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Can someone please explain me the concept of Immunodominant peptide in simple language?? I did read the wiki article but did not understand it clearly. Please help!

(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

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  • $\begingroup$ This article is indeed written in a complicated way. $\endgroup$ – Chris Sep 3 '14 at 6:57
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If you have an antigen (something foreign for the immune system, for example a virus or bacteria) this consists of many different epitopes (immunogenic regions), as shown in the figure below (from the German Wikipedia, Antikörper means antibodies). The antigens are taken up by special cells of the immune system and processed to get small peptides:

enter image description here

To produce highly specific antibodies, the body has to undergo a specific immune reaction against these peptides. In the beginning of this reaction antibodies usually have a rather low affinity (bind only weak) against their antigen. This is changed by the so called affinity maturation in which the antibodies are mutated to make a variety of different new antibodies. These are then again "checked" against the antigen and the ones with a higher affinity are positively selected.

So antibodies with a strong binding to their antigen are favoured against such which have a less strong binding which can lead the selection of only a few antibodies, even if a complex antigen which has many immunogenic peptides is used. This is positive in the way that these antibodies are very effective in directing an immune response against the virus/bacteria but can be critical if the pathogen has a high mutation rate as this leads to a pathogen which does not have this antigen anymore.

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It is about recognizing the intracellular pathogens. Every cell with nucleus splits up some of its intracellular protein to small chunks called oligopeptide (OP hereafter). So if there is an intracellular pathogen inside a cell, then its protein will be split up as well. After that the cell select the OPs it wants to show up on the surface. After an OP is selected, the cell binds it to a protein called MHC1 and sends it to the cell surface. So there is a lot of different MHC1-OP on the surface of every cell with nucleus. An immune cell group called T-cells are recognizing the MHC1 with their T-cell receptor (TCR hereafter). The TCR has a constant part and a variable part. The constant part depends on the species and person, it recognizes the MHC1. The variable part is random, it recognizes the OP. Each (not activated) T-cell has different variable part on the TCR on their surface, so each of them recognizes a different OP set. If a T-cell has strong binding to an intracellular pathogen's OP (IPOP hereafter), then it will be activated and it will destroy the cell infected with the pathogen. If a T-cell has only weak binding to an IPOP, or it recognizes an OP of a harmless own cell, then it won't be activated and it will die after a while, or in the second case it can become a regulator cell, which prevents autoimmune diseases. After the activation the T-cell start to proliferate, it divides many times and these clones try modify their receptor to bind even stronger to the selected IPOP, so they can find and destroy infected cells even more effectively. There is a mechanism in the immune system which prevents the activation of more than a few T-cells with different TCRs against the IPOPs of a single pathogen. So for example against a single pathogen there will be about a dozen different T-cell lines, which recognize a dozen IPOP. These IPOPs are the immunodominant peptides. Ofc. there can be IPOPs which are specific to the pathogen, but the T-cells which recognize them, are not or less activate. Those are the subdominant peptides.

You can find more info about immunodominance on wikipedia.

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