Some aspects concerning conformation of polypeptide chains in proteins.
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 phi and psi torsion angles. In addition a correlation between torsion angle /psi/ and the bond angle tau at C alpha 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 tetrahydrally coordinated C alpha in analogy to the SN2 substitution reaction of the Walden inversion with a trigonal bipyramidal transition state.
D004902:Erythrocruorins; D008968:Molecular Conformation; D009842:Oligopeptides; D010455:Peptides; D011487:Protein Conformation; D011506:Proteins; D014357:Trypsin; D014961:X-Ray Diffraction
D004902:Erythrocruorins; D009842:Oligopeptides; D010455:Peptides; D011506:Proteins; C027661:N,N'-di-tert-butyl-2-(N-(1-phenylethyl)benzamido)malonamide; D014357:Trypsin