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

Abstract

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.

Effect of polyaspartic acid on hydroxyapatite deposition in silk fibroin blend films

“…The amide I and amide II bands for the PASP/SF composite films were shifted from 1658 to 1662 and 1550 to 1542 cm -1 , respectively, and a small sharp peak at 1649 cm -1 appeared, indicating that a partial conformation transition from silk I to silk II structure occurred [11]. After treated with ethanol, the amide I bands were shifted to 1634 cm -1 with a shoulder at 1694 cm -1 , which could be assigned to β-turns [20,21]. Amide II and amide III bands were shifted to 1526 and 1233 cm -1 , respectively.…”

Density Functional Theory Vibrational Frequencies of Amides and Amide Dimers

“…Infrared (IR) spectroscopy is widely used to estimate the secondary structure content of polypeptides and proteins, since many vibrational bands characteristic of the peptide unit are sensitive to their environment . Such studies have benefitted from the advent of techniques such as Fourier self-deconvolution and second-derivative resolution enhancement that allow greater spectral detail to be observed. , In general, α-helical structure gives rise to a single carbonyl stretch band at ∼1650 cm -1 . β-Sheets can give rise to carbonyl stretch bands at ∼1620 cm -1 (strong) and at ∼1690 cm -1 (weak).…”

Influence of Electrostatic Environment on the Vibrational Frequencies of Proteins

“…Secondary structure motifs are important determinants of the infrared (IR) spectra of peptides and proteins . This relationship has led to the development and widespread use of techniques, based on experimentally observed spectra, to calculate secondary structure content for proteins. , These correlations arise from the fundamental physics of the system, and understanding how the IR spectrum of the amide group is affected by its environment is critical for the fullest interpretation of IR experiments. To this end, small amides such as formamide and N -methylacetamide (NMA) have been extensively studied.…”