A coarse-grained model of circular dichroism of proteins

Abstract

Circular dichroism (CD) is a useful technique to investigate the secondary structure of proteins and some other biomolecules like RNA. There are various theoretical approaches intended to correlate the three-dimensional structure to the corresponding CD spectrum and some of them depend on accurate quantum mechanics calculations. Such approaches, however, require an important computational effort. In this work, we present a computationally tractable model that is based on the classical theory of optical activity. In first stage, we estimate a mean polarizability per residue from experiments of molar absorptivity. Then, we determine the complex polarizability that is used together with a protein structure obtained from the Protein Data Bank to calculate the approximate CD spectrum. Our computed spectra are found to be in good agreement with their experimental counterparts. As a result, this model could be utilized to describe conformational changes of a given protein or peptide.