SEARCHING FOR THE SIMPLEST STRUCTURAL UNITS TO DESCRIBE THE 3-DIMENSIONAL STRUCTURE OF PROTEINS

Ab initio computations have been carried out during the past several y ears on diamides of single amino acids (HCO-NHCHR-CONH2 where R=H (gly cine), -CH3 (alanine), -CH(CH3)(2) (valine) and -CH2OH (serine)) explo ring all possible backbone and side chain conformations. Selected conf ormations were studied in our laboratory on threonine (R=CH(CH3)OH), c ystein (R=CH2-SH) and phenylalanine (R=CH2-C5H6) diamides. Tri-, tetra -, penta-, hexa- and hepta-amide systems of poly-L-alanine (H-(CONH-CH CH3-CONH)(n)-H 2 less than or equal to n less than or equal to 6) were also investigated at selected backbone conformations. All these studi es confirmed the results of multidimensional conformation analyses: th e ith amino acid residue in a polypeptide has a maximum of nine (9) di screte backbone conformations. These structures correspond to nine con formational centres on the 2D-Ramachandran map. On the basis of this f inding, it can be shown that the folded secondary structure of any pro tein with known internal coordinates, can be described in terms of the se nine discrete conformation types.