The Mycobacterium tuberculosis Rv2540c DNA sequence encodes a bifunctional chorismate synthase

Background. The emergence of multi- and extensively-drug resistant Mycobacterium tuberculosis strains has created an urgent need for new agents to treat tuberculosis (TB). The enzymes of shikimate pathway are attractive targets to the development of antitubercular agents because it is essential for M. tuberculosis and is absent from humans. Chorismate synthase (CS) is the seventh enzyme of this route and catalyzes the NADH- and FMN-dependent synthesis of chorismate, a precursor of aromatic amino acids, naphthoquinones, menaquinones, and mycobactins. Although the M. tuberculosis Rv2540c (aroF) sequence has been annotated to encode a chorismate synthase, there has been no report on its correct assignment and functional characterization of its protein product. Results. In the present work, we describe DNA amplification of aroF-encoded CS from M. tuberculosis (MtCS), molecular cloning, protein expression, and purification to homogeneity. N-terminal amino acid sequencing, mass spectrometry and gel filtration chromatography were employed to determine identity, subunit molecular weight and oligomeric state in solution of homogeneous recombinant MtCS. The bifunctionality of MtCS was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. The flavin reductase activity was characterized, showing the existence of a complex between FMN ox and MtCS. FMNox and NADH equilibrium binding was measured. Primary deuterium, solvent and multiple kinetic isotope effects are described and suggest distinct steps for hydride and proton transfers, with the former being more rate-limiting. Conclusion. This is the first report showing that a bacterial CS is bifunctional. Primary deuterium kinetic isotope effects show that C4-proS hydrogen is being transferred during the reduction of FMNox by NADH and that hydride transfer contributes significantly to the rate-limiting step of FMN reduction reaction. Solvent kinetic isotope effects and proton inventory results indicate that proton transfer from solvent partially limits the rate of FMN reduction and that a single proton transfer gives rise to the observed solvent isotope effect. Multiple isotope effects suggest a stepwise mechanism for the reduction of FMNox. The results on enzyme kinetics described here provide evidence for the mode of action of MtCS and should thus pave the way for the rational design of antitubercular agents. © 2008 Ely et al; licensee BioMed Central Ltd.

On the Deactivation Mechanisms of Adenine-Thymine Base Pair

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

Exploring the intrinsic polar [4?+?2+] cycloaddition reactivity of gaseous carbosulfonium and carboxonium ions

Gas-phase reactions of model carbosulfonium ions (CH3-S+?=?CH2; CH3CH2-S+?=?CH2 and Ph-S+?=?CH2) and an O-analogue carboxonium ion (CH3-O+?=?CH2) with acyclic (isoprene, 1,3-butadiene, methyl vinyl ketone) and cyclic (1,3-cyclohexadiene, thiophene, furan) conjugated dienes were systematically investigated by pentaquadrupole mass spectrometry. As corroborated by B3LYP/6-311?G(d,p) calculations, the carbosulfonium ions first react at large extents with the dienes forming adducts via simple addition. The nascent adducts, depending on their stability and internal energy, react further via two competitive channels: (1) in reactions with acyclic dienes via cyclization that yields formally [4?+?2+] cycloadducts, or (2) in reactions with the cyclic dienes via dissociation by HSR loss that yields methylenation (net CH+ transfer) products. In great contrast to its S-analogues, CH3-O+?=?CH2 (as well as C2H5-O+?=?CH2 and Ph-O+?=?CH2 in reactions with isoprene) forms little or no adduct and proton transfer is the dominant reaction channel. Isomerization to more acidic protonated aldehydes in the course of reaction seems to be the most plausible cause of the contrasting reactivity of carboxonium ions. The CH2?=?CH-O+?=?CH2 ion forms an abundant [4?+?2+] cycloadduct with isoprene, but similar to the behavior of such alpha,beta-unsaturated carboxonium ions in solution, seems to occur across the C?=?C bond. Copyright (c) 2012 John Wiley & Sons, Ltd.

Phosphonic acid-containing molecules as proton conductors and linkers for hybrid materials

In dieser Arbeit werden zwei Arten von nicht-kovalent verknüpften Netzwerkstrukturen vorgestellt, die aus phosphonsäurehaltigen Molekülen aufgebaut sind. Einerseits sollen diese phosphonsäurehaltigen Moleküle als Protonenleiter in Brennstoffzellen eingesetzt werden. Dies ist durch die Möglichkeit des kooperativen Protonentransports in wasserstoffbrückenhaltigen Netzwerken begründet. Auf der anderen Seite sollen die phosphonsäurehaltigen Moleküle unter Einsatz von Metallkationen zur Darstellung ionischer Netzwerke verwendet werden. In diesem Fall fungieren die phosphonierten Moleküle als Linker in porösen organisch-anorganischen Hybridmaterialien, die sich beispielsweise zur Gasspeicherung eignen.rnEine Brennstoffzelle stellt Energie mit hoher Effizienz und geringer Umweltbelastung bereit. Das Herzstück der Brennstoffzelle ist die Elektrolytmembran, die auch als Separator oder Protonenaustauschmembran (PEM) bezeichnet wird. Es wird davon ausgegangen, daß der Schlüssel zur Weiterentwicklung der PEM-Brennstoffzellen in der Entwicklung von Elektrolyten liegt, die ausschließlich und effizient Protonen transportieren und darüber hinaus chemisch (oxidationsbeständig) und mechanisch stabil sind. Die mechanische Stabilität betrifft insbesondere den Betrieb der Brennstoffzelle bei hohen Temperaturen und niedriger relativer Feuchtigkeit. In dieser Arbeit wird ein neuartiger Ansatz zum Erreichen eines hohen Protonentransports im Festkörper vorgestellt, der auf dem Einsatz kleiner Moleküle beruht, die durch Selbstorganisation eine kontinuierliche protonenleitende Phase erzeugen. Bis jetzt stellt Hexakis(p-phosphonatophenyl)benzol das erste Beispiel eines kristallinen Protonenleiters dar, der im festen Zustand eine hohe und konstante Leistung zeigt. Die Modifizierung von Hexakis(p-phosphonatophenyl)benzol, entweder durch Änderung von para- zu meta-Substitution oder die Einführung von Alkylketten, führt zu Verbindungen geringerer Kristallinität und niedriger Protonenleitfähigkeit.rnIm zweiten Teil der Arbeit wurde 1,3,5-Tris(p-phosphonatophenyl)benzol als Linker in der Synthese von offenen Phosphonat-Netzwerken eingesetzt. Es bilden sich aufgrund der ionischen Wechselwirkung zwischen den positiv geladenen Metallkationen und den negativ geladenen Phosphonsäuregruppen hochstabile Feststoffe. Eines der wichtigsten Ergebnisse dieser Arbeit besteht darin, daß 1,3,5-Tris(p-phosphonatophenyl)benzol als Linker zum Aufbau poröser Hybridmaterialien eingesetzt werden kann. Zum ersten Mal wurde ein dreifach phosphoniertes organisches Molekül zum Aufbau mikroporöser offener Phosphonat-Netzwerke verwendet. Zudem konnte gezeigt werden, daß die Porosität mit dem Wachstumsmechanismus dieser Materialien zusammenhängt. Es ist nur dann möglich ein gleichfalls mikroporöses und kristallines ionisches Netzwerk auf der Grundlage phosphonierter Moleküle zu erhalten, wenn Linker und Konnektor die gleiche Geometrie und Funktionalität besitzen.rn

Effects of sources and meteorology on particulate matter in the Western Mediterranean Basin: An overview of the DAURE campaign

DAURE (Determination of the Sources of Atmospheric Aerosols in Urban and Rural Environments in the Western Mediterranean) was a multidisciplinary international field campaign aimed at investigating the sources and meteorological controls of particulate matter in the Western Mediterranean Basin (WMB). Measurements were simultaneously performed at an urban-coastal (Barcelona, BCN) and a rural-elevated (Montseny, MSY) site pair in NE Spain during winter and summer. State-of-the-art methods such as 14C analysis, proton-transfer reaction mass spectrometry, and high-resolution aerosol mass spectrometry were applied for the first time in the WMB as part of DAURE. WMB regional pollution episodes were associated with high concentrations of inorganic and organic species formed during the transport to inland areas and built up at regional scales. Winter pollutants accumulation depended on the degree of regional stagnation of an air mass under anticyclonic conditions and the planetary boundary layer height. In summer, regional recirculation and biogenic secondary organic aerosols (SOA) formation mainly determined the regional pollutant concentrations. The contribution from fossil sources to organic carbon (OC) and elemental carbon (EC) and hydrocarbon-like organic aerosol concentrations were higher at BCN compared with MSY due to traffic emissions. The relative contribution of nonfossil OC was higher at MSY especially in summer due to biogenic emissions. The fossil OC/EC ratio at MSY was twice the corresponding ratio at BCN indicating that a substantial fraction of fossil OC was due to fossil SOA. In winter, BCN cooking emissions were identified as an important source of modern carbon in primary organic aerosol.

Qualitative Distinction of Autotrophic and Heterotrophic Processes at the Leaf Level by Means of Triple Stable Isotope (C–O–H) Patterns

Foliar samples were harvested from two oaks, a beech, and a yew at the same site in order to trace the development of the leaves over an entire vegetation season. Cellulose yield and stable isotopic compositions (δ13C, δ18O, and δD) were analyzed on leaf cellulose. All parameters unequivocally define a juvenile and a mature period in the foliar expansion of each species. The accompanying shifts of the δ13C-values are in agreement with the transition from remobilized carbohydrates (juvenile period), to current photosynthates (mature phase). While the opponent seasonal trends of δ18O of blade and vein cellulose are in perfect agreement with the state-of-art mechanistic understanding, the lack of this discrepancy for δD, documented for the first time, is unexpected. For example, the offset range of 18 permil (oak veins) to 57 permil (oak blades) in δD may represent a process driven shift from autotrophic to heterotrophic processes. The shared pattern between blade and vein found for both oak and beech suggests an overwhelming metabolic isotope effect on δD that might be accompanied by proton transfer linked to the Calvin-cycle. These results provide strong evidence that hydrogen and oxygen are under different biochemical controls even at the leaf level.

Highly stereoselective decarboxylation of (+)-1-Bromo-1-chloro-2,2,2-trifluoropropanoic acid gives (+)-1-Bromo-1-chloro-2,2,2-trifluoroethane ((+)-Halothane) with retention of configuration

The absolute configuration of the title acid (2) has been determined to be S by X-ray crystallography. Thus, decarboxylation of 2 produces (S)-(+)-halothane with 99% retention of configuration. This behavior is compared to other stereoselective decarboxylation reactions of ?-haloacids from the literature that also give high degrees of retention of configuration when in the form of their quaternary ammonium salts, which contain one proton. The proton of the ammonium salt is necessary to protonate the anionic intermediate formed from decarboxylation. In the absence of this relatively acidic proton, we had previously found that using triethylene glycol (TEG) as both solvent and proton source for the decarboxylation reaction of acid 2 caused poor stereoselectivity. This was in contrast to 1,2,2,2-tetrafluoro-1-methoxypropionic acid (6), which showed a high degree of retention of configuration in TEG. To rationalize this differing behavior we report DFT studies at PCM-B3LYP/6-31++G** level of theory (the results were additionally confirmed with 6-311++G** and aug-cc-pVDZ basis sets). The energy barrier to inversion of configuration of the anionic reaction intermediate of acid 2 (11) is 10.23 kcal/mol. However, we find that the anionic intermediate from acid 6 (10) would rather undergo ?-elimination instead of inversion of configuration. Thus the planar transition state required for inversion of configuration is never reached, regardless of the rate of proton transfer to the anion.

Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy

We have investigated the pH dependence of the dynamics of conformational fluctuations of green fluorescent protein mutants EGFP (F64L/S65T) and GFP-S65T in small ensembles of molecules in solution by using fluorescence correlation spectroscopy (FCS). FCS utilizes time-resolved measurements of fluctuations in the molecular fluorescence emission for determination of the intrinsic dynamics and thermodynamics of all processes that affect the fluorescence. Fluorescence excitation of a bulk solution of EGFP decreases to zero at low pH (pKa = 5.8) paralleled by a decrease of the absorption at 488 nm and an increase at 400 nm. Protonation of the hydroxyl group of Tyr-66, which is part of the chromophore, induces these changes. When FCS is used the fluctuations in the protonation state of the chromophore are time resolved. The autocorrelation function of fluorescence emission shows contributions from two chemical relaxation processes as well as diffusional concentration fluctuations. The time constant of the fast, pH-dependent chemical process decreases with pH from 300 μs at pH 7 to 45 μs at pH 5, while the time-average fraction of molecules in a nonfluorescent state increases to 80% in the same range. A second, pH-independent, process with a time constant of 340 μs and an associated fraction of 13% nonfluorescent molecules is observed between pH 8 and 11, possibly representing an internal proton transfer process and associated conformational rearrangements. The FCS data provide direct measures of the dynamics and the equilibrium properties of the protonation processes. Thus FCS is a convenient, intrinsically calibrated method for pH measurements in subfemtoliter volumes with nanomolar concentrations of EGFP.

Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II

Through the use of site-directed mutagenesis and chemical rescue, we have identified the proton acceptor for redox-active tyrosine D in photosystem II (PSII). Effects of chemical rescue on the tyrosyl radical were monitored by EPR spectroscopy. We also have acquired the Fourier–transform infrared (FT-IR) spectrum associated with the oxidation of tyrosine D and concomitant protonation of the acceptor. Mutant and isotopically labeled PSII samples are used to assign vibrational lines in the 3,600–3,100 cm−1 region to N-H modes of His-189 in the D2 polypeptide. When His-189 in D2 is changed to a leucine (HL189D2) in PSII, dramatic alterations of both EPR and FT-IR spectra are observed. When imidazole is introduced into HL189D2 samples, results from both EPR and FT-IR spectroscopy argue that imidazole is functionally reconstituted into an accessible pocket and that imidazole acts as a chemical mimic for His-189. Small perturbations of EPR and FT-IR spectra are consistent with access to this pocket in wild-type PSII, as well. Structures of the analogous site in bacterial reaction centers suggest that an accessible pocket, large enough to contain imidazole, is bordered by tyrosine D and His-189 in the D2 polypeptide. These data provide evidence that His-189 in the D2 polypeptide of PSII acts as a proton acceptor for redox-active tyrosine D and that proton transfer to the imidazole ring facilitates the efficient oxidation/reduction of tyrosine D.

Identification of the proton pathway in bacterial reaction centers: Both protons associated with reduction of QB to QBH2 share a common entry point

The reaction center from Rhodobacter sphaeroides uses light energy for the reduction and protonation of a quinone molecule, QB. This process involves the transfer of two protons from the aqueous solution to the protein-bound QB molecule. The second proton, H+(2), is supplied to QB by Glu-L212, an internal residue protonated in response to formation of QA− and QB−. In this work, the pathway for H+(2) to Glu-L212 was studied by measuring the effects of divalent metal ion binding on the protonation of Glu-L212, which was assayed by two types of processes. One was proton uptake from solution after the one-electron reduction of QA (DQA→D+QA−) and QB (DQB→D+QB−), studied by using pH-sensitive dyes. The other was the electron transfer kAB(1) (QA−QB→QAQB−). At pH 8.5, binding of Zn2+, Cd2+, or Ni2+ reduced the rates of proton uptake upon QA− and QB− formation as well as kAB(1) by ≈an order of magnitude, resulting in similar final values, indicating that there is a common rate-limiting step. Because D+QA− is formed 105-fold faster than the induced proton uptake, the observed rate decrease must be caused by an inhibition of the proton transfer. The Glu-L212→Gln mutant reaction centers displayed greatly reduced amplitudes of proton uptake and exhibited no changes in rates of proton uptake or electron transfer upon Zn2+ binding. Therefore, metal binding specifically decreased the rate of proton transfer to Glu-L212, because the observed rates were decreased only when proton uptake by Glu-L212 was required. The entry point for the second proton H+(2) was thus identified to be the same as for the first proton H+(1), close to the metal binding region Asp-H124, His-H126, and His-H128.

Conformations and folding of lysozyme ions in vacuo.

Proton transfer reactivity of isolated charge states of the protein hen egg-white lysozyme shows that multiple distinct conformations of this protein are stable in the gas phase. The reactivities of the 9+ and 10+ charge state ions, formed by electrospray ionization of "native" (disulfide-intact) and "denatured" (disulfide-reduced) solutions, are consistent with values calculated for ions in their crystal structure and fully denatured conformations, respectively. Charge states below 8+ of both forms, formed by proton stripping, have similar or indistinguishable reactivities, indicating that the disulfide-reduced ions fold in the gas phase to a more compact conformation.

Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction.

X-ray diffraction experiments revealed the structure of the N photointermediate of bacteriorhodopsin. Since the retinal Schiff base is reprotonated from Asp-96 during the M to N transition in the photocycle, and Asp-96 is reprotonated during the lifetime of the N intermediate, or immediately after, N is a key intermediate for understanding the light-driven proton pump. The N intermediate accumulates in large amounts during continuous illumination of the F171C mutant at pH 7 and 5 degrees Celsius. Small but significant changes of the structure were detected in the x-ray diffraction profile under these conditions. The changes were reversible and reproducible. The difference Fourier map indicates that the major change occurs near helix F. The observed diffraction changes between N and the original state were essentially identical to the diffraction changes reported for the M intermediate of the D96N mutant of bacteriorhodopsin. Thus, we find that the protein conformations of the M and N intermediates of the photocycle are essentially the same, in spite of the fact that in M the Schiff base is unprotonated and in N it is protonated. The observed structural change near helix F will increase access of the Schiff base and Asp-96 to the cytoplasmic surface and facilitate the proton transfer events that begin with the decay of the M state.

Photogenerated o-Azaxylylenes: Mechanistic Studies and Synthetic Applications

This research sets out to build upon excited state o-azaxylylene cycloaddition. The mechanism behind the excitation and cycloaddition process of photogenerated o-azaxylylenes was determined experimentally. Time-correlated single-photon counting, steady-state spectroscopy, triplet quenching experiments, and quantum yield studies provided evidence suggesting that excited state intramolecular proton transfer is followed by intersystem crossing and stepwise addition to the tethered unsaturated pendant. In keeping with the principles of diversity oriented synthesis, a modular approach was taken to gain access to a diverse array of N,O,S-Polyheterocycles which were modified postphotochemically via Suzuki coupling to yield fused biaryls. Cycloaddition products, outfitted with halogens in the aromatic ring of the o-azaxylylene, proved to be reactive with a variety of boronic acids resulting in a rapid growth in structural complexity. A novel procedure was developed that utilized multiple o-azaxylylene cores in a photochemical cascade transformation yielding complex scaffolds of unprecedented topology. The photoprecursors were produced in a one-pot two-step sequence from commercially available starting materials, and upon irradiation yield structures containing up to five fused hetrocyclic rings, and showed complete diastereoselectivity.

Mécanismes de transfert de proton d’une réaction acido-basique en phase aqueuse : une étude ab-initio

Les réactions de transfert de proton se retrouvent abondamment dans la nature et sont des processus cruciaux dans plusieurs réactions chimiques et biologiques, qui se produisent souvent en milieu aqueux. Les mécanismes régissant ces échanges de protons sont complexes et encore mal compris, suscitant un intérêt des chercheurs en vue d’une meilleure compréhension fondamentale du processus de transfert. Le présent manuscrit présente une étude mécanistique portant sur une réaction de transfert de proton entre un acide (phénol fonctionnalisé) et une base (ion carboxylate) en phase aqueuse. Les résultats obtenus sont basés sur un grand nombre de simulations de dynamique moléculaire ab-initio réalisées pour des systèmes de type « donneur-pont-accepteur », où le pont se trouve à être une unique molécule d’eau, permettant ainsi l’élaboration d’un modèle cinétique détaillé pour le système étudié. La voie de transfert principalement observée est un processus ultra-rapide (moins d’une picoseconde) passant par la formation d’une structure de type « Eigen » (H9O4+) pour la molécule d’eau pontante, menant directement à la formation des produits. Une seconde structure de la molécule d’eau pontante est également observée, soit une configuration de type « Zündel » (H5O2+) impliquant l’accepteur de proton (l’ion carboxylate) qui semble agir comme un cul-de-sac pour la réaction de transfert de proton.

Mécanismes de transfert de proton d’une réaction acido-basique en phase aqueuse : une étude ab-initio

Les réactions de transfert de proton se retrouvent abondamment dans la nature et sont des processus cruciaux dans plusieurs réactions chimiques et biologiques, qui se produisent souvent en milieu aqueux. Les mécanismes régissant ces échanges de protons sont complexes et encore mal compris, suscitant un intérêt des chercheurs en vue d’une meilleure compréhension fondamentale du processus de transfert. Le présent manuscrit présente une étude mécanistique portant sur une réaction de transfert de proton entre un acide (phénol fonctionnalisé) et une base (ion carboxylate) en phase aqueuse. Les résultats obtenus sont basés sur un grand nombre de simulations de dynamique moléculaire ab-initio réalisées pour des systèmes de type « donneur-pont-accepteur », où le pont se trouve à être une unique molécule d’eau, permettant ainsi l’élaboration d’un modèle cinétique détaillé pour le système étudié. La voie de transfert principalement observée est un processus ultra-rapide (moins d’une picoseconde) passant par la formation d’une structure de type « Eigen » (H9O4+) pour la molécule d’eau pontante, menant directement à la formation des produits. Une seconde structure de la molécule d’eau pontante est également observée, soit une configuration de type « Zündel » (H5O2+) impliquant l’accepteur de proton (l’ion carboxylate) qui semble agir comme un cul-de-sac pour la réaction de transfert de proton.