Dear Gopikrishna Vempati
there is not an universal best linker. It depends from the protein Size and conformations.
I often used the GSGGGG link which is short and flexible and in my experience only in few case was susceptible to degradations by proteases.
However If you would like to connect big and rigid patners is possible that a longer and in some case also rigid linker could be preferable..
in the following 2 link you can find and overwie of the different linker family and more informations about it
Article Linkers in the structural biology of protein-protein interactions
https://www.sciencedirect.com/science/article/abs/pii/S0169409X12003006
best regards
Manuele
A linker would need to be flexible, an inherently disordered; something like (Gly-Gly-Gly-Gly-Ser)n could have homologous recombination issues; GSAGSAAGSGEF would probably work better, but each protein has its own issues, so try and error...
Miguel Montoya GSAGSAAGSGEF is good choice for flexiable linker, you could also use different codon for the (GGGGS)n linker to avoid homologous recombinaiton. A linker doesn't always need to be flexiable, it could be rigid or cleavable as well, which depends on the protein structures and the experiment design. Here is a review for your reference. Article Fusion Protein Linkers: Property, Design and Functionality
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