Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c
| Autor: | Guillaume Le Breton, Thomas L. C. Jansen, Ana V. Cunha, Jens Bredenbeck, Luuk J. G. W. van Wilderen, Youssef El Khoury |
|---|---|
| Přispěvatelé: | Theory of Condensed Matter, Laboratoire de Bioélectrochimie et Spectroscopie, Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Zernike Institute for Advanced Materials, University of Groningen [Groningen], École normale supérieure de Lyon (ENS de Lyon), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Institut für biophysik (IFP), Goethe-University Frankfurt am Main, École normale supérieure - Lyon (ENS Lyon) |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Infrared
General Physics and Astronomy Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Molecular dynamics symbols.namesake Spectroscopy Fourier Transform Infrared 0103 physical sciences Animals Horses Physical and Theoretical Chemistry Fourier transform infrared spectroscopy Spectroscopy Protein secondary structure 010304 chemical physics biology Chemistry Cytochrome c Cytochromes c Charge density 0104 chemical sciences [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry Crystallography Fourier transform biology.protein symbols Oxidation-Reduction |
| Zdroj: | Journal of Chemical Physics, 154(12):124201. AMER INST PHYSICS Journal of Chemical Physics Journal of Chemical Physics, 2021, 154 (12), pp.124201. ⟨10.1063/5.0039969⟩ Journal of Chemical Physics, American Institute of Physics, 2021, 154 (12), pp.124201. ⟨10.1063/5.0039969⟩ |
| ISSN: | 0021-9606 1089-7690 |
| Popis: | Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|