title: The amide III vibrational circular dichroism band as a probe to detect conformational preferences of alanine dipeptide in water.
abstract: The conformational preferences of blocked alanine dipeptide (ADP), Ac-Ala-NHMe, in aqueous solution were studied using vibrational circular dichroism (VCD) together with density functional theory (DFT) calculations. DFT calculations of three most representative conformations of ADP surrounded by six explicit water molecules immersed in a dielectric continuum have proven high sensitivity of amide III VCD band shape that is characteristic for each conformation of the peptide backbone. The polyproline II (PII ) and αR conformation of ADP are associated with a positive VCD band while β conformation has a negative VCD band in amide III region. Knowing this spectral characteristic of each conformation allows us to assign the experimental amide III VCD spectrum of ADP. Moreover, the amide III region of the VCD spectrum was used to determine the relative populations of conformations of ADP in water. Based on the interpretation of the amide III region of VCD spectrum we have shown that dominant conformation of ADP in water is PII which is stabilized by hydrogen bonded water molecules between CO and NH groups on the peptide backbone.
authors.affiliation: National Institute of Chemistry, Hajdrihova 19,, SI-1000, Ljubljana, Slovenia.
authors.forename: Andreja
authors.initials: A
authors.lastname: Mirtič
authors.forename: Franci
authors.initials: F
authors.lastname: Merzel
authors.forename: Jože
authors.initials: J
authors.lastname: Grdadolnik
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry* / Q000378:metabolism; D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D002942:Circular Dichroism / Q000379:methods*; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D015335:Molecular Probes / Q000737:chemistry*; D011487:Protein Conformation; D017550:Spectroscopy, Fourier Transform Infrared; D013816:Thermodynamics; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D004151:Dipeptides; D015335:Molecular Probes; D014867:Water; C024314:N-acetylalanyl-N-methylamide; D000409:Alanine
keywords: DFT calculations; PII; VCD; alanine dipeptide; backbone conformations; αR; β