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Residue Sequence and Structure in
the Re evaluation the Categorization
of HIV Progression in Subjects Based
on CD4 T cell Decline Rates
Angela Garibaldi & Ryan Willhite
Loyola Marymount University
BIOL 398-01
March 23, 2010
Outline
• Review of previous experiment using CD4
decline rates
• Structure based hypothesis
• Methods and programs used
• Results
• Comparison to More Recent Studies
• References
Recap of past experiment
• Evaluated the categorization of progressors
based on CD4 decline rates
• Analyzed two moderate progressors (6,7) with
rates comparable to non-progressor 13 and
rapid progressor 10.
• Based on divergence and diversity subject 6
did not act as non-progressor
• Subject 7 acted like a rapid progressor.
Hypothesis
• Subject 7’s protein structure and properties
will be more similar to Rapid Progressor
Subject 10 than to Moderate Progressor 5.
• Looking at protein sequences and structure is
a more efficient method of testing our CD4 Tcell decline rate categorization than
nucleotide sequence.
Methods
• Create phylogenetic trees based on amino
acid sequence using Biology Workbench
• Use ProtPram to analyze residue composition
in subjects 6,7,5,10,13
• Select 7, 10, and 5 for time point analysis
– All clones used for selected visits
• Use PSIPRED to analyze secondary structures
of 7, 10 , 5, 13
Phylogenetics based on amino acid
sequence
10 vs 5
10 vs 7
5 vs 7
Subject 6 v 13
Subjects 6 v 7
Subjects 13 v 5
Subjects 6 v 5
ProtParam
Physico-chemical properties of a
protein using ExPASy server
Subject 5 Properties
Subject 6
Subject 7
Subject 10
Overall residue composition
•No significant pattern in Negative/Positive Charged
residues
•Rapid Progressor Subject 10 is the only subject with
Asn as its most prevalent residue
Residue composition over time
•Asn (Asparagine) is a carboxamide and is not an
essential amino acid
•Often found at the beginning and ends of helices
•Provides key sites for N-linked glycosylation
Residue composition over time
• All clones from selected visits were used.
• Subject 10, Rapid Progressor shows Asn as its
prevalent residue over time.
• Subject 7, Moderate Progressor begins with Asn as
prevalent residue
• Subject 10 showed sudden jump in Arg %. This may
be an artifact.
• Negative/Positive Charged residue ratio conserved
over time
Secondary Structure
Subject 7 Visit 5
Subject 10 Visit 6
No Difference!
Subject 5 Visit 5
Subject 13 Visit 6
Conclusion
• The highest percent of amino acids found in the
moderates 5,6, and 7 is (Ile)
• The highest percent of amino acids found in the rapid
10 to compare is (Asn)
• These differences did not equate to significant
secondary structure differences
• While looking at these compositions along with
protein structure is a questionable method of
progressor categorization, it provides insight
regarding qualities of progressors.
More recent study by YS Ho et al
• N-linked Glycosylation (NGL) important in minimizing
virus neutralizing antibody response
• Looked at env gp120 C2-V5 region (includes V3) in
plasma, leukocyte and other compartments
• Significant variation in numbers of NGL sites between
patients
• Found single cell/compartment-specific amino acid
changes and differences in NLG patterns between
plasma and blood leukocytes
Prediction of NGL sites on gp120
• Figure 2. YS Ho et al
V3 Region NGL sites
•V3 region has 1
clearly significant
NGL site along
with 2 lesser NGL
sites
Conclusions in relation to YS Ho
• The dominance of Asn % in Rapid Progressor
amino acid composition across all time points
may lead to the increase of NGL sites
• Dominance of Asn % in Subject 7 during Time
Point 1 suggests subject does share some
Rapid Progressor qualities
• Increase in NGL sites or changes in NGL sites
may be a mechanism of dealing with HIV-1 in
its later stages
– May influence viral recognition by host
antibodies
Future Direction
•Analyze amino acid composition in larger number
of Rapid Progressors for Asn dominance
•Based on subject sequences, predict NGL sites
per individual
•Compare these with that of Non-Progressors
•Analyze the folding patterns of the gp120 protein
based on differences in the V3 region where Asn%
is dominant vs Ile%.
References
• Ho YS, Abecasis AB, Theys K, Deforche K,
Dwyer DE, Charleston M, Vandamme AM, and
Saksena NK. HIV-1 gp120 N-linked
glycosylation differs between plasma and
leukocyte compartments. Virol J 2008 Jan 23; 5
14. doi:10.1186/1743-422X-5-14
pmid:18215327