Comments at CSMP meeting

The project was presented by Ursula Pieper at the annual meeting of the Center for Structures of Membrane Proteins (http://csmp.ucsf.edu/) 2012. The following points have been compiled from the comments and questions during the presentation.

Musings about one-helix membrane proteins

How do we define one?

19 contiguous non-polar residues (lipophilic)
embedded in a total of 26 uncharged residues
(one helix transmembrane)
flu vaccine and weissman lab complexes would be good examples (complex building 1-helix membrane proteins)
would fail with the two helix criteria
oligomeric cases would be missing.

Family assignments

families: claudins
tricellulin
occludin
trp-channels
ach receptor family (nicotinic)
add "suggest missing families" section on web-site.

Homologs

Look at size of bacterial homologs
motif finding programs would find lower sequence identity homologs.

Structure determination feasibility

Amount of total sequence outside the tm domain (large is good).
What criteria should be discussed to assess the feasibility of a successful structure determination?
Bacterial homologs available?
Other criteria:

  • Sequence length
  • Number of cysteine residues
  • Number of methionine residues
  • Secondary structure prediction
  • Disorder prediction
  • Coiled-coil prediction
  • Salilab Feature Sketch would be nice to have as a web-server