potassium ion channel, cell membrane ...

Question

how to locate channel and cell membrane in a ribbon diagram

Answer 1

First, let's think about what type of amino acids will contact the membrane vs the extra- or intracellular space. The cell membrane is made of a phospholipid bilayer. The lipid tails, which make up the inside of the membrane, are hydrophobic. The cell membrane separates the intra- and extracellular spaces, both of which are mostly made of water. Therefore, parts of proteins that contact these regions are hydrophilic.

On a ribbon diagram with labeled amino acids, the transmembrane domains - the regions that usually make ion channels - should be mainly hydrophobic. This is because they cross the bilayer. There are many potassium channel structures. Most have alpha-helices that span the membrane to give the channel structure and help form the pore. These helices are usually symmetrical and surround floppier parts of the protein (lines on a ribbon diagram - non-helical or beta sheets). The floppier parts of the protein make contacts with K ions to help them pass.