A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures

Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.