To add to our discussion last week's chapter (Ch 2), I thought I'd put up something on proton pumps. Below is a video with voice-over giving a simple explanation, and p56-57;59 from Ch 2 has some generic information on ion pumps.
And here is the full 3D structure of 3B8C, a P-type proton pump, determined from X-ray crystallography experiments.
Right-click on the Jmol applet above to interact with the structure (highlight domains, calculate hydrogen bonds, show surface et cetera). If you want to visualise how this might fit into the cell membrane, try colouring residues by charge (e.g Select→Protein→Basic Residues (+), Color→Surfaces→Blue||Color→Structures→Cartoon→Blue ).
(Edit: If the above widget fails, or you want to look examine this in more detail, you can view the structure here.)
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Great work, Tomas. Very nice. Now we need to connect the cartoon with the actual structure.
ReplyDeleteCan you help me find:
the ion channel within this structure?
the 2 sites/residues within the channel which bind and release the protons?
the location of hydrophobic and polar residues relative to the entrance and exit of the ion channel?
On one end of the visualisation, there are ten α-helices lying roughly parallel to each other and packed into a cylinder-like shape. These constitute the core channel, which passes through the membrane. You can select these residues, and colour them by polarity (or lack thereof) to see how this could fit into the lipid bilayer.
ReplyDeleteI had to look up the publication to find the binding sites. D684 is the only negatively charged residue whose side chain sits inside the interior of the channel's transmembrane region, and thus the only one capable of binding protons. N106 - a positively charged residue - is located at the predicted proton ingress pathway. Hydrogen bonding between N106 and D684 causes the binding of H⁺ to D684 to become energetically favourable. When changes in pump conformation bring N106 away from D684, proton binding is no longer favourable and bound H⁺ is released.
Does anyone else want to look at Ross' last question? (If you're keen, you could cut out the channel from the Brookhaven PDB and make a nice hydrophobicity/polarity surface plot...)
(Aside: does anyone know why blogspot forbids <sup> tags?)
Another source for bioinformatics is the Biology Workbench at the San Diego Supercomputer Center:
ReplyDeletehttp://workbench.sdsc.edu/
This is free, has multiple database searching, sequence alignment, and phylogenetic analysis tools. When last I checked, structural bioinformatics was a bit lean. If the workbench doesn't have what you're looking for, then VMD has some structural biology tools. You can get VMD for free at the UIUC Theoretical Biophysics Group (aka Schulten Group) at:
http://www.ks.uiuc.edu/