Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

Area of Science:

• Biophysics
• Computational Chemistry
• Spectroscopy

Background:

• Circular dichroism (CD) spectroscopy is sensitive to protein secondary structure.
• Classical electromagnetic theory, specifically the dipole interaction model, can calculate CD spectra.
• The dipole interaction model, pioneered by J. Applequist, provides a theoretical framework for CD calculations.

Purpose of the Study:

• To present DInaMo, a Fortran package implementing the dipole interaction model for protein CD calculations.
• To assess the accuracy of the DInaMo model in predicting CD spectra for proteins.
• To investigate the impact of atomic approximations on CD prediction accuracy.

Main Methods:

• DInaMo utilizes the dipole interaction model to calculate CD from π-π* transitions of amides.
• The software processes Protein Data Bank (PDB) files, requiring idealized or energy-minimized protein structures.
• Amide chromophores are treated as points with anisotropic polarizability, and aliphatic atoms as points with isotropic polarizability.

Main Results:

• Theoretical CD calculations using DInaMo on 24 proteins showed good agreement with experimental data.
• The model successfully predicted spectral bands with similar morphology and maxima compared to experiments.
• Ignoring hydrogens on methyl groups was found to be a valid approximation, simplifying calculations.

Conclusions:

• DInaMo provides a reliable computational tool for calculating protein CD spectra.
• The dipole interaction model, as implemented in DInaMo, is effective for predicting CD based on protein structure.
• The study validates the use of simplified atomic representations in CD calculations for proteins.