Infrared and vibrational CD spectra of partially solvated [alpha]-helices: DFT-based simulations with explicit solvent

Article Abstract:

The calculations based on the density functional theory (DFT) are used to investigate and analyze the various effects of aqueous solvents on the infrared (IR) and vibrational circular dichroism (CD) spectra of the partially solvated [alpha]-helices. The results show that the amide band-shapes highly depend on the extent of solvation of the helix and the side of contact with the solvent, which shows that the effects of solvation vary from case to case and hence must be studied separately.

Solvents, Alanine, Amides, Structure, Circular dichroism, Report

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Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water

Article Abstract:

Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(sub 10)-helical and 3(sub 1)-helical oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent. The predicted effects of solvent on spectral characteristics are analysed by comparison of the simulated spectra for identical peptides in vacuum and with explicit solvent (water).

Hydrogen bonding, Hydrogen bonds, Oligopeptides

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Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: Correlation between conformational fluctuation and vibrational coupling

Article Abstract:

A combination of molecular dynamics (MD) and density functional theory (DFT) is used for investigating theoretically the vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKLIQ (HBG), stabilized by Aib-Gly turn sequence (B=Aib). The results can provide a consistent description of the origin of amide I IR spectra for a beta-hairpin structure.

Czech Republic, Analysis, Peptides, Molecular dynamics, Atomic properties

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