Cameron Neylon

I'm trying to build a model of the calcium gated potassium channel MthK using the PDB files 1lnq and 2fy8. MthK has a gating domain (rck domain) and a transmembrane domain and works as a tetramer of full length proteins with a tetramer of just rck domain. So I can build the ligand bound (open conformation) from 1lnq by removing residues 19-98 from chains A, B, C, and D. The closed conformation is harder. 2fy8 has the rck domain in the closed conformation but the deposited structure is the asymmetric unit and not the biological unit. What I need to do is build the rck octamer in the closed conformation and then to put that back on top of the transmembrane domain tetramer. Swiss pdb viewer which isn't really cutting the mustard. If anyone can help us by building the models that would be brilliant. Our aim is to determine the structure of these molecules in solution (with detergent) by small angle scattering so good models to compare with data are crucial. Authorship on papers a given - can't offer any money - Cameron Neylon

How fast that needs to be done? I think I can help, but I can start in the middle of the next week. - Pawel Szczesny

Different things for different times. We're putting in the beamtime application next week (Wed) so having a model that we can use to predict scattering would be useful (but not critical) for that. Beamtime won't be until second half of the year at earliest and data analysis will be later again. So if it were possible to get something rough next week that would be brilliant but beyond that its a moderately long term thing. - Cameron Neylon

I cannot promise it's going to be ready for Wed, but if it's only a rough model/picture at least I will try. - Pawel Szczesny

The resolution of SAS is quite low so for prediction something that's just got the shape right is fine. Details of interactions are not so important. The detail can be pinned down later when we have high quality data to compare to. Thanks for your help! - Cameron Neylon

Be interested to hear how this goes. My MODELLER skills are rather rudimentary, unfortunately. So many interesting tools, so little time... - Neil Saunders

Will this end up being the first model by FriendFeed? Good luck folks - Deepak

I didn't think about this in this way, but indeed, it's something... unusual :) If actually that works fine, I'm back to the drawing board with "startup-weekends in science". - Pawel Szczesny

Yes, I am trying different models and tools for finding collaborators. Always try to set up anything so that you can call a null result a result of interest :) - Cameron Neylon