Knowledge-Based Atomic Polarizabilities Used to Model Circular Dichroism Spectra of Proteins

We
present a model of circular dichroism for proteins, which is
mainly based on both the classical theory of optical activity and
a series of effective atomic polarizabilities. Such polarizabilities
are extracted from the analysis of a set of synchrotron radiation
circular dichroism spectra and their corresponding three-dimensional
structures from the Protein Data Bank. Each modeled spectrum is obtained
from the protein atomic coordinates and the identification of its
secondary structure elements. The resulting spectra are in good agreement
with additional experimental data and also with the predictions of
some other models. Among them, only our approach is able to describe
the effect of d-amino acids. Moreover, our model is also
utilized to evaluate protein reconstructions as well as structural
changes.