Dear Crystallographers,


Here is a summary of the methods for oligomeric stablization through 
structure-informed engineered disulfide bonds (thanks to all who responded):


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SSBOND: Although the Google-accesible server seems to be down currently, it 
can still be accessed through  http://129.128.24.248/forms/ssbond.html

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Disufide-by-design: Downloadable from http://cptweb.cpt.wayne.edu/DbD/

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sGAL: Although the server seems to be down, the original paper is at 
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/24/3101

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Mike Thompson's Homebrew Method:

"Also, I have designed intermolecular disulfide bonds using the following 
method (although it is a bit of a hacked up way to do things, but it worked 
well in my situation). Put your PDB files for each chain of the oligomer 
through the following diffusion accessibility server:

http://nihserver.mbi.ucla.edu/diff_acc/

This server will take your PDB file and rewrite the B-factor column with 
values for the diffusion accessibility of each atom. Now you can look at 
your PDB files in PyMol, and if you choose "color by B-factor" you will 
actually be coloring the atoms by diffusion accessibility. Do this for each 
chain of the oligomer separately. Now take those individual chains, colored 
by diff. accessibility and overlay them onto the structure of the oligomer. 
Look for residues whose C(gamma) are both accessible at the surface of each 
chain, and are within reasonable distance for a disulfide bond. You can 
check this by just measuring the distance, or if you want to be more 
precise, you can take several ideal disulfide bonds from other structures 
and compare the distances (and dihedral angles) by overlaying them onto your 
selected residues. If you find a good set of residues that match all the 
criteria I listed, chances are they will be good candidates to disulfide 
bond with each other if mutated to Cys. Remember that with disulfide bonds, 
geometry (dihedral angles) is very important in addition to the bond length. 
I don't recall off the top of my head what values for the dihedral angle and 
bond length are ideal, but this info is readily available in the literature. 
And also, your bond will never form if the gamma position of the side chain 
is buried by surrounding residues (thus, the use of the diff. accessibility 
server - I learned this the hard way by making many unsuccessful mutants). 
Again, this is kind of a drawn out way of doing things compared to just 
throwing your PDB file at a server like sGAL, but I feel that it is a bit 
more rigorous, and it has been successful in my hands."