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

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    • Keywords


      Polypeptides; unperturbed dimensions; characteristic ratio

    • 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/Cf need not always provide information about the flexibility or freedom of rotation of chain units.

    • Author Affiliations


      A R Srinivasan1 V S R Rao2

      1. Department of Physics, University of Madras, Madras - 600025
      2. Indian Institute of Science, Molecular Biophysics Unit, Bangalore - 560012
    • Dates

  • Pramana – Journal of Physics | News

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