FTIR studies of collagen model peptides: complementary experimental and simulation approaches to conformation and unfolding

X-ray crystallography of collagen model peptides has provided high-resolution structures of the basic triple-helical conformation and its water-mediated hydration network. Vibrational spectroscopy provides a useful bridge for transferring the structural information from X-ray diffraction to collagen in its native environment. The vibrational mode most useful for this purpose is the amide I mode (mostly peptide bond C=O stretch) near 1650 cm-1. The current study refines and extends the range of utility of a novel simulation method that accurately predicts the infrared (IR) amide I spectral contour from the three-dimensional structure of a protein or peptide. The approach is demonstrated through accurate simulation of the experimental amide I contour in solution for both a standard triple helix, (Pro-Pro-Gly)10, and a second peptide with a Gly --> Ala substitution in the middle of the chain that models the effect of a mutation in the native collagen sequence. Monitoring the major amide I peak as a function of temperature gives sharp thermal transitions for both peptides, similar to those obtained by circular dichroism spectroscopy, and the Fourier transform infrared (FTIR) spectra of the unfolded states were compared with polyproline II. The simulation studies were extended to model early stages of thermal denaturation of (Pro-Pro-Gly)10. Dihedral angle changes suggested by molecular dynamics simulations were made in a stepwise fashion to generate peptide unwinding from each end, which emulates the effect of increasing temperature. Simulated bands from these new structures were then compared to the experimental bands obtained as temperature was increased. The similarity between the simulated and experimental IR spectra lends credence to the simulation method and paves the way for a variety of applications.