Improving Far UV Circular Dichroism Calculations of Peptides and Proteins with the Dipole Interaction Model
The dipole interaction model (assembled into the computer package DInaMo) uses a classical electromagnetic theory for calculating the far UV circular dichroism (CD) of peptides and proteins. DInaMo reduces all amide chromophores to a single point with anisotropic polarizability and all nonchomophoric aliphatic atoms to points with isotropic polarizability. By determining interactions among the chomophoric and nonchromoporic parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Polarizabilities are largest for the chromophoric points and smaller for the nonchromophoric points with hydrogens having the smallest polarizabilities. It is possible to collapse hydrogen polarizability onto the atom to which it is bound or ignore it in the CD calculation creating a united atom approach. Ignoring CH3 group hydrogens and treating only the π-π∗ transition reproduces experiment in the region of 180 to 210 nm well, showing bands with similar morphology and absorption maxima for the π-π∗ transition. Recent calculations on small peptides and proteins in which both CH3 and CH2 group hydrogens have been ignored seem to produce better CD results than ignoring only the CH3 group hydrogens. Also, preliminary calculations using the mean polarizability values of the CH3 and CH2 groups show some good prospects of further improving the CD calculations with the DinaMo package. In addition, initial calculations indicate that DInaMo has the potential of including the n-π∗ transition in the CD calculations.
2, Supplement 1
Copyright to Biophysical Journal.
Jungong, Akongnwi C.; Soukup, Jenna; Aleksandrov, Tsvetan; Nori, Rahul; Miller, Emma; Uporov, Igor; and Thomasson, Kathryn A., "Improving Far UV Circular Dichroism Calculations of Peptides and Proteins with the Dipole Interaction Model" (2015). Chemistry Faculty Publications. 4.