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

We present the first comprehensive multiscale computational investigation of Resonance Raman, absorption and Circular Dichroism spectra of the resting state of the Deinococcus radiodurans phytochrome. 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[double bond, length as m-dash]C stretching of the double bond involved in the photoisomerization.

• Publication year

  2020

• Venue

  Physical Chemistry, Chemical Physics - PCCP

• Publication date

  2020-04-07

• Fields of study

  Biology, Physics, Chemistry, Materials Science, Environmental Science, Medicine

• Identifiers
  DOI 10.1039/d0cp00372gPMID 32255458
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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