Modeling of phytochrome absorption spectra

Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment

Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.

Correlating Metal Redox Potentials to Co(III)K(I) Catalyst Performances in Carbon Dioxide and Propene Oxide Ring Opening Copolymerization

Carbon dioxide copolymerization is a front-runner CO2 utilization strategy but its viability depends on improving the catalysis. So far, catalyst structure-performance correlations have not been straightforward, limiting the ability to predict how to improve both catalytic activity and selectivity. Here, a simple measure of a catalyst ground-state parameter, metal reduction potential, directly correlates with both polymerization activity and selectivity. It is applied to compare performances of 6 new heterodinuclear Co(III)K(I) catalysts for propene oxide (PO)/CO2 ring opening copolymerization (ROCOP) producing poly(propene carbonate) (PPC). The best catalyst shows an excellent turnover frequency of 389 h-1 and high PPC selectivity of >99 % (50 °C, 20 bar, 0.025 mol% catalyst). As demonstration of its utility, neither DFT calculations nor ligand Hammett parameter analyses are viable predictors. It is proposed that the cobalt redox potential informs upon the active site electron density with a more electron rich cobalt centre showing better performances. The method may be widely applicable and is recommended to guide future catalyst discovery for other (co)polymerizations and carbon dioxide utilizations.

Carbonate precipitation and nitrogen fixation in AMG (Artificial Martian Ground) by cyanobacteria

This article describes experiments performed to study the survival, growth, specific adaptations and bioremediation potential of certain extreme cyanobacteria strains within a simulation of the atmospheric composition, temperature and pressure expected in a future Martian greenhouse. Initial species have been obtained from Mars-analogue sites in Georgia. The results clearly demonstrate that specific biochemical adaptations allow these autotrophs to metabolize within AMG (Artificial Martian Ground) and accumulate biogenic carbon and nitrogen. These findings may thus contribute to the development of future Martian agriculture, as well as other aspects of the life-support systems at habitable Mars stations. The study shows that carbonate precipitation and nitrogen fixation, performed by cyanobacterial communities thriving within the simulated Martian greenhouse conditions, are cross-linked biological processes. At the same time, the presence of the perchlorates (at low concentrations) in the Martian ground may serve as the initial source of oxygen and, indirectly, hydrogen via photo-Fenton reactions. Various carbonates, ammonium and nitrate salts were obtained as the result of these experiments. These affect the pH, salinity and solubility of the AMG and its components, and so the AMG's scanty biogenic properties improved, which is essential for the sustainable growth of the agricultural crops. Therefore, the use of microorganisms for the biological remediation and continuous in situ fertilization of Artificial Martian Ground is possible.

Quantum-based Modeling of Protein-ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen

Modern quantum-based methods are employed to model interaction of the flavin-dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the structure of reactants for the chain of chemical reactions of monooxygenation in the enzyme active site, which is important in drug metabolism. In this case, application of quantum-based approaches is an essential issue, unlike conventional modeling of protein-ligand interaction with force fields using molecular mechanics and classical molecular dynamics methods. We focus on two difficult problems to characterize the structure of reactants in the RutA-FMN-O₂ -uracil complex, where FMN stands for the flavin mononucleotide species. First, location of a small O₂ molecule in the triplet spin state in the protein cavities is required. Second, positions of both ligands, O₂ and uracil, must be specified in the active site with a comparable accuracy. We show that the methods of molecular dynamics with the interaction potentials of quantum mechanics/molecular mechanics theory (QM/MM MD) allow us to characterize this complex and, in addition, to surmise possible reaction mechanism of uracil oxygenation by RutA.

Hydrogen-Bond Network Determines the Early Photoisomerization Processes of Cph1 and AnPixJ Phytochromes

Phytochrome proteins are light receptors that play a pivotal role in regulating the life cycles of plants and microorganisms. Intriguingly, while cyanobacterial phytochrome Cph1 and cyanobacteriochrome AnPixJ use the same phycocyanobilin (PCB) chromophore to absorb light, their excited‐state behavior is very different. We employ multiscale calculations to rationalize the different early photoisomerization mechanisms of PCB in Cph1 and AnPixJ. We found that their electronic S₁, T₁, and S₀ potential minima exhibit distinct geometric and electronic structures due to different hydrogen bond networks with the protein environment. These specific interactions influence the S₁ electronic structures along the photoisomerization paths, ultimately leading to internal conversion in Cph1 but intersystem crossing in AnPixJ. This explains why the excited‐state relaxation in AnPixJ is much slower (ca. 100 ns) than in Cph1 (ca. 30 ps). Further, we predict that efficient internal conversion in AnPixJ can be achieved upon protonating the carboxylic group that interacts with PCB.

Photoelectron Spectroscopy and Theoretical Study on Monosolvated Cyanate Analogue Clusters ECX-·Sol (ECX- = NCSe-, AsCSe-, and AsCS-; Sol = H2O, CH3CN)

Six monosolvated cyanate analogue clusters ECX^-·Sol (ECX^- = NCSe^-, AsCSe^-, and AsCS^-; Sol = H₂O and CH₃CN) were investigated using negative ion photoelectron spectroscopy (NIPES). NIPES experiments show that these clusters possess similar spectra overall compared to their respective isolated ECX^- anions but shift to higher electron binding energy with CH₃CN solvent, stabilizing the excess electrons slightly more than H₂O. For the ECX^-·H₂O series, vertical detachment energies and their increments relative to the bare species are measured to be 3.700/0.370, 3.085/0.415, and 3.085/0.430 eV for NCSe^-, AsCSe^- and AsCS^-, respectively, while the corresponding values in the ECX^-·CH₃CN series are 3.835/0.505, 3.145/0.475, and 3.135/0.480 eV. Ab initio electronic structure calculations indicate that the excess charges were located at the terminal N and Se atoms in NCSe^- and migrated to the central C atom in AsCSe^- and AsCS^-. For NCSe^-, the solvation is driven by the interactions with the two negatively charged terminal ends, while for AsCSe^- and AsCS^-, the solvation revolves around the interactions with the central C atom, where all the excess negative charge is concentrated. Two nearly degenerate isomers for NCSe^-·H₂O are identified, one forming a single strong N···H-O hydrogen bond (HB) and the other featuring a bidentate HB with two hydroxyl H atoms pointing to N and Se ends. In contrast, the negative central C atom in AsCSe^-/AsCS^- allows the formation of a bifurcated HB with H₂O. Similar effects are observed for the acetonitrile case, in which the three H atoms of the methyl group interact with the two negatively charged terminal ends in NCSe^-, while preferring to bind to the central negative carbon atom in AsCSe^-/AsCS^-. The different binding motifs derived in this work may suggest different solvation properties in NCSe^- versus AsCSe^-/AsCS^- with the former anion leading to asymmetric solvation at the N end of the solute, while the latter species creates more "isotropic" solvation around the central C equatorial plane.

The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chromophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive molecular dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway.

Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4

An enhanced interest in the phytochrome-based fluorescent proteins is explained by their ability to absorb and emit light in the far-red and infra-red regions particularly suitable for bioimaging. The fluorescent protein IFP1.4 was engineered from the chromophore-binding domain of a bacteriophytochrome in attempts to increase the fluorescence quantum yield. We report the results of simulations of structures in the ground S₀ and excited S₁ electronic states of IFP1.4 using the methods of quantum chemistry and quantum mechanics/molecular mechanics. We construct different protonation states of the biliverdin (BV) chromophore in the red-absorbing form of the protein by moving protons from the BV pyrrole rings to a suitable acceptor within the system and show that these structures are close in energy but differ by absorption bands. For the first time, we report structures of the minimum energy conical intersection points S₁/S₀ on the energy surfaces of BV in the protein environment and describe their connection to the local minima in the excited S₁ state. These simulations allow us to characterize the deactivation routes in IFP1.4.

Frontiers in Multiscale Modeling of Photoreceptor Proteins

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

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

Molecular dynamics and a multiscale polarizable QM/MM strategy allow reproducing absorption, circular dichroism, and resonance Raman spectra of a bacteriophytochrome.

QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes.

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra.

The Effective Conjugation Length Is Responsible for the Red/Green Spectral Tuning in the Cyanobacteriochrome Slr1393g3

The origin of the spectral shift from a red- to a green-absorbing form in a cyanobacteriochrome, Slr1393g3, was identified by combined quantum mechanics/molecular mechanics simulations. This protein, related to classical phytochromes, carries the open-chain tetrapyrrole chromophore phycocyanobilin. Our calculations reveal that the effective conjugation length in the chromophore becomes shorter upon conversion from the red to the green form. This is related to the planarity of the entire chromophore. A large distortion was found for the terminal pyrrole rings A and D; however, the D ring contributes more strongly to the photoproduct tuning, despite a larger change in the twist of the A ring. Our findings implicate that the D ring twist can be exploited to regulate the absorption of the photoproduct. Hence, mutations that affect the D ring twist can lead to rational tuning of the photoproduct absorption, allowing the tailoring of cyanobacteriochromes for biotechnological applications such as optogenetics and bioimaging.

Competition between two cysteines in covalent binding of biliverdin to phytochrome domains

In this work, we disclose a mechanism of competing chemical reactions of protein assembly for a bacterial phytochrome using modern methods of molecular modeling.

The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful

Bilin-dependent GAF domain photoreceptors cover the whole spectrum of light with their absorbance properties. They can be divided into three groups according to the domain architecture of their photosensory module. Group I and Group II harbor phytochromes with PAS-GAF-PHY and GAF-PHY domain architecture, respectively. Group III consists of stand-alone GAF domain photoreceptors, the cyanobacteriochromes. Crystal structures of all three groups are now available to shed light on possible downstream signaling pathways. Structures of Group I and III photoreceptors in both states display changes in the secondary structures during photoconversion. The knowledge about the photoconversion in phytochromes and CBCRs make them promising targets for applications in life science and synthetic biology.