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 forσ charges and the Hückel MO method forπ charges. The characteristic ratiosC _∞ were computed for all the above polypeptide chains, with different sets of parameters for the peptide unit. The calculated values ofC _∞ are found to be very sensitive to the input peptide geometry. The calculated value of 2·2 forC _∞ 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 ofC _∞ of the polypeptide chains show no correlation with the number of allowed conformations, suggesting that the ratio ofC _∞/C _f need not always provide information about the flexibility or freedom of rotation of chain units.