Quantum theory of the structure and bonding in proteins : Part 14. The serine dipeptide

The energies of the conformations of the serine dipeptide are computed by ab initio molecular orbital theory in order to demonstrate the existence of the hydrogen bonds, torsion barriers and non-bonded repulsions which govern the relative energies of these conformations. The Ramachandran map of the dipeptide is computed and found to resemble closely those of alanine and ethyl glycine. The side-chain maps are them computed and analysed to show the above physical effects in terms of the torsion barrier-free maps.

There is generally good agreement between the experimental and theoretical results in the sense that all three side-chain conformations which are staggered about CC^β (₁ = + 60, 180 and ?60°) are computed to be close in energy and all three values of ₁ occur with similar frequencies in the proteins examined. The fact that serine, unlike all other comparable residues except threonine, tends to favour a ₁ value of + 60° in the bridge region is reproduced clearly by the computations and analysis of the physical factors involved shows that this conformation is stabilised by side chain to backbone hydrogen bonding.