Dear Crystallographers,
Here is a summary of the methods for oligomeric stablization through
structure-informed engineered disulfide bonds (thanks to all who responded):
=============================
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
=============================
Disufide-by-design: Downloadable from http://cptweb.cpt.wayne.edu/DbD/
=============================
sGAL: Although the server seems to be down, the original paper is at
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/24/3101
=============================
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."
