Fusion protein linker - (Feb/04/2011 )

Hi,

For my project I am making a fusion protein out of two DNA binding proteins. To stop the proteins from interfering with one another, my plan is to make a connecting linker protein between them. There doesn’t seem to be much known about linkers for fusion proteins in literature; the main articles I found were about the webprogram LINKER.

Xue F, Gu Z, Feng JA., LINKER: a web server to generate peptide sequences with extended conformation. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W562-5.

Crasto CJ, Feng JA., LINKER: a program to generate linker sequences for fusion proteins. Protein Eng. 2000 May;13(5):309-12.


However the URL to the webprogram that is provided in both articles is offline and so I can not access it. I also found it impossible to reach any of the authors.

Another website I found with some usefull linkers is: http://partsregistry.org/Protein_domains/Linker. I tried a GlycineSerine-rich linker, but now I want to expand my matrix with protein linkers of a different nature to see if they work better. Does anyone of you have experience with protein linkers? I would appreciate it a lot if someone could help me.

With kind regards,

murru

Here's an interesting paper, where they measure FRET using several different linker compositions and lenths.
"An experimental study of GFP-based FRET, with application to intrinsically unstructured proteins." Protein Sci. 2007 Jul;16(7):1429-38. Ohashi T, Galiacy SD, Briscoe G, Erickson HP. PMID 17586775.

Rsm on Sun Feb 6 16:39:52 2011 said:

Thank you very much,

I will probably try one of these linkers.

Does anybody have some further suggestions?