I think that Disulfide by Design, or DbD, is geared toward monomeric proteins (ie. for enhancing stability). I'm sure you could get it to work with an oligomer with a little tinkering, but there is another server called sGAL that may be more like what you're looking for:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/24/3101 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. Good Luck, Mike Thompson ----- Original Message ----- From: "Konstantin v. Korotkov" <k...@u.washington.edu> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, August 23, 2010 4:09:50 PM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Disulfide Designer Program Hello, You could try Disulfide by Design: http://cptweb.cpt.wayne.edu/DbD/ Good luck, Konstantin On Mon, 23 Aug 2010, Jacob Keller wrote: > Dear Crystallographers, > > I remember having heard of a program which takes a given oligomeric assembly, > and suggests optimum disulfides to stablize the complex. Can someone refresh > my memory which program that is, and where it is available? > > Best Regards, > > Jacob Keller > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-kell...@northwestern.edu > ******************************************* > -------------------------- Konstantin Korotkov, Ph.D. Research Scientist University of Washington Department of Biochemistry Box 357742 Seattle, WA 98195-7742 (206)616-4512 k...@u.washington.edu -------------------------- -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
