Colloquium: Prof. Kathryn Thomasson
Prof. Kathryn A. Thomasson
Department of Chemistry
University of North Dakota
Friday Oct 17, 4:00–5:00pm, 211 Witmer Hall. Refreshments at 3:30pm.
The Dipole Interaction Model, a Classical Approach to Protein Circular Dichroism
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. CD is an essential bioinformatic tool for determining protein secondary structure and following the dynamics of folding and unfolding. The dipole interaction model, a theoretical model pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment peptides and 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. Theoretical calculations several peptides and 23 proteins are presented indicating the model does an excellent job in the π−π* region of the far UV spectrum.