Fusion moieties for fusion proteins - (Jun/09/2008 )

Hi there, I'm a beginner to designing fusion proteins so I wanted to know what makes a good linker between two proteins.

I was told that you just string Gly and Ser between them; my understanding is these two are small and inert. Could someone clarify why Gly and Ser? and if there are suitable amino acids? as well as the ordering and number of each (e.g. I see linkers similar to [Gly-Gly-Gly-Ser]x2). And how long should it be?

Thank you very much for your help!

Thinking varies greatly here. Some researchers swear by short linkers (say, GS), others say you need a longer linker (up to 10 residues or even more). As you say, Gly and Ser are used because they are small, essentially inert residues; Gly is good because you don't have any issues of a sidechain causing steric hindrance.
You might get away with an Ala, but you have that nice little CH3 group to consider... I think most researchers have used Gly and Ser for pragmatic reasons, without going into too much detailed investigation of why they work better than other combinations.
Most (All?) of the time, you don't want the fusion partner interacting with your protein of interest, which was why linkers started being used.