Abstract
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.
Highlights
Circular Dichroism (CD) is a powerful structural biology method, critical for examining and evaluating protein conformational changes, protein folding dynamics, and most importantly secondary structural elements in proteins and peptides [1]
The semiempircal quantum matrix method derives from the π-π* transition dipole moment obtained from experiments with N-acetylglycine and propanamide [10,11] and the other parameters (n-π* and transitions connecting π-π* and n-π* excited states) calculated quantum mechanically using the intermediate neglect of differential overlap/spectroscopic (INDO/S) wave functions for N-methylacetamide [12]
Because the dipole interaction model is very sensitive to molecular geometry, it is crucial to optimize any protein structure either by energy minimization or rebuilding the secondary structure based on the torsions extracted from the Protein Data Bank (PDB) file
Summary
Circular Dichroism (CD) is a powerful structural biology method, critical for examining and evaluating protein conformational changes, protein folding dynamics, and most importantly secondary structural elements in proteins and peptides [1]. The semiempircal quantum matrix method derives from the π-π* transition dipole moment obtained from experiments with N-acetylglycine and propanamide [10,11] and the other parameters (n-π* and transitions connecting π-π* and n-π* excited states) calculated quantum mechanically using the intermediate neglect of differential overlap/spectroscopic (INDO/S) wave functions for N-methylacetamide [12] These parameters allow for treating whole peptides and proteins [13,14,15,16,17,18,19,20,21,22,23]. It is a first attempt at applying a united atom approach to the nonchromophoric parts of the protein
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