Enzyme Activity by Design: An Artificial Rhodium Hydroformylase for Linear Aldehydes.

Artificial metalloenzymes (ArMs) are hybrid catalysts that offer a unique opportunity to combine the superior performance of natural protein structures with the unnatural reactivity of transition-metal catalytic centers. Therefore, they provide the prospect of highly selective and active catalytic chemical conversions for which natural enzymes are unavailable. Herein, we show how by rationally combining robust site-specific phosphine bioconjugation methods and a lipid-binding protein (SCP-2L), an artificial rhodium hydroformylase was developed that displays remarkable activities and selectivities for the biphasic production of long-chain linear aldehydes under benign aqueous conditions. Overall, this study demonstrates that judiciously chosen protein-binding scaffolds can be adapted to obtain metalloenzymes that provide the reactivity of the introduced metal center combined with specifically intended product selectivity.

Bioinspired catalyst design and artificial metalloenzymes.

Many bioinspired transition-metal catalysts have been developed over the recent years. In this review the progress in the design and application of ligand systems based on peptides and DNA and the development of artificial metalloenzymes are reviewed with a particular emphasis on the combination of phosphane ligands with powerful molecular recognition and shape selectivity of biomolecules. The various approaches for the assembly of these catalytic systems will be highlighted, and the possibilities that the use of the building blocks of Nature provide for catalyst optimisation strategies are discussed.

Synthesis of hybrid transition-metalloproteins via thiol-selective covalent anchoring of Rh-phosphine and Ru-phenanthroline complexes.

The preparation of hybrid transition metalloproteins by thiol-selective incorporation of organometallic rhodium- and ruthenium complexes is described. Phosphine ligands and two rhodium-diphosphine complexes bearing a carboxylic acid group were coupled to the cysteine of PYP R52G, yielding a metalloenzyme active in the rhodium catalyzed hydrogenation of dimethyl itaconate. The successful coupling was shown by (31)P NMR spectroscopy and ESI mass spectroscopy. In addition wild-type PYP (PYP WT), PYP R52G and ALBP were successfully modified with a (eta(6)-arene) ruthenium(II) phenanthroline complex via a maleimide linker.

The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool.

ArcBA is a two-component regulatory system of Escherichia coli involved in sensing oxygen availability and the concomitant transcriptional regulation of oxidative and fermentative catabolism. Based on in vitro data, it has been postulated that the redox state of the ubiquinone pool is the determinant for ArcB kinase activity. Here we report on the in vivo regulation of ArcB activation, as determined using a lacZ reporter specifically responsive to phosphorylated ArcA. Our results indicate that upon deletion of a ubiquinone biosynthetic enzyme, regulation of ArcB in the anaerobic-aerobic transition is not affected. In contrast, interference with menaquinone biosynthesis leads to inactivation of ArcB during anaerobic growth; this phenotype is fully rescued by addition of a menaquinone precursor. This clearly demonstrates that the menaquinones play a major role in ArcB activation. ArcB shows a complex pattern of regulation when E. coli is titrated through the entire aerobiosis range; ArcB is activated under anaerobic and subaerobic conditions and is much less active under fully aerobic and microaerobic conditions. Furthermore, there is no correlation between ArcB activation and the redox state of the ubiquinone pool, but there is a restricted correlation between the total cellular ubiquinone content and ArcB activity due to the considerable increase in the size of the ubiquinone pool with increasing degrees of aerobiosis. These results lead to the working hypothesis that the in vivo activity of ArcB in E. coli is modulated by the redox state of the menaquinone pool and that the ubiquinone/ubiquinol ratio in vivo surely is not the only determinant of ArcB activity.

Energetics and role of the hydrophobic interaction during photoreaction of the BLUF domain of AppA.

A recently developed method for time-resolved thermodynamic measurements was used to study the photochemical reaction(s) of the BLUF domain of AppA (AppA-BLUF), which has a dimeric form in the ground state, in terms of the energetics and heat capacity changes (DeltaC(p)) in different time domains. The enthalpy change (DeltaH) of the first intermediate that forms within 1 ns after photoexcitation was 38 (+/-8) kJ mol(-1) at 298 K. The heat capacity change (DeltaC(p)) upon formation of this intermediate was positive [1.4 (+/-0.3) kJ mol(-1) K(-1)]. This positive DeltaC(p) suggests that the hydrophobic surface area of AppA-BLUF exposed to the bulk solvent increased. After this initial transition, a dimerization reaction with another ground-state dimer (i.e., tetramer formation) takes place. Upon this reaction, the energy was stabilized to 26 (+/-6) kJ mol(-1) at 298 K. Interestingly, the dimer formation was accompanied by a larger but negative DeltaC(p) [-6.0 (+/-1) kJ mol(-1) K(-1)]. This negative DeltaC(p) might indicate buried hydrophobic residues at the interface of the dimer and/or the existence of trapped water at the interface. We suggest that hydrophobic interactions are the main driving force for the formation of the dimer upon photoactivation of AppA-BLUF.

On the role of aromatic side chains in the photoactivation of BLUF domains.

BLUF (blue-light sensing using FAD) domain proteins are a novel group of blue-light sensing receptors found in many microorganisms. The role of the aromatic side chains Y21 and W104, which are in close vicinity to the FAD cofactor in the AppA BLUF domain from Rhodobacter sphaeroides, is investigated through the introduction of several amino acid substitutions at these positions. NMR spectroscopy indicated that in the W104F mutant, the local structure of the FAD binding pocket was not significantly perturbed as compared to that of the wild type. Time-resolved fluorescence and absorption spectroscopy was applied to explore the role of Y21 and W104 in AppA BLUF photochemistry. In the Y21 mutants, FADH*-W* radical pairs are transiently formed on a ps time scale and recombine to the ground state on a ns time scale. The W104F mutant shows a spectral evolution similar to that of wild type AppA but with an increased yield of signaling state formation. In the Y21F/W104F double mutant, all light-driven electron-transfer processes are abolished, and the FAD singlet excited-state evolves by intersystem crossing to the triplet state. Our results indicate that two competing light-driven electron-transfer pathways are available in BLUF domains: one productive pathway that involves electron transfer from the tyrosine, which leads to signaling state formation, and one nonproductive electron-transfer pathway from the tryptophan, which leads to deactivation and the effective lowering of the quantum yield of the signaling state formation. Our results are consistent with a photoactivation mechanism for BLUF domains where signaling state formation proceeds via light-driven electron and proton transfer from the conserved tyrosine to FAD, followed by a hydrogen-bond rearrangement and radical-pair recombination.

Tetramer formation kinetics in the signaling state of AppA monitored by time-resolved diffusion.

The photoreaction kinetics of the BLUF domain of AppA(5-125) was studied by monitoring time-dependence of an apparent diffusion coefficient (D) using the pulsed laser-induced transient grating technique. It was found that D of the photoproduct is time-dependent. From the concentration dependence of the reaction rate, it was concluded that the BLUF domain of AppA forms a dimer upon the photoexcitation. Since AppA exists as a dimeric form in the ground state, this dimerization reaction indicates the tetramer formation in the signaling state. From the slope of the plot of observed rate constants (k(obs)) against the AppA concentration, the second order rate constant is determined to be approximately 2.5 x 10(5) M(-1) s(-1), which is approximately 4 orders in magnitude lower than the diffusion controlled reaction. It indicates that a relative orientation of the protein molecules during the dimerization process causes additional constraints, which slow down the reaction rate.

On the mechanism of activation of the BLUF domain of AppA.

AppA, a transcriptional antirepressor, regulates the steady expression of photosynthesis genes in Rhodobacter sphaeroides in response to high-intensity blue light and to redox signals. Its blue-light sensing is mediated by an N-terminal BLUF domain, a member of a novel flavin fold. The photocycle of this domain (AppA(5-125)) includes formation of a slightly red-shifted long-lived signaling state, which is formed directly from the singlet excited state of the flavin on a subnanosecond time scale [Gauden et al. (2005) Biochemistry 44, 3653-3662]. The red shift of the absorption spectrum of this signaling state has been attributed to a rearrangement of its hydrogen-bonding interactions with the surrounding apoprotein. In this study we have characterized an AppA mutant with an altered aromatic amino acid: W104F. This mutant exhibits an increased lifetime of the singlet excited state of the flavin chromophore. Most strikingly, however, it shows a 1.5-fold increase in its quantum yield of signaling state formation. In addition, it shows a slightly increased rate of ground-state recovery. On top of this, the presence of imidazole, both in this mutant protein and in the wild-type BLUF domain, significantly accelerates the rate of ground-state recovery, suggesting that this rate is limited by rearrangement of (a) hydrogen bond(s). In total, an approximately 700-fold increase in recovery rate has been obtained, which makes the W104F BLUF domain of AppA, for example, suitable for future analyses with step-scan FTIR. The rate of ground-state recovery of the BLUF domain of AppA follows Arrhenius kinetics. This suggests that this domain itself does not undergo large structural changes upon illumination and that the structural transitions in full-length AppA are dominated by interdomain rearrangements.

The solution structure of the AppA BLUF domain: insight into the mechanism of light-induced signaling.

The transcriptional antirepressor AppA from the photosynthetic bacterium Rhodobacter sphaeroides senses both the light climate and the intracellular redox state. Under aerobic conditions in the dark, AppA binds to and thereby blocks the function of PpsR, a transcriptional repressor. Absorption of a blue photon dissociates AppA from PpsR and allows the latter to repress photosynthesis gene expression. The N terminus of AppA contains sequence homology to flavin-containing photoreceptors that belong to the BLUF family. Structural and chemical aspects of signal transduction mediated by AppA are still largely unknown. Here we present NMR studies of the N-terminal flavin-binding BLUF domain of AppA. Its solution structure adopts an alpha/beta-sandwich fold with a beta alpha beta beta alpha beta beta topology, which represents a new flavin-binding fold. Considerable disorder is observed for residues near the chromophore due to conformational exchange. This disorder is observed both in the dark and in the light-induced signaling state of AppA. Furthermore, we detect light-induced structural changes in a patch of surface residues that provide a structural link between light absorption and signal-transduction events.

Photocycle of the flavin-binding photoreceptor AppA, a bacterial transcriptional antirepressor of photosynthesis genes.

The flavoprotein AppA from Rhodobacter sphaeroides contains an N-terminal domain belonging to a new class of photoreceptors designated BLUF domains. AppA was shown to control photosynthesis gene expression in response to blue light and oxygen tension. We have investigated the photocycle of the AppA BLUF domain by ultrafast fluorescence, femtosecond transient absorption, and nanosecond flash-photolysis spectroscopy. Time-resolved fluorescence experiments revealed four components of flavin adenine dinucleotide (FAD) excited-state decay, with lifetimes of 25 ps, 150 ps, 670 ps, and 3.8 ns. Ultrafast transient absorption spectroscopy revealed rapid internal conversion and vibrational cooling processes on excited FAD with time constants of 250 fs and 1.2 ps, and a multiexponential decay with effective time constants of 90 ps, 590 ps, and 2.7 ns. Concomitant with the decay of excited FAD, the rise of a species with a narrow absorption difference band near 495 nm was detected which spectrally resembles the long-living signaling state of AppA. Consistent with these results, the nanosecond flash-photolysis measurements indicated that formation of the signaling state was complete within the time resolution of 10 ns. No further changes were detected up to 15 micros. The quantum yield of the signaling-state formation was determined to be 24%. Thus, the signaling state of the AppA BLUF domain is formed on the ultrafast time scale directly from the FAD singlet excited state, without any apparent intermediate, and remains stable over 12 decades of time. In parallel with the signaling state, the FAD triplet state is formed from the FAD singlet excited state at 9% efficiency as a side reaction of the AppA photocycle.

Chromophore composition of a heterologously expressed BLUF-domain.

Upon heterologous expression of the BLUF (for: Blue-Light sensing Using Flavin) domain from AppA, a transcriptional anti-repressor from Rhodobacter sphaeroides, in Escherichia coli, photoactive holo-protein is formed through non-covalent binding of a flavin. Whereas it is generally assumed that FAD is the physiological chromophore of this photo-perception domain in vivo, E. coli can (and does) insert, depending on the growth conditions, all naturally occurring flavins, i.e. riboflavin, FMN and FAD into this protein domain. The nature of the particular flavin bound affects the photochemical- and particularly the fluorescence properties of the N-terminal domain of this photosensory protein.

Initial characterization of the primary photochemistry of AppA, a blue-light-using flavin adenine dinucleotide-domain containing transcriptional antirepressor protein from Rhodobacter sphaeroides: a key role for reversible intramolecular proton transfer from the flavin adenine dinucleotide chromophore to a conserved tyrosine?

The flavin adenine dinucleotide (FAD)-containing photoreceptor protein AppA (in which the FAD is bound to a novel so-called BLUF domain) from the purple nonsulfur bacterium Rhodobacter sphaeroides was previously shown to be photoactive by the formation of a slightly redshifted long-lived intermediate that is thought to be the signaling state. In this study, we provide further characterization of the primary photochemistry of this photoreceptor protein using UV-Vis and Fourier-transform infrared spectroscopy, pH measurements and site-directed mutagenesis. Available evidence indicates that the FAD chromophore of AppA may be protonated in the receptor state, and that it becomes exposed to solvent in the signaling state. Furthermore, experimental data lead to the suggestion that intramolecular proton transfer (that may involve [anionic] Tyr-17) forms the basis for the stabilization of the signaling state.