Amide I Raman optical activity of polypeptides: fragment approximation.
Vibrational optical activity (VOA) is an important property used to determine the absolute configuration of a chiral molecule in condensed phases. In particular, vibrational circular dichroism and Raman optical activity (ROA) are two representative VOA measurement techniques that have been extensively used to study structures and dynamics of biomolecules. Recently, the amide I vibrational circular dichroism of polypeptides was theoretically described by using fragment approximation methods, which are based on the assumption that amide I VOA can be described as a linear combination of those of constituent fragment peptide units. Here, we develop a fragment approximation theory applicable to numerical simulations of Raman and Raman optical activity spectra for the amide I vibrations in polypeptides. For an alanine dipeptide and pentapeptide analogs, we carried out density functional theory calculations of polarizability, magnetic dipole-, and electric quadrupole-ROA tensors. Numerically simulated spectra using the fragment approximation are directly compared to density functional theory results. Furthermore, the simulated ROA spectra of alanine-based right-handed alpha-helix and polyproline II polypeptides are directly compared to the previously reported experimental results. The agreements were found to be excellent, which suggests that the fragment approximation method developed for the numerical simulation of ROA spectrum of polypeptide in solution is valid and useful.
Choi
Jun-Ho
JH
Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Republic of Korea.
Cho
Minhaeng
M
D000577:Amides / Q000737:chemistry; D003198:Computer Simulation; D008956:Models, Chemical; D009904:Optical Rotation; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012996:Solutions; D013059:Spectrum Analysis, Raman / Q000379:methods*; D013237:Stereoisomerism
D000577:Amides; D010455:Peptides; D012996:Solutions