Comparing theoretical and experimental backbone-dependent sidechain conformational preferences for linear, branched, aromatic and polar residues Original Research Article

An Ecepp-3 conformational study based on a φ-ψ grid search with sidechain minimization was carried out on the N-acetyl N′-methyl amides of four representative amino acids: Met, Phe, Ile, and Ser, and the distribution of ξ1 backbone-dependent rotamer preferences was compared with the similar distribution obtained from the backbone-dependent rotamer library for proteins developed by Dunbrack and Karplus (J. Mol. Biol. 230 (1993) 543). The experimental distribution is best reproduced theoretically in the case of the linear sidechain of Met, reasonably well for the bulky sidechains of the aromatic Phe and asymmetrically β-branched Ile, and only partially for the short polar sidechain of Ser. In the case of the Ser dipeptide the difference is accounted for by the missing H bonds.