If I understand well the first part, you will have a mixture of homo and heterodimers in all conditions.

Actually this might be a way of not having more than dimers. Imagine that another Cys different than 136 forms homodimers; then you culd end up with heterotrimers or tetramers formed by at least one Igbeta homodimer

The second question: definitely "yes". Not familiar with this specific CD protein, i.e. I wonder whether these Cys are close to membranes or on the outside or in the inside (extra or intracellularly oriented). Depending on where Cys are located you must or not design a peptide able to enter into the cell (in you work with living cells).

Thank you for your elaborations Rafael.

The peptide is, up until now, meant to work on the cell surface as it will mainly deal with extra-cellular domain of the BCR including CD79.

Also, what I can understand from your answer to the second part is that If I can find/design a peptide to interact with cys136 residue, it will prevent the formation of both dimers (homo and hetero) due to deterring disulphide bond from being formed, and thus, no conformation changes will happen nor signal initiated/transduced by Ig-alpha&beta heterodimer. If this is correct, it will is so great information for the project.

Yes to the first part. However, I wonder whether monomers may still be somehow "functional"

By they way another possibility is to use dithiotreitol or betamercaptoethanol to disrupt S-S bonds but this may be affect your assays (or perhaps not).

On the point about whether monomers are still functional, what I understood about BCR is that, due to, oligomerization of its three parts (IgM, CD79a&b), the signals are initiated. Our hypothesis is to prevent this dimerzation of CD79a&b so that no conformation changes happen (BCR oligomer will not be formed); hence no signals initiated. I hope I got your question correctly, otherwise, please correct me.

Furthermore regarding dithiotreitol or betamercaptoethanol, I think we should not use them as the project is all about peptides as a new approach, given, its higher safety and much less cost than mAbs, also and higher affinity than small molecules. Stability issues may still be a problem , but less than few years ago, thanks to some new relevant technologies.

Yes this was my point (first issue)

Concerning betamercaptoethanol, yes it may affect the assays.

Best of luck

Thank you for your wishes and helpful inputs

I just want to know which of three binding sites of CD79b is involved in dimerization?

I got three binding sites when I run CD79b into peptiMap web-server (which identify/predict the binding sites on protein services). Are there any clues which of these sites responsible/takes part in dimerization so that I try to find peptides that interact with it and prevent dimerization?

I have attached a table of the AA residues of each of the three sites

obtained by PeptiMap.

Hi Rafael,

You stated earlier that ''you will have a mixture of homo and heterodimers in all conditions''. This information is important for my research and a basis for some deductions, such as Ig-alpha is posed just near the dimerization interface of chain A&B of Ig-beta. Also, it could be a good strategy if we design a peptide that dock in the dimerzation interface, and hence have a great potential to prevent dimerations/conformation change.

For the purpose of referencing my research, I would appreciate if you can provide me with a reference paper about the information saying '' a mixture of homo and heterodimer can be available in all conditions''.