binding site
Post-translational modifications linear progressors occur
near or on the co-receptor binding site
The Entry of HIV Involves Specific
Interactions between gp120, CD4, and
the Co-receptor
• Kwong et al. (1998) solved the
crystal structure of
– gp120 (red)
– CD4 (yellow)
– An antibody that binds similarly
to the co-receptor (blue and
aqua)
• Gp120 is crucial for fusion of HIV-1
to cell surface
– Positioning
– Timing
• CD4 binding induces
conformational change in gp120
Structure of gp120 Core
Kwong, et, al 1998
Previous investigation revealed
differences in diversity and divergence in
DNA sequence of gp120 V3 variants
• Patients with high CD4 decline had greater diversity
and divergence in DNA sequence of gp120 V3
variants than patients with high variability in CD4
count
• Are there amino acid changes that lead to structural
differences in gp120 between patients with a rapid
CD4+ T cell decline versus patients with high CD4+ T
Cell variability?
Linear Progressors
High Variability
Differences in Amino Acid Sequences
were observed between the Linear and
High Variability Groups
• Multiple sequence alignments based on amino acid
sequences were generated for each subject using the
clones from the first four visits
• Determined consensus sequence for each subject
• Determined the sequence(s) with most differences
from consensus sequence for each subject
High Variability group has fewer differences
between sequences and less divergence in
sequences
Subject 12
High Variability group has fewer differences between
sequences and less divergence in sequences
Subject 8
D
High Variability group has fewer differences between
sequences and less divergence in sequences
Subject 6
Linear Progressors had More Nonconservative
Substitutions
Subject
4
Linear Progressors had More Nonconservative
Substitutions
Subject
10
Structure-Based Sequence Alignment of Core
Gp120
Predicted Secondary Structures of the
gp120 V3 Region shows six beta sheets
and one alpha helix
High Variability shows six beta sheets and
one alpha helix Subject 6
Subject 8
Subject 12
Linear Progressors show six beta sheets
and one or two alpha helices
Subject 4
Subject 10
High Variability Participants had Amino Acid
Substitutions Occur on the Protein Surface
Surface
Surface
Binding Site
Surface
Key:
•Blue: Single, fully conserved residues
•Green: Conservation of strong groups
•Purple: Conservation of weak groups
•Black: No consensus
Linear Progressor Participants Had a
Greater Number of Nonconservative Amino
Acid Substitutions Located on Binding Sites
Binding Site
Binding Site
Binding Site Surface
Key:
•Blue: Single, fully conserved residues
•Green: Conservation of strong groups
•Purple: Conservation of weak groups
•Black: No consensus
Linear Progressor Participants Have Greater
Major Amino Acid Changes on Protein
Binding Sites
Key:
•Blue: Single, fully conserved residues
•Green: Conservation of strong groups
•Purple: Conservation of weak groups
•Black: No consensus
Linear Progessor Participant Displaying Nonconservative
Amino Acid Substitution Located on Binding Site
Sites of Post Translational Modification:
Linear Progressors Have Slightly Greater
Post Translational Modifications than High
Variability
The Linear Progressor group was different from
the High Variability group on a number of
different measures
• Linear progressors
– had greater number of amino acid sequence differences
– greater amount of nonconserved amino acid substitutions
– had greater number of major amino acid changes in CD4-binding
regions
– showed greater post-translational modifications
• This could indicate greater structural differences in linear
progressors
• Further studies could examine protein structural differences
variants within gp41 region
Pancera et al. (2010) examined the region
where gp120 interacts with gp41
• This region had not been explored by earlier studies
(Kwong et al)
• gp120 elements proximal to gp41 completed a 7
stranded Beta sandwich
• Facilitated movement between outer domain and
gp41
• Kwong et al. also observed a conformational change
with the virus in the v3 region
• This corroborates with Pancera’s observed changes
in the gp41
Conclusion
•
•
•
•
•
•
•
Entry of HIV-1 involves the binding of gp120 to CD4
receptor and co-receptors
There are structural differences in the V3 region of HIV-1
gp120 between participants with rapid CD4+ T cell decline
and patients with high CD4+ T Cell variability
The diversity and divergence of gp120 V3 region Amino
Acid sequences is higer in linear progressors
Presented differences in secondary structure between linear
and high variability
Amino acid changes take place on the surface of gp120
and near the co-receptor binding site
Post-translational modifications linear progressors occur
near or on the co-receptor binding site
Pancera et al & Kwong et al observed conformational
changes in the gp41 and V3 region
References
• Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J,
and Hendrickson WA. Structure of glycoprotein in
complex with the CD4 receptor and a neutralizing human
antibody. Nature 1998 Jun 18; 398(6686) 648-59.
• Pancera M, Majeed S, Ban YE, Chen L, Huang CC, Kong
L, Kown YD, Stuckey J, Zhou T, Robinson JE, Schief WR,
Sodroski J, Wyatt R, and Kwong PD. Structure of HIV-1
gp120 with gp41-interactive region reveals layered
envelope architecture and basis of conformational
mobility. Proc Natl Acad Sci USA 2010 doi:10.1073