Hi Janusz

Probably nobody knows or if investigated the results are "occluded".

Apart from S-S and the collagen cross-links the other you mentioned are, at present, considered (in general terms) of low physiological abundance and/or of low physiological relevance. 

Dear Janusz,

My brief comment here is limited to the formation and identification of isoaspartyl bonds since we probably were the first to show how 2D NMR could be used to identify and quantitate  two isoforms of a protein (calbindin. D9k) and assess changes in the local and global conformation ( Biochemistry, vol 28 ,pp 8646-8653 ; 1989).  Deamidation and the formation of isopeptide linkages is probably more common than many realize and is a hurdle in quality assurance in the commercial production of biologicals. As you probably know the deamidation of a Asn-Gly linkage primarily takes place via a cyclic imide intermediate that can open up in two ways. Either to form a normal Asp-Gly linkage or to form an isoaspartyl linkage.  Since this results in an increased negative charge of the protein their existance is most easily detected through isoelectric focusing techniques - and may be missed in other separation methods insensitive to charge.

As mentioned above  2D 1H NMR is a powerful technique to not only identify the presence but also the structural perturbations in multiple forms of a protein in solution. In the case of Calbindin D9k is was shown that the structural perturbation through isoaspartyl linkage formation was highly localized and with small effects on the global 3D structure. 

All the best

Sture

Hi Janusz, many of the crosslinking mechanism you mention occur outside the cell.

Most collagen related crosslinking occur outside the cell (transglutaminases, lysyl oxidases etc)

Inside the cell you have ubiquitin ligase crosslinking. The S-S crosslinking of 2 different proteins inside cells is not extensive since cells are full of glutathione. 

NH-COOH