Elucidating the role of structural fluctuations, intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome
| Main Authors: | Macaluso, Veronica, Cupellini, Lorenzo, Salvadori, Giacomo, Lipparini, Filippo, Mennucci, Benedetta |
|---|---|
| Format: | Article |
| Terbitan: |
, 2020
|
| Online Access: |
https://zenodo.org/record/4742723 |
Daftar Isi:
- We present the first comprehensive multiscale computational investigation of Resonance Raman (RR), absorption and Circular Dichroism (CD) spectra of the resting state of the dimeric phy- tochrome of Deinococcus radiodurans. 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 4.5μs 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. From simulations, we find a transient H-bond network within the binding pocket of the chromophore that, unexpect- edly, do not significantly affect the absorption and CD spectra. In parallel, we characterize the vibrations which are more strongly coupled to the excitation confirming the important role of the hydrogen-out-of-plane mode of the vinyl C-H in between C and D rings together with the expected C=C stretching of the double bond involved in the photoisomerization.