Portal de Periódicos da CAPES

Introducing Dinamo: A Package for Calculating Protein Circular Dichroism using Classical Electromagnetic Theory

2013; Elsevier BV; Volume: 104; Issue: 2 Linguagem: Inglês

10.1016/j.bpj.2012.11.1299

1542-0086

Boris Anyangwa Sango, Neville Y. Forlemu, Sandeep Pothuganti, Rahul Nori, Yvonne E. Bongfen, Kathryn A. Thomasson,

Glycosylation and Glycoproteins Research

The dipole interaction model is a classical electromagnetic theory that has successfully been able to reproduce the experimental circular dichroism (CD) for the π-π∗ transitions for peptides and proteins. This theoretical model, pioneered by Jon B. Applequist, has been assembled into a package DInaMo that is written in C and Fortran allowing for treatment of whole proteins. The program reads Protein Data Bank formatted files of structures generated by molecular mechanics and molecular dynamics. Simple crystal structures need to at least be energy minimized for use in the model because they do not contain all the hydrogens. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromphoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of the CD spectrum for each molecule. Theoretically predicted CD for a variety proteins (lysozyme, myoglobin, insulin, and collagen) are compared with synchrotron radiation CD data. Theory agrees with experiment showing bands with similar morphology and absorption maxima for the π-π∗ transitions.