Protein motifs

Ashok Aiyar aiyar at
Sat Aug 8 11:02:47 EST 1998

On Sat, 8 Aug 1998 10:53:25 -0400,
Mary P. Remington (mremingt at wrote:
>2.  In fusing the two proteins together (I have only done this on paper so
>far) I have introduced two additional amino acids between the two
>proteins.  Will this affect the fusion  protein?  Are there any rules of
>thumb regarding spacer amino acids between proteins?  

There is an excellent paper from Patrick Argos on oligopeptides
that are candidates for use in fusing two proteins, based on the
sequence of peptide linkers present within domains of naturally
occuring proteins.  I have cited the reference below.

Argos, P.  An investigation of oligopeptides linking domains in protein 
    tertiary structures and possible candidates for general gene fusion. 
    J. Mol. Biol. 211:943-958 (1990).

I have used an oligopeptide whose sequence was designed on the basis of
the work cited above to fuse a 400 a.a protein to a 700 a.a protein. 
The expressed fusion was intact, and retained the activities of each
of it's members.  The oligopeptide that I used was "GQSGPGG".

I have also seen a number of papers where two proteins were fused by a
tetra-glycine linker.

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at

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