I have a sequence for a coiled coil and I wish to build a homology model for it. The coiled coil is a homo tetramer with each chain containing 8 repeats of the same alpha helical sequence. There is a structure for the structure of the repeat and the biological assembly of the coiled coil containing the 24 repeats. How can I create one structure of the entire coiled coil with all repeats in a PDB file?
Hi Alex,
I suggest that you may align your homology model to the template tetramer one by one.
Yoshinobu Ishikawa what would be the best way to make such an alignment?
Virtually any version of PyMol will permit you to make a good quality homology-based structure alignment. Basically all you need to do is
a) load the crystallized tetramer as one molecule,
b) read in the modeled versions of each of the four homologous target chains (let's call them ModelA, ModelB, ModelC and ModelD),
c) define each of the crystallized monomer chains as separate selections (let's call them CrysA, CrysB, CrysC and CrysD), then
d) align each of the modeled chains to the crystal chains via the 'align' command (e.g., "align ModelA, CrysA" and so forth).
I'm leaving out a few minor details, but it's not much harder than that.
I'd recommend using https://swissmodel.expasy.org/ to make your models (it handles modelling quaternary structure very well).
For alignment, i'd recommend using UCSF Chimera's MatchMaker feature, which is very easy to use.
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