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

New Fourier transform infrared based computational method for peptide secondary structure... 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 β‐turns and α‐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. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 95–108, 2001 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Biopolymers Wiley

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

Simonetti, Mario; Di Bello, Carlo
Biopolymers , Volume 62 (2) – Jan 1, 2001
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References (41)

Publisher
Wiley
Copyright
Copyright © 2001 John Wiley & Sons, Inc.
ISSN
0006-3525
eISSN
1097-0282
DOI
10.1002/bip.1002
pmid
11288058
Publisher site
See Article on Publisher Site

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 β‐turns and α‐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. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 95–108, 2001

Journal

Biopolymers – Wiley

Published: Jan 1, 2001

Keywords: FTIR spectroscopy; peptide conformation; H → D exchange; secondary structures; β‐turns

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