Cyanobacteriochromes (CBCRs) are photoreceptor proteins that photoconvert between two parent states and thereby regulate various biological processes. An intriguing property is their variable ultraviolet−visible (UV−vis) absorption that covers the entire spectral range from the far-red to the near-UV region and thus makes CBCRs promising candidates for optogenetic applications. Here, we have studied Slr1393, a CBCR that photoswitches between red-and green-absorbing states (Pr and Pg, respectively). Using UV−vis absorption, fluorescence, and resonance Raman (RR) spectroscopy, a further orange-absorbing state O 600 that is in thermal equilibrium with Pr was identified. The different absorption properties of the three states were attributed to the different lengths of the conjugated π-electron system of the phycocyanobilin chromophore. In agreement with available crystal structures and supported by quantum mechanics/molecular mechanics (QM/MM) calculations, the most extended conjugation holds for Pr whereas it is substantially reduced in Pg. Here, the two outer pyrrole rings D and A are twisted out of the plane defined by inner pyrrole rings B and C. For the O 600 state, the comparison of the experimental RR spectra with QM/MM-calculated spectra indicates a partially distorted ZZZssa geometry in which ring A is twisted while ring D and the adjacent methine bridge display essentially the same geometry as Pr. The quantitative analysis of temperature-dependent spectra yields an enthalpy barrier of ∼30 kJ/mol for the transition from Pr to O 600 . This reaction is associated with the movement of a conserved tryptophan residue from the chromophore binding pocket to a solvent-exposed position.

A bacterial phytochrome reversibly interconverts between a parallel and antiparallel dimeric arrangement during photoconversion.

Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.

It is demonstrated how the second-quantization formulation of multi-mode dynamics leads to expressions for vibrational density matrices. The properties and different representations of these matrices are discussed. Diagonalizing the one-mode density matrices defines a set of natural modals for each vibrational mode. The theory and first implementation of the iterative natural modals (ItNaMo) method for correlated vibrational-structure models is presented. In the ItNaMo method, natural modals are used as basis functions for a subsequent correlated calculation. This optimization of the one-mode basis is repeated until the changes in the basis functions become sufficiently small. Ground-state and excited-state energy calculations are presented for water, formaldehyde, and ethylene. It is shown that using optimized coordinates for the water calculation makes the occupation numbers converge to zero much faster and thereby allows for large reductions in the required number of basis functions. For the higherorder wave-function models the ItNaMo method results in smaller energy errors compared to full vibrational configuration interaction (FVCI) and thereby facilitates a more accurate description of the wave function.

Light sensing allows organisms to adapt to constantly changing environmental factors. Phytochromes constitute a widespread biological photoreceptor family that typically interconvert between two photostates called Pr (red light-absorbing) and Pfr (far-red light-absorbing). Despite the vast structural information reported on phytochromes, the lack of full-length structures at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here we present three crystallographic structures from the plant pathogen Xanthomonas campestris virulence regulator bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structural findings, combined with mutational, biochemical and computational studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level, from the isomerization of the chromophore and the β-sheet/α-helix tongue transition to the remodeling of the quaternary assembly of the protein.