Why are peptide bonds important for the secondary structure of proteins?
Basically, the way they have limited rotation, the way they hydrogen-bond to each other in a specific pattern... those factors provide the "leverage" over what kind of secondary structure the protein takes up.
If peptide bonds didn't have the key properties they have, the secondary structure could look like anything and the protein wouldn't care. The protein starts caring when it knows that it can fall apart without the key properties of the peptide bond being the way they are.
The key properties of a peptide bond are that:
#~40%#double bond character makes it rigid, limiting the #"C"_alpha-"N"#bond rotation.
- It's thermodynamically unstable, but kinetically stable, meaning that its hydrolysis/cleavage will not occur in our lifetimes. (That's good, because then we would literally fall apart.)
- It has a hydrogen-bond acceptor (the carbonyl) and a hydrogen-bond donor (the
The limited rotation, steric strain of particular amino acid sidechains, as well as the
The most important kinds of secondary structures are the
If you use the right-hand rule, the
According to the Ramachandran plot below, there are few combinations of
Anything not within the green is impossible, except for Glycine, and Proline has more limited combinations due to its ring "sidechain". These limitations overall are due to steric strain/interference and the limited rotation of the peptide bond itself.