New Fourier transform infrared based computational method for peptide secondary structure determination. I. Description of method.
Fourier transform infrared (FTIR) experiments in dimethylsulfoxide, a solvent incapable of H donation, demonstrate that H --> D isotopic replacement on the amide side of peptide bonds involves modifications of both the position and intensity of the amide I band. The effect of the isotopic substitution is particularly significant in the 1710-1670 and 1670-1650 cm(-1) regions, which are generally associated with beta-turns and alpha-helices. This behavior, attributed to the existence of intramolecular H-bonds in the polypeptide chain, is directly correlated to the presence of different secondary structures. Utilizing the effects induced by isotopic substitution, a method for the quantitative determination of the percentage of intramolecular H-bonds and the correlated secondary structures is proposed. The method consists of three principal steps: resolution of the fine structure of the amide I band with the determination of the number and position of the different components; reconstruction of the experimentally measured amide I band as a combination of Gaussian and Lorentzian functions, centered on the wave numbers set by band-narrowing methods, through a curve-fitting program; and quantitative determination of the population of the H-bonded carbonyls and the correlated secondary structures by comparison of the integrated intensities pertaining to the components with homologous wave numbers before and after isotopic exchange. The method is tested on a synthetic fragment of proocytocin that was previously analyzed by NMR techniques using the same solvent systems.
Simonetti
M
M
Department of Chemical Processes Engineering, University of Padova, Via Marzolo 9, 35131 Padua, Italy.
Di Bello
C
C
D003903:Deuterium; D004121:Dimethyl Sulfoxide / Q000494:pharmacology; D008958:Models, Molecular; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012997:Solvents / Q000494:pharmacology; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods
D010455:Peptides; D012997:Solvents; D003903:Deuterium; D004121:Dimethyl Sulfoxide