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Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy


Buhrke, David; Michael, Norbert; Hamm, Peter (2022). Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America, 119(31):e2206400119.

Abstract

Significance
Two-dimensional infrared absorption (2D-IR) spectroscopy is severely limited in its application to larger proteins due to broad and overlapping signals in the amide I region. Here, we overcome this limitation and isolate couplings between pairwise two single-molecular groups in the biotechnologically relevant phytochrome Agp1 (510 aa) by calculating light-induced difference spectra. In phytochromes, the photoactivation of a cofactor with a relatively small structural change triggers a large-scale refolding of big parts of the protein, but the mechanism of that interaction is not understood. We observe cross-peaks in the 2D-IR spectra that are directly related to the changing dipole coupling between the cofactor and the part of the protein that refolds, suggesting that both sites stabilize each other mutually.
Abstract
Phytochromes are ubiquitous photoreceptor proteins that undergo a significant refolding of secondary structure in response to initial photoisomerization of the chromophoric group. This process is important for the signal transduction through the protein and thus its regulatory function in different organisms. Here, we employ two-dimensional infrared absorption (2D-IR) spectroscopy, an ultrafast spectroscopic technique that is sensitive to vibrational couplings, to study the photoreaction of bacterial phytochrome Agp1. By calculating difference spectra with respect to the photoactivation, we are able to isolate sharp difference cross-peaks that report on local changes in vibrational couplings between different sites of the chromophore and the protein. These results indicate inter alia that a dipole coupling between the chromophore and the so-called tongue region plays a role in stabilizing the protein in the light-activated state.

Abstract

Significance
Two-dimensional infrared absorption (2D-IR) spectroscopy is severely limited in its application to larger proteins due to broad and overlapping signals in the amide I region. Here, we overcome this limitation and isolate couplings between pairwise two single-molecular groups in the biotechnologically relevant phytochrome Agp1 (510 aa) by calculating light-induced difference spectra. In phytochromes, the photoactivation of a cofactor with a relatively small structural change triggers a large-scale refolding of big parts of the protein, but the mechanism of that interaction is not understood. We observe cross-peaks in the 2D-IR spectra that are directly related to the changing dipole coupling between the cofactor and the part of the protein that refolds, suggesting that both sites stabilize each other mutually.
Abstract
Phytochromes are ubiquitous photoreceptor proteins that undergo a significant refolding of secondary structure in response to initial photoisomerization of the chromophoric group. This process is important for the signal transduction through the protein and thus its regulatory function in different organisms. Here, we employ two-dimensional infrared absorption (2D-IR) spectroscopy, an ultrafast spectroscopic technique that is sensitive to vibrational couplings, to study the photoreaction of bacterial phytochrome Agp1. By calculating difference spectra with respect to the photoactivation, we are able to isolate sharp difference cross-peaks that report on local changes in vibrational couplings between different sites of the chromophore and the protein. These results indicate inter alia that a dipole coupling between the chromophore and the so-called tongue region plays a role in stabilizing the protein in the light-activated state.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Scopus Subject Areas:Health Sciences > Multidisciplinary
Uncontrolled Keywords:Multidisciplinary
Language:English
Date:2 August 2022
Deposited On:04 Jan 2023 09:53
Last Modified:29 Mar 2024 02:37
Publisher:National Academy of Sciences
ISSN:0027-8424
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1073/pnas.2206400119
Project Information:
  • : FunderNational Science Foundation
  • : Grant ID200020B_188694
  • : Project Title
  • Content: Accepted Version
  • Content: Published Version
  • Licence: Creative Commons: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)