Bernhard Dederer

Some Aspects Concerning Conformation of Polypeptide Chains in Proteins

Abstract The structure of (S)-N,N′-di-tert-butyl-2-[N-(1-phenylethyl)benzamido] malonamide contains two fragments of a polypeptide chain. This compound therefore can be taken as a model substance for details of protein conformation. In the crystalline state one peptide chain of the model molecule incorporates a hydrogen bond between two adjacent nitrogen atoms in the backbone. The acceptor for the hydrogen is the pz-orbital at the proton accepting nitrogen. The occurence of such hydrogen bonds in proteins might explain some correlations found between φ and ψ torsion angles. In addition a correlation between torsion angle ψ and the bond angle τ at Cα in the backbone of polypeptide chains could be established. The model substance also contains a “frozen” back side attack of a C = O group on the tetrahedrally coordinated Cα in analogy to the SN2 substitution reaction of the Walden inversion with a trigonal bipyramidal transition state.