I am interested in the question whether exposure to protein A might create antibodies that also bind to protein B.

I am wondering whether, if the antigen of protein A is a conformational epitope, it would still be possible to predict (or at least guess at) the reaction against protein B with only a sequence comparison.

This might be possible if the subunits are long enough and if there are enough of them, which is why I ask about their length and number.

  • $\begingroup$ You seem to be using the word "subunit" in a manner that conflicts with that used with respect to protein structure. Do you mean short stretches of primary structure that contribute to the epitope? $\endgroup$ – David Oct 8 '18 at 21:52
  • $\begingroup$ Yes, I guess that's what I mean. I took that term from the definition of conformational epitope at wikipedia: "A conformational epitope is a sequence of sub-units (usually amino acids) composing an antigen that come in direct contact with a receptor of the immune system." $\endgroup$ – BlindKungFuMaster Oct 9 '18 at 7:41

I found this paper that analyzes 111 antigen-antibody x-ray crystal structures.

They find that in their dataset that "the large majority of Ag structures (86.5%) have CRS ranging from 20 to 229 aa." CRS stands for contact regions span which they define as "the minimum contiguous amino acid sequence containing all CRs of an Ag or Ab and represents the size of a complete structural epitope or paratope, inclusive of CR and the minimum set of supporting residues required for proper conformation." further on they mention that "The average and median CRS of all 111 Ag structures is 125 and 95 aa, respectively." and "the majority of the structures do indeed have epitope CRs that are clustered together in short, contiguous stretches ranging from 2 to 12 aa, longest contiguous sequence of CR being 5"

I hope this helps.


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