Q on synthetic oligopeptides for antibody production

Wolfgang Schechinger u7k0201 at sunmail.lrz-muenchen.de
Wed Jul 19 12:35:55 EST 1995


If anyone could give me a short hint:

I thought of synthesizing some small peptides (10-25 mers) to produce antibodies against an 
enzyme of which the gene (and protein-) sequence is known (instead of isolating the protein and 
using it for an immunisation). The crucial point is, as I believe, to select regions from the 
protein structure that are on the 'outside' of the folded protein and thus accessible to 
antibody binding.

Is there a way to determine or predict which part of a protein sequence is likely to appear on 
the 'outside' of the folded protein (a rough algorithm based estimation e.g.)?

Or do I simply have to select hydrophilic regions of the sequence (it's a periphal membrane 
protein when active - probably attached to the membrane by another protein - and found in the 
cytosol when inactive) because they are likely to be neccesary for keeping the enzyme in 

Is there a better chance to be successful if selecting a region near the N- or the C-terminus 
or in the middle?

Should I avoid selecting regions that are known or supposed to be binding sites for other 
proteins or domains for substrates?

I already have been conducting a medline research but did'nt find anything appropriate yet 
(protein and (synthe* or design) and (antibod* and production), so I'm now posting to this 

What do you think? I appreciate ANY comment. Maybe you know a good book or journal article or 
have experince of your own. Please mail, too.

Thanks a lot in advance!

Wolfgang Schechinger
Institute for Diabetes Research
Koelner Platz 1
80804 Munich
Phone + 49 (89) 30 79 31 24
Fax   + 49 (89) 30 81 733
email u7k0201 at sunmail.lrz-muenchen.de

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