I am preparing a fusion protein for the production of protein drug in plant expression system. As I am planning to use several function domains in one construct, therefore I wanna put flexible linkers between them. I have seen in some literature that sometimes flexible linkers of this type of sequence are used: (Gly-Gly-Gly-Gly-Ser)n . Can an expert in the field confirm that which is the most suitable flexible linker can be used? What would be the optimal length?
Thank you for your help.
agree with the above, I prefer shorter (Gly-Gly-Gly-Ser)n with n=3 minimum as you don't want it too hydrophobic - but generally length will still be an empirical observation so you'll have to clone in a few choices there
I have tried to play with quite a few different kinds of linkers. In one case (GGGS)n with n=1 has worked fine for me. Too many repeats can be tricky in some cases during PCR amplification or get shortened by recombination (could be an issue in plants).
I have also seen poly-Asparagine linkers for fusion proteins. A vector to make MBP fusion protein, chose poly-N over GS rich linkers.
I have played with some rigid linkers and "nunchuks". ( I do see that you are specifically looking for flexible linkers).
Something like GAAAAAAAAAAG as rrigid linker and GAAAA(GS)1-2AAAAG as nunchuk can be tried.
In literature, poly proline linkers and E/R linkers like EEEERRMK have been also shown to work as rigid linkers.
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