Effect of variations in peptide parameters and charges on the unperturbed dimensions of polypeptide chains

Abstract

The net charges on various atoms of poly (L-alanine), polyglycine, poly (N-methyl-L-alanine) and poly (N-methylglycine) were computed using the MOLCAO method of Del Re for σ charges and the Hückel MO method for π charges. The characteristic ratios C_∞ were computed for all the above polypeptide chains, with different sets of parameters for the peptide unit. The calculated values of C_∞ 8 are found to be very sensitive to the input peptide geometry. The calculated value of 2.2 for C_∞ 8 of poly (N-methylglycine) obtained with set-3 parameters (derived from a crystal structure containing prolyl residue) is closer to the experimental value of 1.8±0.2 than the value of 2.7 obtained with set 1 (Pauling-Corey parameters), suggesting that the peptide parameters of N-substituted aminoacids have close similarity to set 3 rather than to set 1. The calculated values of C_∞ 8 of the polypeptide chains show no correlation with the number of allowed conformations, suggesting that the ratio of C_∞/C _τ need not always provide information about the flexibility or freedom of rotation of chain units.