We present the first comprehensive multiscale computational investigation of Resonance Raman, absorption and Circular Dichroism spectra of the resting state of theDeinococcus radioduransphytochrome. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5 μs MD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. A good agreement with experiments is found for all the three spectra. Moreover, we find a transient H-bond network within the binding pocket of the biliverdin chromophore that, unexpectedly, does not significantly affect the spectra. In parallel, we characterize the vibrations that are more strongly coupled to the biliverdin excitation, confirming the important role of the hydrogen-out-of-plane mode of its vinyl C-H together with the expected C=C stretching of the double bond involved in the photoisomerization.

Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome

Cupellini L.;Salvadori G.;Lipparini F.;Mennucci B.
2020-01-01

Abstract

We present the first comprehensive multiscale computational investigation of Resonance Raman, absorption and Circular Dichroism spectra of the resting state of theDeinococcus radioduransphytochrome. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5 μs MD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. A good agreement with experiments is found for all the three spectra. Moreover, we find a transient H-bond network within the binding pocket of the biliverdin chromophore that, unexpectedly, does not significantly affect the spectra. In parallel, we characterize the vibrations that are more strongly coupled to the biliverdin excitation, confirming the important role of the hydrogen-out-of-plane mode of its vinyl C-H together with the expected C=C stretching of the double bond involved in the photoisomerization.
2020
Macaluso, V.; Cupellini, L.; Salvadori, G.; Lipparini, F.; Mennucci, B.
File in questo prodotto:
File Dimensione Formato  
paper.pdf

Open Access dal 24/03/2021

Tipologia: Documento in Post-print
Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 5.04 MB
Formato Adobe PDF
5.04 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11568/1042640
Citazioni
  • ???jsp.display-item.citation.pmc??? 4
  • Scopus 14
  • ???jsp.display-item.citation.isi??? 13
social impact