Structural Immunology
Fall 2006
last modified: 8/24/06
Practical Matters
- See Tynette Hills in the Biochemistry Department office in order
to register for GBCH724.
- Meeting time, day, and location: (tentatively) Thursdays,
2-4 pm in Med School, Rm. 6301.
- Prerequisite: Permission of instructor, Sam Landry, Ph.D, Rm
6055, landry@tulane.edu
Summary
This year the course will involve literature research and
bioinformatics data mining in order to correlate antigen
three-dimensional structure with CD4+ helper T-cell epitope
immunodominance. The course director has identified several
proteins for which appropriate information is available.
Participants will be asked to research the immunology on one or more of
the proteins, analyze the structure(s) and epitope-mapping data, and
co-author a paper to be submitted for publication. The following
papers serve as examples:
- S.J. Landry. Local Protein
Instability Predictive of Helper T-cell
Epitopes, Immunology Today 18,
527-532 (1997). Link
to PubMed entry
- G. Dai, N.K. Steede, and S.J. Landry. Allocation of
helper T-cell epitope immunodominance according to three-dimensional
structure
in the human immunodeficiency virus type I envelope glycoprotein gp120,
Journal of Biological Chemistry 276,
41913-41920 (2001). Link
to PubMed entry
- S. J. Landry. The
Relationship of T-Cell Epitopes and Allergen Structure, in Food Allergy, S. J. Maleki, A. W. Burks,
R. M. Helm, Eds. (ASM Press, Washington D.C., 2006) pp. 123-159. Link to Tulane Blackboard for
access to copyrighted documents
Paper Outline
Preliminary
Title: Allocation of CD4+ epitopes according to structure in
[your protein]
Journal
format: Journal of Immunology (ISI impact factor in
2005: 6.9)
Introduction (Some
topics may not be necessary, and the order is flexible.)
- What are the “immune correlates to protection”,
i.e., what
components of the immune response are necessary for protection against
disease?
- What information suggests that CD4+ T-cell
immune responses to your
antigen are protective?
- [Allergen] What information suggests that
individuals are
allergic to your protein (for example, as opposed to other proteins in
the same
pollen)?
- How are people exposed to the protein? What tissue encounters the protein first?
- How is the protein disposed in its natural state
(cell-surface, etc.)?
- Describe the protein’s structure, biosynthesis,
and regulation.
- Describe what is known about B-cell and T-cell
epitopes in
the protein.
- Compare and contrast antigen processing and
presentation of
CD4+ vs. CD8+ T-cell epitopes
- Describe the relationship of protein
structure/stability/flexibility and proteolytic breakdown (antigen
processing)
- Describe methods of analyzing protein
stability/flexibility,
including crystallographic B-factors and COREX/BEST residue stability
- Summarize the findings of your work
Methods
- Specify the sources of CD4+ epitope data
- Describe the assignment of epitope scores to
amino acid
residues
- Describe the calculation of the COREX/BEST
profile,
including values of adjustable parameters (ensemble generation by
exhaustive enumeration
or Monte Carlo sampling, entropy weighting factor, temperature, window
size,
minimum window size)
- Describe method of correlating epitope score
with
structural data and the analysis of statistical significance
- Describe the analysis of sequence entropy, i.e.,
the
sequences used and method of selection
Results
- Describe the variability in epitope maps among
individual
animals or human subjects
- Note the number and average width of peaks in
the profile of
epitope scores.
- Compare the profile of B-factors to the profile
of epitope
score: numbers of peaks, locations
- Describe the analysis of correlation (B-factor
and epitope
score) vs. offset, and specify the P-values for the maximum
correlations
[r(max)]
- Describe the profile of COREX/BEST residue
stability and
compare it to the B-factor profile
- Compare the profile of residue stabilities to
the profile of
epitope score: numbers of peaks, locations
- Describe the analysis of correlation (residue
stability and
epitope score) vs. offset, and specify the P-values for the r(max)
Discussion
- Compare number of peaks of epitope score with
the average
number of epitopes observed in the individual.
- Conclude that the correlation of epitope score
with
stability/flexibility suggests that structure directs antigen
processing and
that epitopes tend to be located [offset at r(max)] residues
N-terminal/C-terminal from stable/flexible segments of the protein
- Discuss the locations of B-factor maxima and
residue-stability
minima (probable sites of proteolytic processing) in the ribbon diagram
of the X-ray crystal structure. Are they
in loops, turns, or domain linkers?
- What are the implications of CD4+ epitope
allocation
according to structure in the protein? Compare
the profiles of B-factor, residue stability, and
epitope score
to the profile of sequence entropy. Are
cross-reactive CD4+ T-cell responses more or less likely as a result of
structure-based epitope dominance? Does
this increase or decrease the likelihood of disease?