title: Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent.
abstract: Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins at very low temperatures, but overestimate the effects of solvent on the protein spectra at ambient temperatures, where the peptide-water hydrogen bonds are weakened by thermal motion.
authors.affiliation: Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Turner
authors.forename: Jan
authors.initials: J
authors.lastname: Kubelka
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D002942:Circular Dichroism / Q000379:methods; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry*; D013055:Spectrophotometry, Infrared / Q000379:methods; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D010455:Peptides; D012997:Solvents; D014867:Water; C019529:polyalanine