Optimized precursor to simplify assignment transfer between backbone resonances and stereospecifically labelled valine and leucine methyl groups: application to human Hsp90 N-terminal domain.

Methyl moieties are highly valuable probes for quantitative NMR studies of large proteins. Hence, their assignment is of the utmost interest to obtain information on both interactions and dynamics of proteins in solution. Here, we present the synthesis of a new precursor that allows connection of leucine and valine pro-S methyl moieties to backbone atoms by linear 13C-chains. This optimized 2H/13C-labelled acetolactate precursor can be combined with existing 13C/2H-alanine and isoleucine precursors in order to directly transfer backbone assignment to the corresponding methyl groups. Using this simple approach leucine and valine pro-S methyl groups can be assigned using a single sample without requiring correction of 1H/2H isotopic shifts on 13C resonances. The approach was demonstrated on the N-terminal domain of human HSP90, for which complete assignment of Ala-ß, Ile-δ1, Leu-δ2, Met-ε, Thr-γ and Val-γ2 methyl groups was obtained.

Hybrid Amyloid-Based Redox Hydrogel for Bioelectrocatalytic H2 Oxidation.

An artificial amyloid-based redox hydrogel was designed for mediating electron transfer between a [NiFeSe] hydrogenase and an electrode. Starting from a mutated prion-forming domain of fungal protein HET-s, a hybrid redox protein containing a single benzyl methyl viologen moiety was synthesized. This protein was able to self-assemble into structurally homogenous nanofibrils. Molecular modeling confirmed that the redox groups are aligned along the fibril axis and are tethered to its core by a long, flexible polypeptide chain that allows close encounters between the fibril-bound oxidized or reduced redox groups. Redox hydrogel films capable of immobilizing the hydrogenase under mild conditions at the surface of carbon electrodes were obtained by a simple pH jump. In this way, bioelectrodes for the electrocatalytic oxidation of H2 were fabricated that afforded catalytic current densities of up to 270 µA cm-2 , with an overpotential of 0.33 V, under quiescent conditions at 45 °C.

CH3-specific NMR assignment of alanine, isoleucine, leucine and valine methyl groups in high molecular weight proteins using a single sample.

A new strategy for the NMR assignment of aliphatic side-chains in large perdeuterated proteins is proposed. It involves an alternative isotopic labeling protocol, the use of an out-and-back (13)C-(13)C TOCSY experiment ((H)C-TOCSY-C-TOCSY-(C)H) and an optimized non-uniform sampling protocol. It has long been known that the non-linearity of an aliphatic spin-system (for example Ile, Val, or Leu) substantially compromises the efficiency of the TOCSY transfers. To permit the use of this efficient pulse scheme, a series of optimized precursors were designed to yield linear (13)C perdeuterated side-chains with a single protonated CH3 group in these three residues. These precursors were added to the culture medium for incorporation into expressed proteins. For Val and Leu residues, the topologically different spin-systems introduced for the pro-R and pro-S methyl groups enable stereospecific assignment. All CH3 can be simultaneously assigned on a single sample using a TOCSY experiment. It only requires the tuning of a mixing delay and is thus more versatile than the relayed COSY experiment. Enhanced resolution and sensi-tivity can be achieved by non-uniform sampling combined with the removal of the large JCC coupling by deconvolution prior to the processing by iterative soft thresholding. This strategy has been used on malate synthase G where a large percentage of the CH3 groups could be correlated directly up to the backbone Ca. It is anticipated that this robust combined strategy can be routinely applied to large proteins.

Scrambling free combinatorial labeling of alanine-ß, isoleucine-δ1, leucine-proS and valine-proS methyl groups for the detection of long range NOEs.

Specific isotopic labeling of methyl groups in proteins has greatly extended the applicability of solution NMR spectroscopy. Simultaneous labeling of the methyl groups of several different amino acid types can offer a larger number of useful probes that can be used for structural characterisations of challenging proteins. Herein, we propose an improved AILV methyl-labeling protocol in which L and V are stereo-specifically labeled. We show that 2-ketobutyrate cannot be combined with Ala and 2-acetolactate (for the stereo-specific labeling of L and V) as this results in co-incorporation incompatibility and isotopic scrambling. Thus, we developed a robust and cost-effective enzymatic synthesis of the isoleucine precursor, 2-hydroxy-2-(1'-[(2)H2], 2'-[(13)C])ethyl-3-keto-4-[(2)H3]butanoic acid, as well as an incorporation protocol that eliminates metabolic leakage. We show that application of this labeling scheme to a large 82 kDa protein permits the detection of long-range (1)H-(1)H NOE cross-peaks between methyl probes separated by up to 10 Å.

A Ruthenium(II)-Copper(II) Dyad for the Photocatalytic Oxygenation of Organic Substrates Mediated by Dioxygen Activation.

Dioxygen activation by copper complexes is a valuable method to achieve oxidation reactions for sustainable chemistry. The development of a catalytic system requires regeneration of the Cu(I) active redox state from Cu(II). This is usually achieved using extra reducers that can compete with the Cu(II)(O2) oxidizing species, causing a loss of efficiency. An alternative would consist of using a photosensitizer to control the reduction process. Association of a Ru(II) photosensitizing subunit with a Cu(II) pre-catalytic moiety assembled within a unique entity is shown to fulfill these requirements. In presence of a sacrificial electron donor and light, electron transfer occurs from the Ru(II) center to Cu(II). In presence of dioxygen, this dyad proved to be efficient for sulfide, phosphine, and alkene catalytic oxygenation. Mechanistic investigations gave evidence about a predominant (3)O2 activation pathway by the Cu(I) moiety.

ubiI, a new gene in Escherichia coli coenzyme Q biosynthesis, is involved in aerobic C5-hydroxylation.

Coenzyme Q (ubiquinone or Q) is a redox-active lipid found in organisms ranging from bacteria to mammals in which it plays a crucial role in energy-generating processes. Q biosynthesis is a complex pathway that involves multiple proteins. In this work, we show that the uncharacterized conserved visC gene is involved in Q biosynthesis in Escherichia coli, and we have renamed it ubiI. Based on genetic and biochemical experiments, we establish that the UbiI protein functions in the C5-hydroxylation reaction. A strain deficient in ubiI has a low level of Q and accumulates a compound derived from the Q biosynthetic pathway, which we purified and characterized. We also demonstrate that UbiI is only implicated in aerobic Q biosynthesis and that an alternative enzyme catalyzes the C5-hydroxylation reaction in the absence of oxygen. We have solved the crystal structure of a truncated form of UbiI. This structure shares many features with the canonical FAD-dependent para-hydroxybenzoate hydroxylase and represents the first structural characterization of a monooxygenase involved in Q biosynthesis. Site-directed mutagenesis confirms that residues of the flavin binding pocket of UbiI are important for activity. With our identification of UbiI, the three monooxygenases necessary for aerobic Q biosynthesis in E. coli are known.

Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins.

The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D2O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d10. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.

Photocatalyzed sulfide oxygenation with water as the unique oxygen atom source.

In our research program aiming to develop new ruthenium-based polypyridine catalysts for oxidation we were interested in combining a photosensitizer and a catalytic fragment within the same complex to achieve catalytic light-driven oxidation. To respond to the lack of such conjugates, we report here a new catalytic system capable of using light to activate water molecules in order to perform selective sulfide oxygenation into sulfoxide via an oxygen atom transfer from H(2)O to the substrate with a TON of up to 197 ± 6. On the basis of electrochemical and photophysical studies, a proton-coupled electron-transfer process yielding to an oxidant Ru(IV)-oxo species was proposed. In particular, the synergistic effect between both partners in the dyad yielding a more efficient catalyst compared to the bimolecular system is highlighted.

Studies of inhibitor binding to the [4Fe-4S] cluster of quinolinate synthase.

Stop for NadA! A [4Fe-4S] enzyme, NadA, catalyzes the formation of quinolinic acid in de novo nicotinamide adenine dinucleotide (NAD) biosynthesis. A structural analogue of an intermediate, 4,5-dithiohydroxyphthalic acid (DTHPA), has an in vivo NAD biosynthesis inhibiting activity in E. coli. The inhibitory effect can be explained by the coordination of DTHPA thiolate groups to a unique Fe site of the NadA [4Fe-4S] cluster.

A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins.

A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[(13)C]glucose and subsaturating amounts of 2-[(13)C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional (1)H-(13)C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.

A dyad as photocatalyst for light-driven sulfide oxygenation with water as the unique oxygen atom source.

With the objective to convert light energy into chemical oxidation energy, a ruthenium-based dyad constituted of the assembly of a photosensitizer and a catalytic fragment was synthesized. Upon irradiation with blue LEDs, and in the presence of an electron acceptor, the complex is able to catalyze selective sulfide oxygenation involving an oxygen atom transfer from water to the substrate. Electrochemical and photophysical studies highlighted a proton-coupled electron transfer (PCET) to access to a high valent oxidant Ru(IV) oxo species.

LEAFY protein crystals with a honeycomb structure as a platform for selective preparation of outstanding stable bio-hybrid materials.

Well-organized protein assemblies offer many properties that justify their use for the design of innovative bionanomaterials. Herein, crystals of the oligomerization domain of the LEAFY protein from Ginkgo biloba, organized in a honeycomb architecture, were used as a modular platform for the selective grafting of a ruthenium-based complex. The resulting bio-hybrid crystalline material was fully characterized by UV-visible and Raman spectroscopy and by mass spectrometry and LC-MS analysis after selective enzymatic digestion. Interestingly, insertion of complexes within the tubular structure affords an impressive increase in stability of the crystals, eluding the use of stabilizing cross-linking strategies.

Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination.

Quinolinate synthase (NadA) is a [4Fe-4S] cluster-containing enzyme involved in the formation of quinolinic acid, the precursor of the essential NAD coenzyme. Here, we report the synthesis and activity of derivatives of the first inhibitor of NadA. Using multidisciplinary approaches we have investigated their action mechanism and discovered additional specific inhibitors of this enzyme.

New polydentate ligand and catalytic properties of the corresponding ruthenium complex during sulfoxidation and alkene epoxidation.

Bis(diimine)-ruthenium complexes constitute a class of catalysts with good activity for oxidation reactions, such as sulfoxidation and epoxidation. The synthesis and the full characterization of a new ruthenium complex bearing an original pentadentate ligand (L5pyr for 2,6-bis-(6-ethyl-2,2'-bipyridyl)-pyridine) is reported. Comparison of its activity with regard to[Ru(bpy)2(CH3CN)2](2+) and [Ru(bpy)2(py)(CH3CN)](2+) during alkene and sulfide oxidation allowed us to conclude that the addition of a fifth pyridine ligand in the coordination sphere improves the efficiency of the catalyst. Moreover, under these oxidation conditions a hydroxylation of the ligand L5pyr led to a better activity than its analogue [Ru(bpy)2(py)(CH3CN)](2+), especially during epoxidation of alkenes by PhI(OAc)2.

Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA.

NadA is a multifunctional enzyme that condenses dihydroxyacetone phosphate (DHAP) with iminoaspartate (IA) to generate quinolinic acid (QA), the universal precursor of the nicotinamide adenine dinucleotide (NAD(P)) cofactor. Using X-ray crystallography, we have (i) characterized two of the reaction intermediates of QA synthesis using a "pH-shift" approach and a slowly reacting Thermotoga maritima NadA variant and (ii) observed the QA product, resulting from the degradation of an intermediate analogue, bound close to the entrance of a long tunnel leading to the solvent medium. We have also used molecular docking to propose a condensation mechanism between DHAP and IA based on two previously published Pyrococcus horikoshi NadA structures. The combination of reported data and our new results provide a structure-based complete catalytic sequence of QA synthesis by NadA.

An optimized isotopic labelling strategy of isoleucine-γ2 methyl groups for solution NMR studies of high molecular weight proteins.

An efficient synthetic route is proposed to produce 2-hydroxy-2-ethyl-3-oxobutanoate for the specific labelling of Ile methyl-γ(2) groups in proteins. The (2)H, (13)C-pattern of the biosynthetic precursor has been designed to optimize magnetization transfer, in large proteins, between these important structural probes and their corresponding backbone nuclei.

Synthesis, electrochemical and photophysical properties of heterodinuclear Ru-Mn and Ru-Zn complexes bearing ambident Schiff base ligand.

While ruthenium tris(diimine) complexes have been extensively studied, this is not the case with ruthenium bis(diimine)X(2) complexes where X represents a pyridinyl-based ligand. The synthesis of a new complex ([2][PF(6)](2)) bearing two ambident Schiff base ligands (HL) constituted by the assembly of phenol and pyridinyl moieties is reported. Thanks to the heteroditopic property of HL, compound [2](2+) was used as an original metalloligand for the coordination of a redox-active (Mn(III)) and redox-inactive (Zn(II)) second metal cation affording three heterodinuclear complexes, namely, [(bpy)(2)Ru(2)Mn(acac)][PF(6)](2) ([3][PF(6)](2); acac = acetylacetonate), [(bpy)(2)Ru(2)Mn(OAc)][PF(6)](2) ([4][PF(6)](2), OAc = acetate), and [(bpy)(2)Ru(2)Zn][PF(6)](2) ([5][PF(6)](2)). The influence of the second metal with regard to the photophysical and electrochemical properties of the ruthenium bis(diimine)X(2) subunit was then investigated. In the case of Ru(II)-Mn(III) heterodinuclear complexes, a partial quenching of the luminescence was observed as a consequence of an efficient electron transfer process from the ruthenium to the manganese. EPR and spectrophotometric analyses of the oxidized species resulting from the one-electron oxidation of compounds [3](2+) and [4](2+) showed the formation of a Mn(IV) species for [3](2+) and an organic free radical for [4](2+).

Involvement of mitochondrial ferredoxin and para-aminobenzoic acid in yeast coenzyme Q biosynthesis.

Yeast ubiquinone or coenzyme Q(6) (Q(6)) is a redox active lipid that plays a crucial role in the mitochondrial electron transport chain. At least nine proteins (Coq1p-9p) participate in Q(6) biosynthesis from 4-hydroxybenzoate (4-HB). We now show that the mitochondrial ferredoxin Yah1p and the ferredoxin reductase Arh1p are required for Q(6) biosynthesis, probably for the first hydroxylation of the pathway. Conditional Gal-YAH1 and Gal-ARH1 mutants accumulate 3-hexaprenyl-4-hydroxyphenol and 3-hexaprenyl-4-aminophenol. Para-aminobenzoic acid (pABA) is shown to be the precursor of 3-hexaprenyl-4-aminophenol and to compete with 4-HB for the prenylation reaction catalyzed by Coq2p. Yeast cells convert U-((13)C)-pABA into (13)C ring-labeled Q(6), a result that identifies pABA as a new precursor of Q(6) and implies an additional NH(2)-to-OH conversion in Q(6) biosynthesis. Our study identifies pABA, Yah1p, and Arh1p as three actors in Q(6) biosynthesis.