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CBS >> CBS Courses >> Immunological Bioinformatics Course >> Course Programme 2008 >> Exercise 6

Proteasome specificity

The purpose of this exercise is to see i) the effect of proteasome and TAP in determining immunodominancy and ii) the selection pressure caused by proteasome and TAP to generate immune escape mutants.

Prediction methods

You can use NetChop 3.0 to make proteasomal cleavage predictions. Note that the 20S-3.0 webserver has been trained on in vitro digest data generated by the constitutive proteasome. The NetChop Cterm 3.0 webserver has been trained on CTL epitope data, and can thus be expected to mostly describe the specificity of the immuno-proteasome. You can thus estimate the difference between the two types of proteasomal cleavage using the two NetChop methods.

A recent paper by Peters, et al proposed a matrix method for predicting TAP binding affinity for ligands upto 20 aa. Using this matrix, you can predict log(IC50) values for TAP binding, t, by:

t=mat(1,N1) + mat(2,N2) + mat(3,N3) + mat(9,C),

where N1, N2 and N3 are the first three positions in the peptide, and C is the last position. Remember that a low IC50 value means strong binding to TAP. A low matrix entry indicates that an amino acid is well suited for TAP binding. You can use this formula to understand how TAP binding affects antigen presentation!

Q1: What does the formula given for TAP binding efficiency tell us about the properties of TAP binding?

Effect of processing in immunodominance hierarchies

Acidic protein 2 (PA) from influenza A virus contain several epitopes that can be presented by mouse H-2Db allele. Using NetMHC .
Identify possible 10mers that could become immunodominant epitopes.

Among the first 4 likely epitopes (according to MHC predictions) in PA protein, check which one has the best TAP binding. Remember a TAP ligand does not need to be a 10-mer. (Calculate 10-12 mers).
Can this peptide be an immunodominant epitope?

Check which of the top 4 peptides are predicted to be generated correctly in their C-terminal by the immuno-proteasome (use NetChop-3.0 C-term).

Q2: Combining all three predictons (MHC, proteasome and TAP), which epitope according to you should be the immunodominant one?

Q3: Chen et al. have found that the immunodominant epitope ranks lower when the immunoproteasome activity is inhibited. Can you explain why? (Use NetChop-20S)

Immune escape

HIV-1 is a rapidly evolving virus. One factor that forces the virus to evolve is the immune response of the host. In this exercise we will analyse the data of Allen, et al. which studied the immune escape variants in individuals carrying HLA-A3 molecules. The two immunodominant epitopes are from p17 (part of Gag) protein: KK9 epitope (positions 18-26) and RK9 epitope (positions 20-28). The main mutations found in patients are K->R (position 26) and K->(Q,T,R) (position 28).
Q4: What is the effect of mutation at position 26 for KK9 epitope on the immune response?
Q5: What is the effect of mutation at position 28 for RK9 epitope on the immune response?
You can use NetTAP to make prediction of TAP transport NetChop-3.0 to generate proteasomal cleavage prediction, and NetMHC to predict peptide MHC binding.


This file was last modified Thursday 12th 2008f June 2008 09:59:42 GMT