Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit

Abstract

Potential energies of conformation of a dipeptide unit with butyl, seryl, threonyl, eysteinyl, and valyl side groups have been computed by using classical energy expressions. The presence of a γ-atom introduces characteristic restrictions on the backbone rotational angles φ and ψ the γ-atom itself is restricted to three staggered positions about the C^α-C^β bond. The important results are that a γ-carbon in position I (χ¹ ⋍ 60°) cannot be accommodated in the standard right-and left-handed α-helices, whereas a γ-oxygen or sulfur could easily be accommodated in the right-handed α-helix. Further, a γ-carbon or a heteroatom in position II (χ¹ ⋍ 180^°) does not favor a conformation ψ ⋍ 180^°, compared to two other positions. The valyl side group significantly reduces the allowed φ and ψ values and energetically prefers a α-conformation compared to right-or left-handed α-helical conformations. The less favorable α-helical conformation is possible only for γ (III, II) combination of the valyl residue. The observed φ, ψ, and χ¹ values of all the amino acid residues in the three protein molecules, lysozyme, myoglobin, and chymotrypsin are compared with the theoretical predictions and the agreement is excellent. The results bring out the important fact that even in large molecules, the conformation of local segments are predominantly governed by the short-range intramolecular interactions.