Theoretical studies of time-resolved spectroscopy of protein folding

Recently, we have made significant improvements in the accuracy of calculations of the circular dichroism of proteins from first principles. The quality of these calculations (especially at 220 nm, a key wavelength, where the intensity of the band correlates well with the helical content of polypeptides) has given us confidence to use such calculations to analyse nanosecond molecular dynamics simulations of the folding of polypeptides. We use this combined approach to explore the influence of dynamics on the circular dichroism spectroscopy of polypeptides. We apply it to equilibrium molecular dynamics simulations of two beta-sheet proteins with similar structures, but differing circular dichroism spectra. We analyse a molecular dynamics simulation of the acid-unfolding of myoglobin. For both alpha-helical and beta-sheet conformations, we find that changes in dihedral angles of 30 degrees can change intensities of bands in circular dichroism spectra by up to 5000 degree cm2 dmol(-1). Thus, in isolation, moderate differences in circular dichroism spectra cannot be interpreted uniquely in terms of conformational changes. Examination of individual structures allows us to dissect the influence of conformation on the calculated circular dichroism spectra. Our results are aimed at providing a deeper understanding of the optical properties of proteins. An atomic level connection between molecular dynamics simulations and optical spectroscopy is increasingly desirable as theoretical and experimental studies begin to probe protein folding events reliably on the nanosecond timescale.