New Fourier transform infrared based computational method for peptide secondary structure determination. I. Description of method

Fourier transform infrared (FTIR) experiments in dimethylsulfoxide, a solve nt incapable of H donation, demonstrate that H --> D isotopic replacement o n the amide side of peptide bonds involves modifications of both the positi on and intensity of the amide I band. The effect of the isotopic substituti on is particularly significant in the 1710-1670 and 1670-1650 cm(-1) region s, which are generally associated with beta -turns and alpha -helices. This behavior, attributed to the existence of intramolecular H-bonds in the pol ypeptide chain, is directly correlated to the presence of different seconda ry structures. Utilizing the effects induced by isotopic substitution, a me thod for the quantitative determination of the percentage of intramolecular H-bonds and the correlated secondary structures is proposed. The method co nsists of three principal steps: resolution of the fine structure of the am ide I band with the determination of the number and position of the differe nt components; reconstruction of the experimentally measured amide I band a s 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 intens ities pertaining to the components with homologous wave numbers before and after isotopic exchange. The method is tested on a synthetic fragment of pr oocytocin that was previously analyzed by NMR techniques using the same sol vent systems. (C) 2001 John Wiley & Sons, Inc.