Studies on the conformation of amino acids. X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit

Abstract

Backbone-side group conformations of amino acid residues including one or two δ-carbons in the side group have been investigated. Conformational energies of norvalyl, leucyl, phenylalanyl, tyrosyl, tryptophenyl, and histidinyl side groups in a dipeptide unit have been calculated by using classical energy expressions. The side group conformations about the C^α-C^⓼ and C^β-C^γ bonds are restricted to specific values of the respective rotational angles. Thus, most favourable positions of γ- and δ-atoms of a linear side-chain (norvalyl) are restricted to (γ_I, δ_II) (γ_II, δ_I), (γ_II, δ_II), (γ_III, δ_II), and (γ_III, δ_III), whereas those of the side-chain branching at a sp³ γ-atom (leueyl) are further restricted. It is also shown that there is a definite correlation between the orientations of the two peptide planes and that of the planar group of the aromatic side chain of phenylalanyl type residues. The studies bring out an important fact that while the γ-atoms have definite and characteristic effects on the backbone rotational angles φ and ψ, the δ atoms and beyond have no effects on the preferred φ and ψ values. Thus, the preferred backbone conformations are independent of the preferred side group conformations beyond the γ-atom and vice versa. The observed φ, ψ, χ¹, and χ² values of amino acids, simple peptides, and of the three protein molecules lysozyme, myoglobin, and chymotrypsin have been compared with the theoretical predictions, and the agreement is found to be excellent.