Arrangement of fibril side chains studied by molecular dynamics and simulated infrared and vibrational circular dichroism spectra.

Highly ordered assemblies of β-sheet-forming peptide and protein fibrils have been the focus of much attention because of their multiple and partially unknown biological functions, in particular as related to degenerative neuronal disorders. Recently, vibrational circular dichroism (VCD) spectra have been shown to provide a unique means of detection for such extended structures utilizing modes of the peptide main chain backbone. In the case of poly-glutamic acid, surprising VCD responses were also found for side chain modes. In this study, in an attempt to explain this latter observation and obtain a link between fibrillar structure and its optical spectral properties, molecular dynamics (MD) methods are used to model the geometry and dynamics of assemblies containing repeating β-strands of Glu(n). A crystal-like model was adopted for the MD structure simulations. Infrared and VCD spectra for segments of MD modeled fibrillar geometries were first calculated using density functional theory (DFT), and then, those parameters were applied to larger structures by means of Cartesian coordinate transfer (CCT) of atomic tensors from the segments. The computations suggest the side chains exhibit residual conformational constraints, resulting in local coupling giving rise to non-negligible VCD intensity, albeit with an overall broad distribution. Calculated spectral distributions are qualitatively consistent with the experimental results but do differ in magnitude. The possibility of realistic modeling of vibrational spectra significantly broadens the potential for application of optical spectroscopies in structural studies of these aggregated biopolymers.