Computation and Analysis of Protein Circular Dichroism Spectra

Publisher Summary This chapter presents computation and analysis of protein circular dichroism (CD) spectra. The origins of electronic CD in proteins, theoretical methods for computing protein CD, and empirical analysis of CD for estimating structural composition of proteins are described. The phenomenon of CD involves the absorption of light and it can be considered as a special type of absorption spectroscopy. The CD spectra of proteins are generally divided into three wavelength ranges, based on the energy of the electronic transitions that dominate in the given range. The basic approach used to compute the CD of complex systems, such as proteins and nucleic acids, is the divide and conquer approach. In addition to the isotropic atomic polarizabilities, the anisotropic polarizability of the first electrically allowed peptide transition was included in the dipole interaction model for protein CD calculations. Polarizability anisotropy data for simple amides were used for obtaining polarizability parameters. It is found that the CD spectrum of the typical β sheet has a negative band near 215-nm and a positive band near 198 nm.