Recently, a question was asked by Ed Stokes about finding tryptophan residues in the antigen binding pockets of IgG molecules. One suggestion was to pull all of the IgG sequences out of GenBank to see what could be seen. I would like to suggest an alte
rnate, admittedly "lower tech" approach.
There is a book (now actually in three volumes) published by the US Govt. Printing Office entitled "Sequences of Proteins of Immuno- logical Interest" edited by Kabat et al. The advantage of this book over a collection of GenBank sequences is that the e
ditors have layed out the sequences (both DNA and protein) logically and with easy-to-find landmarks.
In Ed's case, he would look under the section entitled "Immuno- globin Variable Regions." There, the sequences are laid out with labels for framework and CDR (hypervariable) subregions. While this simplifies finding the CDRs (which are the antigen-bind
ing portions of the antibody), it still requires the intrepid researcher to manually look for tryptophan residues. Call it "good news, bad news..."
I can only hope that some relational database guru (or some whiz kid working on a senior project) will soon allow us to ask a data-base questions such as "Show Ig sequences that contain tryptophan residues in the CDR regions."
Mark
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| Mark W. Ravera |
| Sandoz Research Institute |
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