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Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra.

ABSTRACT: Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed ?/? proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.

SUBMITTER: Baldassarre M

PROVIDER: S-EPMC6331840 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra.

Baldassarre Maurizio M Li Chenge C Eremina Nadejda N Goormaghtigh Erik E Barth Andreas A

Molecules (Basel, Switzerland) 20150710 7

Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spec ...[more]

PMID: 26184143

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Project description:In the present paper, the photophysical properties of metallocene-4-amino-1,8-naphthalimide-piperazine molecules (1-M2+), as well as their oxidized and protonated derivatives (1-M3+, 1-M2+-H+, and 1-M3+-H+), where M = Fe, Co, and Ni, were studied via DFT and TD-DFT, employing three functionals, i.e., PBE0, TPSSh, and wB97XD. The effect of the substitution of the transition metal M on their oxidation state, and/or the protonation of the molecules, was investigated. The present calculated systems have not been investigated before and, except for the data regarding their photophysical properties, the present study provides important information regarding the effect of geometry and of DFT methodology on absorption spectra. It was found that small differences in geometry, specifically in the geometry of N atoms, reflect significant differences in absorption spectra. The common differences in spectra due to the use of different functionals can be significantly increased when the functionals predict minima even with small geometry differences. For most of the calculated molecules, the main absorption peaks in visible and near-UV areas correspond mainly to charge transfer excitations. The Fe complexes present larger oxidation energies at 5.4 eV, whereas Co and Ni complexes have smaller ones, at about 3.5 eV. There are many intense UV absorption peaks with excitation energies similar to their oxidation energies, showing that the emission from these excited states can be antagonistic to their oxidation. Regarding the use of functionals, the inclusion of dispersion corrections does not affect the geometry, and consequently the absorption spectra, of the present calculated molecular systems. For certain applications, where there is a need for a redox molecular system including metallocene, the oxidation energies could be lowered significantly, to about 40%, with the replacement of the iron with cobalt or nickel. Finally, the present molecular system, using cobalt as the transition metal, has the potential to be used as a sensor.

Dataset Information

Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra.

Publications

Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra.

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