AMINO-ACID CONFORMATIONAL-ANALYSES OF PROTEINS (ACAP PROGRAM)

The secondary structure analysis of proteins is a powerful tool, effic iently supporting spectroscopic (CD, IR, NMR) and biochemical research projects. However, the precise location of the different secondary st ructural elements in a sequence incorporates some subjectivity. A line arized notation of a uniform and objective description of protein back bone structures was developed. This involves a three-dimensional to on e-dimensional transformation (3D --> 1D). The classification is based on a step-by-step comparison performed between reference conformers (a lso called template values) and backbone sub-conformations of the prot ein. The readily provided structure templates may be modified, but the procedure still remains objective and uniform. This linearized notati on of protein structures provides a description of the three-dimension al backbone conformation without relying on the traditional concept of secondary structure. Previously, the sequence analysis (primary struc ture) of proteins resulted in the identification of the 20 natural ami no acid residues. Similarly, the backbone conformation analysis of the same proteins confirmed the presence of nine basically different subc onformers. This recognition and the application of the linearized nota tion of the 3D structure makes easier the comparison of proteins at th e levels of primary to tertiary structure.