I want to create a higher-order structure of a designated substructure (see Figure). Along the edges of the octahedron, I would like to link the trimers with disulfide bonds (potentially with other interactions). Is there any good (computational) method to calculate which amino acid would best be replaced by cysteine to form the most stable disulfide bonds? I used Chimera for this model so far but I'm open for other programs.
Hi Stefan,
I think modeling the disulfides in Chimera will probably work fine. I wrote a program a while ago to engineer disulfide bonds into protein structures. I've attach a PDF of the paper on this program. If you have a PDB model of your trimer, I can run it and see if there are any sites that jump out as especially suitable for disulfides. You can reach me at [email protected]
Randy
My guess is that you may need to perform ab initio quantum chemical calculations of the substructure using higher levels of theory (DFT calculation). You may try first with RHF/6-31G(d,p) level followed by further higher levels to find out consistency of the bond lengths .
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