How do alpha helices form and why are they the predominent structure found in transmembrane domains?
Generally speaking, a helix is a very simple structural motif which helps the monomers (amino acids) be in a conformation with minimal energy penalties due to steric effects. The secondary structure of proteins depends on the amino acid sequence (primary structure) and the environment. The protein backbone has lots of peptides bonds and their NH and CO groups need to make as many hydrogen bonds as possible. In water you can have some H-bonds forming with water. However in a hydrophobic environment, such as the lipid bilayer, you can’t have such H-bonds; all H-bonds have to come from peptide bonds and the system has to be such that no groups are left “facing” the lipids, without having an interacting partner. How could a peptide sequence cross the lipid bilayer? First of all it would require amino acids with hydrophobic side-chais interacting with the lipids-otherwise the energy penalty is huge. Still the backbone needs to form H-bonds. Since the groups can interact only with each other
