open access publication

Article, 2024

Importance of Polarizable Embedding for Absorption Spectrum Calculations of Arabidopsis thaliana Cryptochrome 1

The Journal of Physical Chemistry B, ISSN 1520-5207, 1520-6106, Volume 128, 26, Pages 6283-6290, 10.1021/acs.jpcb.4c02168

Contributors

Frederiksen, Anders 0000-0001-6712-2975 [1] Gerhards, Luca 0000-0002-8404-2421 [1] Reinholdt, Peter 0000-0003-2406-700X [2] Kongsted, Jacob 0000-0002-7725-2164 [2] Solov'Yov, Ilia A 0000-0002-8626-145X (Corresponding author) [1]

Affiliations

  1. [1] Carl von Ossietzky University of Oldenburg
    2. [NORA names: Germany; Europe, EU; OECD];
  2. [2] University of Southern Denmark
    3. [NORA names: SDU University of Southern Denmark; University; Denmark; Europe, EU; Nordic; OECD]

Abstract

Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD), a chromophore within cryptochromes, absorbs blue light, initiating electron transfer processes that lead to a biological signaling cascade. A key step in this cascade is the formation of the FAD semiquinone radical (FADH•), characterized through a specific red-light absorption. The absorption spectra of FADH• in cryptochromes are, however, significantly different from those recorded for the cofactor in solution, primarily due to protein-induced shifts in the absorption peaks. This study employs a multiscale approach, combining molecular dynamics (MD) simulations with quantum mechanical/molecular mechanical (QM/MM) methodologies, to investigate the influence of protein dynamics on embedded FADH• absorption. We emphasize the role of the protein's polarizable environment in the shaping of the absorption spectrum, crucial for accurate spectral predictions in cryptochromes. Our findings provide valuable insights into the absorption process, advancing our understanding of cryptochrome functioning.

Keywords

Arabidopsis, FADH, QM/MM, absorption, absorption peak, absorption process, absorption spectra, absorption spectrum calculations, adenine dinucleotide, approach, avian magnetoreception, biological signaling cascades, blue light, calculations, cascade, chromophore, circadian rhythm, cofactor, cryptochrome, cryptochrome 1, cryptochrome function, dinucleotide, dynamics, electron, electron transfer process, environment, findings, flavin, flavin adenine dinucleotide, flavoprotein, formation, function, importance, influence, influence of protein dynamics, light, magnetoreception, methodology, molecular dynamics, multiscale approach, peak, polarizability, polarizable environment, prediction, process, protein, protein dynamics, quantum mechanical/molecular mechanical (QM/MM, radicals, red light absorption, rhythm, semiquinone radical, shift, signaling cascades, solution, spectra, spectral predictions, spectrum calculations, study, transfer process

Funders

  • Deutsche Forschungsgemeinschaft
  • Volkswagen Foundation

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