Steric Effects Govern the Photoactivation of Phytochromes

Falklöf, Olle; Durbeej, Bo

doi:10.1002/cphc.201501080

Cited by 26 publications

(23 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the phy and opsin proteins, isomerization produces similar effects, strengthening the hypothesis that Δ V 1 > 0 reflects mainly steric and geometric rearrangements. Recently, quantum mechanics/molecular mechanics calculations on Deinococcus radiodurans BphP ( Dr BphP) have shown that steric effects are indeed a key factor in determining isomerization selectivity and efficiency, when the bilin chromophore is embedded within the protein . In Sy Cph1‐R, two different D‐ring geometries exists, one of which is thought to be planar (silent) and the second has a pretwisted C15 = C16 double bond induced by HB to H290 (active); as a consequence of pretwisting, the latter has a much higher Φ I = 0.29 ( vs 0.03 for the former) .…”

Section: Discussionmentioning

confidence: 99%

Time‐Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome‐Related Photoreceptors

Losi

Bonomi

Michael

et al. 2017

Photochem & Photobiology

View full text Add to dashboard Cite

Time-resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light-induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20 ns and 5 μs. Here, we report PA measurements on diverse photochromic bilin-binding photoreceptors of prokaryotic origin: (1) the chromophore-binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full-length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub-ns scale, reflecting the low photoisomerization quantum yield (<0.2). This "prompt" step is accompanied by a positive ΔV = 5-12.5 mL mol . Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3-G for which ΔV = +4.5 mL mol is followed by a time-resolved, energy-conserving contraction ΔV = -11.4 mL mol , τ = 180 ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3-G.

show abstract

Section: Discussionmentioning

confidence: 99%

Time‐Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome‐Related Photoreceptors

Losi

Bonomi

Michael

et al. 2017

Photochem & Photobiology

View full text Add to dashboard Cite

show abstract

“…Building on the same benchmark study, the QM region included the BV chromophore and the side chain of Cys24 to which it is linked. Recently, this scheme has also been used to explain why the most favorable double‐bond photoisomerization of BV in Dr BphP is the one occurring at C15−C16 …”

Section: Figurementioning

confidence: 99%

“…Recently, this scheme has also been used to explain why the most favorable doublebond photoisomerization of BV in DrBphP is the one occurring at C15ÀC16. [33] First, the structures of native DrBphP and of DrBphP with either of nitrogens A, B or C deprotonated (the latter three forms are henceforth denoted n A DrBphP, n B DrBphP and n C DrBphP; see Figure 2) were relaxed by performing geometry optimizations with the QM region described with the B3LYP functional. The procedure to consider only potential-energy minimum structures of the different forms, instead of ensembles of structures sampled from classical molecular dynamics (MD) trajectories, has a three-fold rationale.…”

Section: Computational Identification Of Pyrrole Ring C As the Prefermentioning

confidence: 99%

Computational Identification of Pyrrole Ring C as the Preferred Donor for Excited‐State Proton Transfer in Bacteriophytochromes

Falklöf

Durbeej

2018

ChemPhotoChem

Self Cite

View full text Add to dashboard Cite

The engineering of bacteriophytochrome photoreceptors into near‐infrared fluorescent proteins is a promising route toward deep‐tissue imaging of living cells with many challenges ahead. One key objective is to increase the fluorescence quantum yields, which are limited by competing non‐radiative relaxation processes involving not only the well‐known double‐bond photoisomerization of the tetrapyrrole chromophore, but also a potential excited‐state proton transfer from the chromophore to the protein. Motivated by the lack of mechanistic knowledge about this proton transfer, we here use hybrid quantum mechanics/molecular mechanics methods to investigate three possible scenarios for how the process is initiated. Through calculated excited‐state pKa values of the chromophore inside the protein matrix of Deinococcus radiodurans bacteriophytochrome, it is found that pyrrole ring C is a much more likely donor for excited‐state proton transfer than rings A and B, which are also possible donors discussed in the literature. This finding offers a starting point for establishing a strategy to strengthen the fluorescence of engineered bacteriophytochromes through biochemical inhibition of the proton transfer.

show abstract

“…The red pigment derived from organism is an important member in the family of dyestuff from biomass. Pyrrole structure microbial pigment, called prodigiosin, recently have become a research hotspot for its bright colors and antibacterial function [8,9]. This pigment was a kind of intracellular metabolite.…”

Section: Introductionmentioning

confidence: 99%

Bio-Preparation and Regulation of Pyrrole Structure Nano-Pigment Based on Biomimetic Membrane

et al. 2019

View full text Add to dashboard Cite

Microbial pigments, regarded as the most potential biomass pigments, have lately attracted increasing attention in textile dyeing due to their sustainability and cleaner production. The pyrrole structure microbial pigment, called prodigiosin, recently have become a research hotspot for its bright colors and antibacterial function. However, in most case the extraction and preparation are time-consuming and expensive processes since these kinds of microbial pigments are intracellular metabolites. In order to promote the application of microbial pigments in textile dyeing, a novel idea of preparing dye liquid of pyrrole structure pigments based on fermentation broth was put forward via increasing the proportion of extracellular pigments. A model membrane platform was established with a planar lipid bilayer to investigate transmembrane transport of microbial pigments and permeability barrier of cell membrane. The nano-dispersion of pigments was produced as the dye liquor owing to high-throughput transmembrane transfer of intracellular pigments and the increase of extracellular pigments proportion. The results indicated that the size and surface electrical properties of the pigments had contributed much to the mass transfer. It is also showed that transmembrane transmission of the intracellular pigments could be regulated by physical and chemical methods. With the improvement of transmembrane transfer efficiency of microbial pigments and the proportion of extracellular pigments, the complicated biological separation process could be avoided and the application of microbial pigments in textile dyeing can be promoted.

show abstract

Steric Effects Govern the Photoactivation of Phytochromes

Cited by 26 publications

References 44 publications

Time‐Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome‐Related Photoreceptors

Time‐Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome‐Related Photoreceptors

Computational Identification of Pyrrole Ring C as the Preferred Donor for Excited‐State Proton Transfer in Bacteriophytochromes

Bio-Preparation and Regulation of Pyrrole Structure Nano-Pigment Based on Biomimetic Membrane

Contact Info

Product

Resources

About