Amino spedfic interactions

We assume that, after the protein has entered the proteasome, the protein-proteasome interaction is characterized by a spatially periodic asymmetric potential U(x) with the period P equal to the distance between amino adds in the protein. In reality there is a basic periodicity, namely the periodidty of the protein (or peptide) backbone, that is superposed by a nonperiodic (in our sense irregular) part that is attributed to the amino add-spedfic residues. Below we consider also the influence of the nonperiodic constituent. The spatial asymmetry results from breaking the symmetry by entering the proteasome from one end, as well as from the C — N asymmetry of the protein (or peptide) backbone. Figure 14.3 (left) plots several examples of such asymmetric periodic potential. The detailed form of the asymmetric periodic interaction potential is of less importance for this qualitative study. 

Houghten, R. A., General method for the rapid solid-phase synthesis of large numbers of peptides Spedficity of antigen-antibody interaction at the level of individual amino acids, Proc. Natl. Acad. Sci. USA 1985, 82, 5131-5135... 

The above conaderations ate described in fiiller detail in previous papers [6,7] and indicate that macromolecules assuming a single chirality conformation can show chiroptical properties characteristic of the conformation itself. Moreover, if chromophores are present in the side chains specific chiroptical properties can arise from dipole-dipole dectronic interactions among these chromophores disposed along the chirally arranged backbone. This situation is cleariy shown in poly-a-amino adds, in which spedfic and typical chiroptical properties are assodated with spedfic and typcal conformations (a-helix, -structures, random coil) [8]. 

Indeed, poly (U-G) and poly (U-Aza G) direct the incorporation of the same amino adds (the spedfidty is not altered) into polypeptides, but poly (U-Aza G) is less efficient when added to a subcellular protein-synthesis system derived from E. coli. With codons containing two Aza G, the interaction between the amino-acyl-transfer RNA and the triplet is so weakened that the translation may be interrupted, giving incompl polypeptide chains, which remain attached to the ribosomes. Ibis has been demonstrated in cell-free systems derived from aza-guanine-treated B. cereus. This also explains the differences observed by Chantreime between the d ree of inhibition of global protein synthesis and that of spedfic enzymes. 

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