Searching for the simplest structural units to describe the three-dimensional structure of proteins

Abstract

Abstract Ab initio computations have been carried out during the past several years on diamides of single amino acids (HCO-NHCHR-CONH2 where R=H (glycine), -CH3 (alanine), -CH(CH3)2 (valine) and -CH2OH (serine)) exploring all possible backbone and side chain conformations. Selected conformations were studied in our laboratory on threonine (R=CH(CH3)OH), cystein (R=CH2-SH) and phenyl-alanine (R=CH2-CH5H6) diamides. Tri-, tetra-, penta-, hexa- and hepta-amide systems of poly-L-alanine (H-(CONH-CHCH3-CONH)n-H 2n6) were also investigated at selected backbone conformations. All these studies confirmed the results of multidimensional conformation analyses: the jth amino acid residue in a polypeptide has a maximum of nine (9) discrete backbone conformations. These structures correspond to nine conformational centres on the 2D-Ramachandran map. On the basis of this rinding, it can be shown that the folded secondary structure of any protein with known internal coordinates, can be described in terms of these nine...