Hi, I couldnt find anywhere the exact percentage or amount of cysteine need to be present for my protein to be considered as cysteine rich. May I know the exact number/ percentage? for example >1%
Dear Fatin Safiudin ,
This is of course virtually impossible to say since the diversity of species and numerous families of proteins is impressively high but perhaps the following paper answers your question somewhat (see enclosed files):
Fahey, R.C., Hunt, J.S. & Windham, G.C. On the cysteine and cystine content of proteins. J Mol Evol10, 155–160 (1977). https://doi.org/10.1007/BF01751808
And the rather old but perhaps still relevant paper:
Malcolm H. Smith, The amino acid composition of proteins, Journal of Theoretical Biology, Volume 13, 1966, Pages 261-282, https://doi.org/10.1016/0022-5193(66)90021-X
So, a very rough rule would be above 1% Cysteines in your protein might classify it as a Cys-rich protein.
Best regards.
In addition to the interesting papers mentioned by Rob Keller, you may also want to consider the case where a protein contains a Cys-rich domain - i.e. there is some kind of local compositional bias. There are different definitions for compositional bias (e.g. probabilistic, complexity/entropy-based, or empirical) and all of them use some form of arbitrary threshold (e.g. in the form of a score/test statistic, a p-value etc.). So, when referring to this phenomenon (amino acid richness) it is important to make clear which definition was used to enable meaningful comparisons. Of course, extreme cases (e.g. homopolymeric sequences of sufficient length, like CCCCCCCCCC) will be detected as Cys-rich with any definition, but more subtle cases will depend on the definition used - and its internal parameters. The same issues apply to global compositional bias.
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