TABLE 3.

Quantitative comparison of predicted PMP-1 variant models versus hPF-4

PeptidePEFaPPSAbMPCAcln PdPSAe
Ser1-PMP-1−0.235,142 ± 620.006−15.762,600
Asp1-PMP-1−0.215,142 ± 1510.007−18.282,900
hPF-4−0.224,034 ± 670.007−15.762,100
  • a PEF, positional energy function (in kiloteslas). Mean residue energies are indicated for peptides in their monomeric forms. See Materials and Methods.

  • b PPSA, partial positive surface area (in angstroms squared) (25). Peptide (monomeric form) motion was simulated by molecular dynamics at 310 K. The mean partial positive surface area ± standard deviation was computed for the resulting ensemble of peptide conformers. The partial positive surface area is a measure of the amount of peptide surface that carries a net positive charge. Since the side chains of the peptides are in motion at realistic temperatures, the use of molecular dynamics provides a realistic estimate of the properties of the peptides.

  • c MPCA, most positive charged atom, defined as the charge on the most positively charged atom divided by the sum of all positive charges. The quantity is a unitless ratio.

  • d ln P, logarithm of the partition coefficient based on Hansch relationships. The HINT program was used to estimate this parameter by the dictionary method (31).

  • e PSA, polar surface area (in angstroms squared).