Dear all,
one of my proteins (human) of interest does not has any lysines (K). I was wondering if this is frequent in the overall proteome of mammals... or in organisms in general. Is there an easy way to look for this info in protein repositories, such as SWISSPROT... Is the total absence of K relevant for some functional aspects of the proteins.
In advance many thanks for any of your thoughts on that.
Best regards,
Jose
Hi Jose,
the fact that your are astounded by the lack of lysines in your protein already implies that the total absence of a certain amino acid is not the average case and that this might well be linked to the function of the protein. So you are totally right.
Lysine is abundant in proteins needing positive charge to have affinity for anions - like DNA, which is essentially a large anion. So you would find lysine in DNA-binding motifs and likewise one might hypthesize that a protein lacking lysine was selected in evolution for negative charge... How this is linked to the physiological function can only be speculated on with more information on your protein.
Best,
Peter
Dear Peter,
Many thanks for your reply to address my doubts... It is interesting, because the protein I was refering to is a a transcriptional co-activator (but does not bind DNA directly).
Cheers,
Jose
Hm, interesting... it would make sense if protein/protein-interactions in the vicinity of DNA (co-activators e.g.) would not rely on Coulomb-interactions (attractive effect of positive/negative charges), since this feature would recruit them directly to the DNA. So, maybe the protein does not have any Lysines in order to prevent binding to DNA and so to indirectly increase the affinity to proteins in environments abundant with DNA... Search for hydrophobic patches on the surface of your protein, this could be a possible interaction site with the activator (interaction by hydrophobic interactions instead of charge)- but this ist just a guess.
Do not forget, that Lys is not the only positively charged amino acid. YOu should check as well Arg and to lesser extent His.Analysis of the overall net charge would be interesting. If it still contains acidic amino acids Glu and Asp, it will be negatively charged, similarly to DNA. But that would make more sense for some negative regulator (competing for binding with DNA). Only if it bound actually to repressor, that would increase expression and thus appear as co-activator.
But this is just wild guessing without more information.
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