Helicity, circular dichroism and molecular dynamics of proteins

In protein unfolding studies, reduction in circular dichroism (CD) at 222 nm has been interpreted as loss of helicity. Estimates of the helicity of a protein from its CD spectrum are calibrated by reference to X-ray crystal structures, based on the assumption that the mean residue ellipticity at 222 nm is directly proportional to the number of residues in a helix. We have examined various influences on the CD at 222 nm, using molecular dynamics simulations to provide the structural detail required. We have found that the fragmentation of long helices, without a reduction in the number of helical residues, significantly reduces the mean residue ellipticity at 222 nm. The dynamical motion of the protein and the precise conformation of helical residues also play an important role. We discuss the implications of these factors to the interpretation of CD for the partial unfolding of apomyoglobin.