On the molecular structure of the phytochrome chromophore: X-ray analysis of two 2,3-dihydrobilatriene-abc derivatives

The molecular and crystal structures of the two 2,3-dihydrobilatrienes-abc1 and2, representing model compounds for the phytochrome chromophore, were determined by X-ray crystallography at 97 K. Crystals of the racemate1 contain disordered regions. Both molecules are found to be ofall-(Z) configuration, assuming a helical conformation. The acidic hydrogen atoms are localized at the nitrogen atoms of rings A, C and D. A summary of the geometries of unsaturated five-membered rings as observed in four accurate low-temperature crystal structures of bilatrienes-abc is given.Herrn Prof.Josef Schurz zum 60. Geburtstag gewidmet.     

Determination of the chromophore structures in the photoinduced reaction cycle of phytochrome

The chromophore structures in the parent states Pr and Pfr as well as in the photocycle intermediate Lumi-R of oat phytochrome phyA are determined by comparison of the experimental resonance Raman spectra with calculated Raman spectra that have been obtained by density functional theory calculations (B3LYP) using scaled force fields. The spectra were calculated for various tetrapyrrole geometries including more than twenty different methine bridge isomers. For the parent states Pr and Pfr the best agreement in terms of vibrational frequencies, isotopic shifts, and Raman intensities was achieved with the ZZZasa and ZZEssa geometry, respectively. For the first intermediate Lumi-R, the chromophore geometry is concluded to be the ZZEasa configuration. These finding imply that the primary step of the photoactivation of phytochrome is the Z/E isomerization of the C-D methine bridge double bond, whereas the single bond remains in the anti conformation. The subsequent transition to the physiologically active state Pfr includes a (partial) single bond rotation of the A-B methine bridge.     

Biosynthesis of phycobilins. Formation of the chromophore of phytochrome, phycocyanin and phycoerythrin

Phycobiliproteins play important roles in photomorphogenesis and photosynthesis. The light-absorbing chromophores of the phycobiliproteins are linear tetrapyrroles (bilins) very similar in structure to the mammalian bile pigments. 5-Aminolaevulinate (5-ALA) is the first committed intermediate in phycobilin synthesis. The biosynthesis of 5-ALA, destined for phycobilins, occurs via the five-carbon pathway, now well established for tetrapyrrole synthesis in plants and distinct from the mammalian pathway. The phycobilins are formed by reduction of biliverdin which results from the synthesis and degradation of haem. This haem is an essential intermediate in the biosynthesis of phycobilins. Phycocyanobilin, the blue-green pigment found in certain algae and cyanobacteria, is formed from biliverdin via phytochromobilin, the chromophore of phytochrome. This leads to the likelihood that phytochromobilin is formed as an end product, or intermediate, in the synthesis of all phycobilins.     

Interactions between chromophore and protein in phytochrome identified by novel oxa-, thia- and carba-chromophores

Abstract Six new bilin chromophores of the plant photoreceptor phytochrome have been synthesized, carrying at the photoisomerizing ring D an oxygen or a sulfur atom or a methylene group instead of the pyrrole nitrogen atom. These furanone-, thiophenone- or cyclopentenone-containing compounds bound covalently to the recombinant apophytochrome phyA of Avena sativa. The novel chromoproteins showed hypsochromically shifted absorption spectra with respect to native phytochrome and a strongly diminished photochemical activity, but a three- to four-fold higher fluorescence quantum yield. These results demonstrate that, on the one hand, also ring D-modified chromophores can be forced into a partially extended structure, required for incorporation into the apoprotein binding pocket and covalent binding. On the other hand, the modifications introduced into ring D of the chromophores strongly impede the formation of stable far red-absorbing forms of plant photoreceptor phytochrome (P(fr)-form) of the chromoproteins, highlighting especially the role of the pyrrole nitrogen atom and hydrogen bonding for the precise interactions between that part of the chromophore and the protein for the P(fr)-formation.     

Synthesis and characterization of a metal-to-polyoxometalate charge transfer molecular chromophore

[P(4)W(35)O(124){Re(CO)(3)}(2)](16-) (1), a Wells-Dawson [α(2)-P(2)W(17)O(61)](10-) polyoxometalate (POM)-supported [Re(CO)(3)](+) complex containing covalent W(VI)-O-Re(I) bonds has been synthesized and characterized by several methods, including X-ray crystallography. This complex shows a high visible absorptivity (ε(470 nm) = 4000 M(-1) cm(-1) in water) due to the formation of a Re(I)-to-POM charge transfer (MPCT) band. The complex was investigated by computational modeling and transient absorption measurements in the visible and mid-IR regions. Optical excitation of the MPCT transition results in instantaneous (<50 fs) electron transfer from the Re(I) center to the POM ligand.     

Heteronuclear NMR investigation on the structure and dynamics of the chromophore binding pocket of the cyanobacterial phytochrome Cph1

Structural changes of the chromophore in phytochrome proteins associated with its photocycle are still not fully understood. We use heteronuclear NMR to investigate the conformation and dynamics of the chromophore in the binding pocket of the cyanobacterial phytochrome Cph1. On the basis of distance information obtained from three-dimensional nuclear Overhauser enhancement (3D-NOESY) spectra using the photochemically intact photosensory module of Cph1 we demonstrate that the chromophore is in the ZZZssa form in the P(r) (red absorbing form) state and the ZZEssa form in the P(fr) (far-red absorbing form) state of the protein. While ZZZssa for the P(r) state is in agreement with a recently determined X-ray structure, no comparable information for the P(fr) state of photochemically intact phytochrome has been available up to now. In addition, the chromophore in the binding pocket of Cph1 exhibits a notable mobility, which is distinctly different in the two photostates.     

Rapid topography mapping of scalar fields: Large molecular clusters

An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CP's) of small systems. It is further applied to large molecular clusters viz. (H(2)O)(25), (C(6)H(6))(8) and also to a unit cell of valine crystal at MP2∕6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincare?-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.     

Photochemistry of visual pigment chromophore models by ab initio molecular dynamics

Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck-Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approach--torsion angle following--is discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and selective photochemistry, which is in agreement with photophysical measurements on rhodopsin analogues. We conclude that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.     

The amide-aromatic-ring system : An inherently dissymmetric chromophore

Two cyclic peptide like compounds, cyclo-anthranoyl-L- prolyl (1) and cyclo-homoanthranoyl-L-prolyl (2) have been synthesized and investigated by UV spectroscopy and measurement of circular dichroism. Compound 1 of entirely rigid conformation with two N-CO groups conjugated to the aromatic ring, Ar-NH-CO left handed helical, Ar-CO-N right handed helical, shows a very strong positive Cotton effect centered around 250 nm and a strong negative one centered around 227 nm. Compound 2, which has only one conjugated skewed electron system, Ar-NH-CO, can exist in two different stable conformations, one of them being left handed, the other one right handed helical. It also shows a strong positive Cotton effect centered around 235 nm. Since from earlier ¹³C NMR data the latter was concluded to be the preferred conformation, a right handed helical sense of the amide bond-aromatic ring system is likely to correlate with a positive Cotton effect of this inherently dissymmetric chromophore.     

The chromophore of asFP595: a theoretical study

We investigate the electronic and structural properties of the chromophore of the asCP/asFP595, a newly discovered protein of the (green) fluorescent protein family. The use of theoretical methods with different degrees of accuracy and efficiency (DFT, TDDFT, CASSCF and perturbative corrections) allows us to compare the properties of a large number of hypothetic molecular models for the chromophore. The models are sorted on the basis of the relative stability and through a comparison with the experimental values of the excitation energy. Our study indicates that the most probable structure of the photoactive moiety in the protein and in water is the one resulting from the GFP-like rather than the "alternative" cyclization scheme.     

The Si-B chromophore: A joint experimental and theoretical investigation

Silylboranes with aromatic substituents linked to boron and silicon exhibit an unexpected absorption band in the UV-Vis spectral region. When polar groups were introduced, a marked solvatochromic effect was observed in their fluorescence emission spectra, revealing a strong excited state dipole moment. Semi-empirical MNDO/d and AM1 calculations showed that, upon UV excitation, the polarity of the Si-B bond increased and the aromatic π-electrons migrated toward the Si-B bond, consistent with experimental observations.     

Assignments of the Pfr-Pr FTIR difference spectrum of cyanobacterial phytochrome Cph1 using 15N and 13C isotopically labeled phycocyanobilin chromophore

The reversible red and far-red light-induced transitions of cyanobacterial phytochrome Cph1 from Synechocystis PCC 6803 were investigated by Fourier transform infrared (FTIR) difference spectroscopy. High-quality light-induced Pfr-Pr difference FTIR spectra were recorded for the 58 kDa N-terminal domain of Cph1 by repetitive photochemical cycling and signal averaging. The Pfr-Pr difference spectra in H(2)O and D(2)O were very similar to those previously reported for full-length 85 kDa Cph1.(1) Published assignments were extended by analysis of the effects of (13)C and (15)N isotope substitutions at selected sites in the phycocyanobilin chromophore and by (15)N global labeling of the protein. The Pfr-Pr difference spectra were dominated by an amide I peak/trough at 1653 cm(-1)(+)/1631 cm(-1)(-) and a smaller amide II band at 1554 cm(-1). Labeling effects allowed specific chromophore assignments for the C(1)=O (1736 cm(-1)(-)/1724 cm(-1)(+)) and C(19)=O (1704 cm(-1)(-)) carbonyl vibrations, C=C vibrations at 1589 cm(-1)(+), and bands at 1537(-), 1512(+), 1491(-), 1163(+), 1151(-), 1134(+), 1109(-), and 1072(-) cm(-1) that must involve chromophore C-N bonds. A variety of additional changes were insensitive to isotope labeling of the chromophore. Effects of (15)N labeling of the protein were used to tentatively assign some of these to specific amino acid changes. Those insensitive to (15)N labeling included a protonated aspartic or glutamic acid at 1734 cm(-1)(-)/1722 cm(-1)(+) and a cysteine at 2575 cm(-1)(+)/2557 cm(-1)(-). Bands sensitive to (15)N protein labeling at 1487 cm(-1)(+)/1502 cm(-1)(-) might arise from trytophan and bands at 1261 cm(-1)(+)/1244 cm(-1)(-) and 1107 cm(-1)(-)/1095 cm(-1)(+) might arise from a histidine environment or protonation change. These assignments are discussed in light of the 15Z-E photoisomerization model of phototransformation and the associated protein conformational changes.     

The "benzothiazine" chromophore of pheomelanins: a reassessment

The characteristic absorption and photochemical properties of pheomelanins are generally attributed to "benzothiazine" structural units derived biogenetically from 5-S-cysteinyldopa. This notion, however, conveys little or no information about the structural chromophores responsible for the photoreactivity of pheomelanins. At pH 7.4, natural and synthetic pheomelanins show a defined maximum around 305 nm, which is not affected by reductive treatment with sodium borohydride, and a monotonic decrease in the absorption in the range 350-550 nm. These features are not compatible with a significant proportion of structural units related to 2H-1,4-benzothiazine and 2H-1,4-benzothiazine-3-carboxylic acid, the early borohydride-reducible pheomelanin precursors featuring absorption maxima above 340 nm. Rather, these features would better accommodate a contribution by the nonreducible 3-oxo-3,4-dihydrobenzothiazine (lambdamax 299 nm) and benzothiazole (lambdamax 303 nm) structural motifs, which are generated in the later stages of pheomelanogenesis in vitro. This conclusion is supported by a detailed liquid chromatography/UV and mass spectrometry monitoring of the species formed in the oxidative conversion of 5-S-cysteinyldopa to pheomelanin, and would point to a critical reassessment of the commonly reported "benzothiazine" chromophore in terms of more specific and substantiated structural units, like those formed during the later stages of pheomelanin synthesis in vitro.     

Appraisal of through-bond and through-space substituent effects via molecular electrostatic potential topography

Through-bond (TB) and through-space (TS) substituent effects in substituted alkyl, alkenyl, and alkynyl arenes are quantified separately using molecular electrostatic potential (MESP) topographical analysis. The deepest MESP point over the aromatic ring (V(min)) is considered as a probe for monitoring these effects for a variety of substituents. In the case of substituted alkyl chains, the TS effect (79.6%) clearly dominates the TB effect, whereas in the unsaturated analogues the TB effect (～55%) overrides the TS effect.     

Two native pools of phytochrome A in monocots: Evidence from fluorescence investigations of phytochrome mutants of rice

Fluorescence investigations of phytochrome (phy) in rice (Oryza sativa L. cv. Nipponbare) mutants deficient in phyA, phyB and phyA plus phyB were performed. Total content of the pigment (P(tot)) and its spectroscopic and photochemical characteristics were determined in different parts of the dark-grown and far-red light (FR)-grown coleoptiles. Spectroscopically, phyA in the phyB mutant was identical to phyA in the wild-type (WT) and the extent of the conversion from Pr to lumi-R at 85 K was the same for phyA in both lines and varied similarly, depending on the part of the coleoptile used. The latter finding proved that phyA in rice is heterogeneous and comprises two phyA populations, phyA' and phyA". Functional properties of phyA were also determined. In the dark the phyB mutant had a higher content of phyA, inactive protochlorophyllide (Pchlide633) and active protochlorophyllide (Pchlide655) than WT and its coleoptile was longer, indicating that phyB may affect the development of WT seedlings in the dark. Constant FR drastically reduced the content of phyA, Pchlide633 and Pchlide655 and brought about coleoptile shortening and appearance of the first leaf, whereas pulsed FR of equal fluence was less effective. This suggested that the reactions were primarily of the high irradiance responses type, which are likely to be mediated by phyA'. The effects on protochlorophyllide biosynthesis and growth responses type were more pronounced in the phyB mutant than in the WT seedlings, which can be connected with the higher phyA' content in the phyB mutant and/or phyB interference with its action in WT seedlings. In the phyA mutant induction of Pchlide633 and Pchlide655 biosynthesis was observed under constant FR, indicating that phyC may be responsible for this effect.