Immunological Bioinformatics 2010 Exam! ! ! Wednesday, 23 June 2010

10 Questions of 3 points each1 Exercise Question of 10 points 7 pages

Name:____________________________________________________________

Student number: ___________________

General questions (Q1-Q10 = 75%)Q1:What is shown in the figure below (circle the correct answer)

MHC class I + ligand! MHC classII + ligand! Antibody + ligand!

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Q2:We use binding data to train our prediction methods.We have a training set consisting of 965 peptides with corresponding biochemically measured affinities. 325 of these have a measured binding affinity stronger than (i.e., the IC50 value is below) 500 nM. We will train Artificial Neural Networks to predict the binding affinity. For this we set op a 5-fold cross-validation training scheme. How many peptides will be used for training in each of the five training rounds: (circle the correct answer)

1. 652. 2603. 7724. 965

DatabasesWe want to check if the following peptide that is residing in the SARS corona virus protein is an epitope:

FIAGLIAIV

Use the IEDB database (not predictors) we have been using, to verify if this peptide have been shown to be/be a part of (substring) an epitope. If not write No or write the full found epitope sequence and in case of T cell epitopes write the specific HLA allele(s).

Q3:

Class I/CTL epitope

ClassII/Helper epitope

Linear Bcell epitope

Discontinuous (Non_peptidic) Bcell epitope

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Supertypes and logosQ4:We already saw that there were MHC alleles in monkeys that were similar to human alleles. Now we want to investigate if also mice share similarities with humans.One of the most used laboratory mouse strains are named BALB/c and have the following MHC alleles:

H-2-Kd, H-2-Dd and H-2-Ld

Now find out which of these have the most similar human class I supertype representative based on their peptide binding preferences. Write the one Mouse-Human allele pair that you find are the most similar:

Human HLA:

Mouse MHC:

TAPQ5:Having this peptide generated by the proteasome:

CEPTIIERNITE

Which sub-peptide (shorter, continuos part of the full peptide) will have the biggest chance of being a TAP binder using Björn Petersʼ SMM matrix given below.

sub-peptide:

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PredictionsWe have done some immunological predictions using this Neuraminidase protein sequence originating from a Danish influenza patient:

>gi|156691880|gb|ABU92776.1| neuraminidase [Influenza A virus (A/Denmark/101/2006(H3N2))]MNPNQKIITIGSVSLTISTICFFMQIAILITTVTLHFKQYEFNPPPNNQVMLCEPTIIERNITEIVYLTNTTIEKEICPKLAEYRNWSKPQCSITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNVHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGDDKNATASFIYNGRLVDSIVSWSKEILRTQESECVCINGTCTVVMTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINIKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDVWMGRTISEKSRSGYETFKVIEGWSNPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI

Q6:We have predicted potential 15mer T helper epitopes for DRB1*0401, DRB1*1501, and  DRB1*0101 using NetMHCIIpan(see output here)

Which are the 3 best binding peptides to each allele

Q7:We have predicted the affinity of HLA-A*0201, HLA-A*0301 and HLA-B*0702 binding of 10mers using NetMHCpan.(See output ) herehttp://www.cbs.dtu.dk/cgi-bin/webface?jobid=netmhcpan,4C21CF0C038FCB84http://www.cbs.dtu.dk/cgi-bin/webface?jobid=netmhcpan,4C21CF0C038FCB84

Which are the best three binding peptides to each allele

Q8:A) Which of the above two types of peptides (HLA-A or HLA-DRB1 binding) should also

be tested for for correct proteasomal cleavage and TAP binding.

B) Looking at the NetChop output, linked here, which of the relevant peptides have an acceptable cleavage prediction: (Write the sequences)

Q9:Look at the output from CPHModels when submitting the Neuraminidase sequence. The output is linked here.

A) Which PDB entry is the best hit: PBD: Chain:

B) Is this likely to be a close homolog? Yes No (Circle the correct)

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C) How many residues in the aligned area differs between your template and your model?

Q10:We have submitted the model to DiscoTope and the result is linked here.

We have also submitted the template structure which is linked here.

A) Which of the two structures have the most predicted B cell epitopes?

Template! ! ! CPHmodel model (circle the correct answer)

B) Does the positions of difference in epitope assignment always correlate with the positions of sequence difference between the two proteins?

Yes No! ! ! (circle the correct answer)

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Exercise question (25%)continues over more pages

We have chosen the following envelope protein as a potential Herpes simplex vaccine candidate.

>gi|9629400|ref|NP_044621.1| envelope protein UL20 [Human herpesvirus 1]MTMRDDLPLVDRDLVDEAAFGGEEGELPLEEQFSLSSYGTSDFFVSSAYSRLPPHTQPVFSKRVILFLWSFLVLKPLEMVAAGMYYGLTGRVVAPACILAAIVGYYVTWAVRALLLYVNIKRDRLPLSAPVFWGMSVFLGGTALCALFAAAHETFSPDGLFHFIATNQMLPPTDPLRTRALGIACAAGASMWVAAADSFAASANFFLARFWTRAILNAPVAF We have prepared NetCTLpan and NetMHCIIpan outputs.

How many different epitopes do you find

Helper epitopes:CTL epitopes:

How big a part of the population in Northern Ireland will be covered by this vaccine? We will consider the 10 most frequent HLA-A, HLA-B, and HLA-DRB1 alleles, respectively. Use the statistics from allelefrequencies.net (login lunde, password cbsdtu).

Remember that digits more than 4 does not have functional meaning thus the frequencies of HLA-A*680101 must be added to HLA-A*680102 to get the total allele frequency of HLA-A*6801.(N in a allele name means non-functional)Here is a link to the relevant frequencies:

Helper epitopes:! ! ! ! % of the populationCTL epitopes:! ! ! ! ! % of the population

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In order to check for B cell epitopes first check for a 3D structure in the PDB database using BLAST.

What is your best hit?

PDBname: Chain ID:E-value:

Will this structure be a good template:

We have made a homology model using CPHModel which is linked here.

Which template are used?PDBname:Chain ID:

In order to test for potential B cell epitopes we have used the model for DiscoTope predictions and the sequence for BepiPred predictions.

How many Residues are predicted to be in epitopes by BepiPred?

How many Residues are predicted to be in epitopes by DiscoTope?

How many are in both?

THE END!

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