Question

Why are peptide bonds important for the secondary structure of proteins?

Answer 1

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:

• Its `~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 `"N"-"H"`).

The limited rotation, steric strain of particular amino acid sidechains, as well as the `phi` (`"C"_alpha-"N"`) and `psi` (`"C"-"C"_alpha`) torsion/dihedral angles limit the number of secondary structures a protein can take up.

The most important kinds of secondary structures are the `alpha`-helix and the `beta`-sheet.

If you use the right-hand rule, the `alpha`-helix coils counterclockwise, and the `i`th and `i+4`th amino acid sidechains interact via a hydrogen-bonding interaction at about `"2.8 angstroms"` away. These interactions help maintain its secondary structure. Also, the structure is such that the hydrophobic sidechains are inside, and the hydrophilic sidechains are outside, further determining its structure.

The `beta`-sheet, on the other hand, has the amino acid sidechains alternating in and out, and you get similar hydrogen-bonding interactions between sheets, and the antiparallel sheets are slightly more stable.

According to the Ramachandran plot below, there are few combinations of `phi` and `psi` angles a protein's secondary structure can take up:

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.