title: Simulation of the amide I infrared spectrum in photoinduced peptide folding/unfolding transitions.
abstract: The amide I' infrared spectrum of a α-helical photoswitchable peptide is calculated here by means of a mixed quantum mechanics/molecular dynamics theoretical-computational methodology based on the perturbed matrix method (PMM). The contribution of specific residues to the total spectrum is also analyzed and the results compared to previous experimental spectroscopic data, obtained by means of site-specific isotope labeling at different residues, resulting in good agreement. One of the residues (Ala7) shows atypical spectroscopic behavior in both the experimental and calculated spectra, i.e., the folded-state amide I' band is shifted to higher frequencies than the unfolded-state one, while the other residues show the opposite behavior. The calculations reveal the origin of this uncommon spectroscopic trend and point to a crucial role of the molecular switch, the presence of which perturbs the conformational sampling of the peptide. Indeed, infrared spectra of the same peptide calculated in the absence of the molecular switch show that the single-residue spectrum of Ala7 does not have any distinguishing feature, resembling the spectra of the other analyzed residues.
authors.affiliation: Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila , via Vetoio (Coppito 1), 67010 Coppito (AQ), Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Zanetti-Polzi
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Aschi
authors.forename: Andrea
authors.initials: A
authors.lastname: Amadei
authors.forename: Isabella
authors.initials: I
authors.lastname: Daidone
mesh_terms: D000577:Amides / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D055668:Photochemical Processes; D017510:Protein Folding; D058767:Protein Unfolding; D011789:Quantum Theory; D013055:Spectrophotometry, Infrared
chemical_list: D000577:Amides; D010455:Peptides