Redox and pH gradients drive amino acid synthesis in iron oxyhydroxide mineral systems.

Iron oxyhydroxide minerals, known to be chemically reactive and significant for elemental cycling, are thought to have been abundant in early-Earth seawater, sediments, and hydrothermal systems. In the anoxic Fe2+-rich early oceans, these minerals would have been only partially oxidized and thus redox-active, perhaps able to promote prebiotic chemical reactions. We show that pyruvate, a simple organic molecule that can form in hydrothermal systems, can undergo reductive amination in the presence of mixed-valence iron oxyhydroxides to form the amino acid alanine, as well as the reduced product lactate. Furthermore, geochemical gradients of pH, redox, and temperature in iron oxyhydroxide systems affect product selectivity. The maximum yield of alanine was observed when the iron oxyhydroxide mineral contained 1:1 Fe(II):Fe(III), under alkaline conditions, and at moderately warm temperatures. These represent conditions that may be found, for example, in iron-containing sediments near an alkaline hydrothermal vent system. The partially oxidized state of the precipitate was significant in promoting amino acid formation: Purely ferrous hydroxides did not drive reductive amination but instead promoted pyruvate reduction to lactate, and ferric hydroxides did not result in any reaction. Prebiotic chemistry driven by redox-active iron hydroxide minerals on the early Earth would therefore be strongly affected by geochemical gradients of Eh, pH, and temperature, and liquid-phase products would be able to diffuse to other conditions within the sediment column to participate in further reactions.

The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa.

Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α-helix with unstructured N- and C-terminal tails, and binds to the ß1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70 ) and the stress sigma factor holoenzyme (EσS ) in vitro, but has a greater impact on EσS . In both cases, SutA appears to affect intermediates in the open complex formation and its N-terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.

Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions.

Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.

CO Coupling Chemistry of a Terminal Mo Carbide: Sequential Addition of Proton, Hydride, and CO Releases Ethenone.

The mechanism originally proposed by Fischer and Tropsch for carbon monoxide (CO) hydrogenative catenation involves C-C coupling from a carbide-derived surface methylidene. A single molecular system capable of capturing these complex chemical steps is hitherto unknown. Herein, we demonstrate the sequential addition of proton and hydride to a terminal Mo carbide derived from CO. The resulting anionic methylidene couples with CO (1 atm) at low temperature (-78 °C) to release ethenone. Importantly, the synchronized delivery of two reducing equivalents and an electrophile, in the form of a hydride (H- = 2e- + H+), promotes alkylidene formation from the carbyne precursor and enables coupling chemistry, under conditions milder than those previously described with strong one-electron reductants and electrophiles. Thermodynamic measurements bracket the hydricity and acidity requirements for promoting methylidene formation from carbide as energetically viable relative to the heterolytic cleavage of H2. Methylidene formation prior to C-C coupling proves critical for organic product release, as evidenced by direct carbide carbonylation experiments. Spectroscopic studies, a monosilylated model system, and Quantum Mechanics computations provide insight into the mechanistic details of this reaction sequence, which serves as a rare model of the initial stages of the Fischer-Tropsch synthesis.

Proton-hydride tautomerism in hydrogen evolution catalysis.

Efficient generation of hydrogen from renewable resources requires development of catalysts that avoid deep wells and high barriers. Information about the energy landscape for H2 production can be obtained by chemical characterization of catalytic intermediates, but few have been observed to date. We have isolated and characterized a key intermediate in 2e(-) + 2H(+) → H2 catalysis. This intermediate, obtained by treatment of Cp*Rh(bpy) (Cp*, η(5)-pentamethylcyclopentadienyl; bpy, κ(2)-2,2'-bipyridyl) with acid, is not a hydride species but rather, bears [η(4)-Cp*H] as a ligand. Delivery of a second proton to this species leads to evolution of H2 and reformation of η(5)-Cp* bound to rhodium(III). With suitable choices of acids and bases, the Cp*Rh(bpy) complex catalyzes facile and reversible interconversion of H(+) and H2.

Lewis Acid Enhancement of Proton Induced CO2 Cleavage: Bond Weakening and Ligand Residence Time Effects.

Though Lewis acids (LAs) have been shown to have profound effects on carbon dioxide (CO2) reduction catalysis, the underlying cause of the improved reactivity remains unclear. Herein, we report a well-defined molecular system for probing the role of LA additives in the reduction of CO2 to carbon monoxide (CO) and water. Mo(0) CO2 complex (2) forms adducts with a series of LAs, demonstrating CO2 activation that correlates linearly with the strength of the LA. Protons induce C-O cleavage of these LA adducts, in contrast to the CO2 displacement primarily observed in the absence of LA. CO2 cleavage shows dependence on both bond activation and the residence time of the bound small molecule, demonstrating the influence of both kinetic and thermodynamic factors on promoting productive CO2 reduction chemistry.

Modulating the Folding Landscape of Superoxide Dismutase†1 with Targeted Molecular Binders.

Amyotrophic lateral sclerosis, or Lou Gehrig's disease, is characterized by motor neuron death, with average survival times of two to five years. One cause of this disease is the misfolding of superoxide dismutase 1 (SOD1), a phenomenon influenced by point mutations spanning the protein. Herein, we used an epitope-specific high-throughput screen to identify a peptide ligand that stabilizes the SOD1 native conformation and accelerates its folding by a factor of 2.5. This strategy may be useful for fundamental studies of protein energy landscapes as well as designing new classes of therapeutics.

Total Synthesis and Characterization of 7-Hypoquinuclidonium Tetrafluoroborate and 7-Hypoquinuclidone BF3 Complex.

Derivatives of the fully twisted bicyclic amide 7-hypoquinuclidone are synthesized using a Schmidt-Aubé reaction. Their structures were unambiguously confirmed by X-ray diffraction analysis and extensive spectroscopic characterization. Furthermore, the stability and chemical reactivity of these anti-Bredt amides are investigated. 7-Hypoquinuclidonium tetrafluoroborate is shown to decompose to a unique nitrogen bound amide-BF3 complex of 7-hypoquinuclidone under anhydrous conditions and to react instantaneously with water making it one of the most reactive amides known to date.

Lewis acid promoted titanium alkylidene formation: off-cycle intermediates relevant to olefin trimerization catalysis.

Two new precatalysts for ethylene and α-olefin trimerization, (FI)Ti(CH2SiMe3)2Me and (FI)Ti(CH2CMe3)2Me (FI = phenoxy-imine), have been synthesized and structurally characterized by X-ray diffraction. (FI)Ti(CH2SiMe3)2Me can be activated with 1 equiv of B(C6F5)3 at room temperature to give the solvent-separated ion pair [(FI)Ti(CH2SiMe3)2][MeB(C6F5)3], which catalytically trimerizes ethylene or 1-pentene to produce 1-hexene or C15 olefins, respectively. The neopentyl analogue (FI)Ti(CH2CMe3)2Me is unstable toward activation with B(C6F5)3 at room temperature, giving no discernible diamagnetic titanium complexes, but at -30 °C the following can be observed by NMR spectroscopy: (i) formation of the bis-neopentyl cation [(FI)Ti(CH2CMe3)2](+), (ii) α-elimination of neopentane to give the neopentylidene complex [(FI)Ti(═CHCMe3)](+), and (iii) subsequent conversion to the imido-olefin complex [(MeOAr2N═)Ti(OArHC═CHCMe3)](+) via an intramolecular metathesis reaction with the imine fragment of the (FI) ligand. If the reaction is carried out at low temperature in the presence of ethylene, catalytic production of 1-hexene is observed, in addition to the titanacyclobutane complex [(FI)Ti(CH(CMe3)CH2CH2)](+), resulting from addition of ethylene to the neopentylidene [(FI)Ti(═CHCMe3)](+). None of the complexes observed spectroscopically subsequent to [(FI)Ti(CH2CMe3)2](+) is an intermediate or precursor for ethylene trimerization, but notwithstanding these off-cycle pathways, [(FI)Ti(CH2CMe3)2](+) is a precatalyst that undergoes rapid initiation to generate a catalyst for trimerizing ethylene or 1-pentene.

An initial event in the insect innate immune response: structural and biological studies of interactions between ß-1,3-glucan and the N-terminal domain of ß-1,3-glucan recognition protein.

In response to invading microorganisms, insect ß-1,3-glucan recognition protein (ßGRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Here we report on the nuclear magnetic resonance (NMR) solution structure of the N-terminal domain of ßGRP (N-ßGRP) from Indian meal moth (Plodia interpunctella), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. NMR and isothermal calorimetric titrations of N-ßGRP with laminarihexaose, a glucose hexamer containing ß-1,3 links, suggest a weak binding of the ligand. However, addition of laminarin, a glucose polysaccharide (~6 kDa) containing ß-1,3 and ß-1,6 links that activates the proPO pathway, to N-ßGRP results in the loss of NMR cross-peaks from the backbone (15)N-(1)H groups of the protein, suggesting the formation of a large complex. Analytical ultracentrifugation (AUC) studies of formation of the N-ßGRP-laminarin complex show that ligand binding induces self-association of the protein-carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (~102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to submicromolar concentrations. The structural model thus derived from this study for the N-ßGRP-laminarin complex in solution differs from the one in which a single N-ßGRP molecule has been proposed to bind to a triple-helical form of laminarin on the basis of an X-ray crystallographic structure of the N-ßGRP-laminarihexaose complex [Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., and Yamaguchi, Y. (2011) J. Biol. Chem. 286, 29158-29165]. AUC studies and phenoloxidase activation measurements conducted with the designed mutants of N-ßGRP indicate that electrostatic interactions involving Asp45, Arg54, and Asp68 between the ligand-bound protein molecules contribute in part to the stability of the N-ßGRP-laminarin macro complex and that a decreased stability is accompanied by a reduced level of activation of the proPO pathway. An increased level of ß-1,6 branching in laminarin also results in destabilization of the macro complex. These novel findings suggest that ligand-induced self-association of the ßGRP-ß-1,3-glucan complex may form a platform on a microbial surface for recruitment of downstream proteases, as a means of amplification of the initial signal of pathogen recognition for the activation of the proPO pathway.

Get5 carboxyl-terminal domain is a novel dimerization motif that tethers an extended Get4/Get5 complex.

Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyzes the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3. Get5 forms a homodimer mediated by its carboxyl domain. We show here that a conserved motif exists within the carboxyl domain. A high resolution crystal structure and solution NMR structures of this motif reveal a novel and stable helical dimerization domain. We additionally determined a solution NMR structure of a divergent fungal homolog, and comparison of these structures allows annotation of specific stabilizing interactions. Using solution x-ray scattering and the structures of all folded domains, we present a model of the full-length Get4/Get5 complex.

Characterization and dynamics of substituted ruthenacyclobutanes relevant to the olefin cross-metathesis reaction.

The reaction of the phosphonium alkylidene [(H(2)IMes)RuCl(2)=CHP(Cy)(3))](+) BF(4)(-) with propene, 1-butene, and 1-hexene at -45 °C affords various substituted, metathesis-active ruthenacycles. These metallacycles were found to equilibrate over extended reaction times in response to decreases in ethylene concentrations, which favored increased populations of α-monosubstituted and α,α'-disubstituted (both cis and trans) ruthenacycles. On an NMR time scale, rapid chemical exchange was found to preferentially occur between the ß-hydrogens of the cis and trans stereoisomers prior to olefin exchange. Exchange on an NMR time scale was also observed between the α- and ß-methylene groups of the monosubstituted ruthenacycle (H(2)IMes)Cl(2)Ru(CHRCH(2)CH(2)) (R = CH(3), CH(2)CH(3), (CH(2))(3)CH(3)). EXSY NMR experiments at -87 °C were used to determine the activation energies for both of these exchange processes. In addition, new methods have been developed for the direct preparation of metathesis-active ruthenacyclobutanes via the protonolysis of dichloro(1,3-bis(2,4,6-trimethylphenyl)-2-imidazolidinylidene)(benzylidene) bis(pyridine)ruthenium(II) and its 3-bromopyridine analogue. Using either trifluoroacetic acid or silica-bound toluenesulfonic acid as the proton source, the ethylene-derived ruthenacyclobutane (H(2)IMes)Cl(2)Ru(CH(2)CH(2)CH(2)) was observed in up to 98% yield via NMR at -40 °C. On the basis of these studies, mechanisms accounting for the positional and stereochemical exchange within ruthenacyclobutanes are proposed, as well as the implications of these dynamics toward olefin metathesis catalyst and reaction design are described.

Characterization of the ABC methionine transporter from Neisseria meningitidis reveals that lipidated MetQ is required for interaction.

NmMetQ is a substrate-binding protein (SBP) from Neisseria meningitidis that has been identified as a surface-exposed candidate antigen for meningococcal vaccines. However, this location for NmMetQ challenges the prevailing view that SBPs in Gram-negative bacteria are localized to the periplasmic space to promote interaction with their cognate ABC transporter embedded in the bacterial inner membrane. To elucidate the roles of NmMetQ, we characterized NmMetQ with and without its cognate ABC transporter (NmMetNI). Here, we show that NmMetQ is a lipoprotein (lipo-NmMetQ) that binds multiple methionine analogs and stimulates the ATPase activity of NmMetNI. Using single-particle electron cryo-microscopy, we determined the structures of NmMetNI in the presence and absence of lipo-NmMetQ. Based on our data, we propose that NmMetQ tethers to membranes via a lipid anchor and has dual function and localization, playing a role in NmMetNI-mediated transport at the inner membrane and moonlighting on the bacterial surface.

Kinetics and products of the acid-catalyzed ring-opening of atmospherically relevant butyl epoxy alcohols.

Epoxydiols are produced in the gas phase from the photo-oxidation of isoprene in the absence of significant mixing ratios of nitrogen oxides (NO(x)). The reactive uptake of these compounds onto acidic aerosols has been shown to produce secondary organic aerosol (SOA). To better characterize the fate of isoprene epoxydiols in the aerosol phase, the kinetics and products of the acid-catalyzed ring-opening reactions of four hydroxy-substituted epoxides were studied by nuclear magnetic resonance (NMR) techniques. Polyols and sulfate esters are observed from the ring-opening of the epoxides in solutions of H(2)SO(4)/Na(2)SO(4). Likewise, polyols and nitrate esters are produced in solutions of HNO(3)/NaNO(3). In sulfuric acid, the rate of acid-catalyzed ring-opening is dependent on hydronium ion activity, sulfate ion, and bisulfate. The rates are much slower than the nonhydroxylated equivalent epoxides; however, the hydroxyl groups make them much more water-soluble. A model was constructed with the major channels for epoxydiol loss (i.e., aerosol-phase ring-opening, gas-phase oxidation, and deposition). In the atmosphere, SOA formation from epoxydiols will depend on a number of variables (e.g., pH and aerosol water content) with the yield of ring-opening products varying from less than 1% to greater than 50%.

Total synthesis and evaluation of 22-(3-azidobenzoyloxy)methyl epothilone C for photoaffinity labeling of beta-tubulin.

The total synthesis of 22-(3-azidobenzoyloxy)methyl epothilone C is described as a potential photoaffinity probe to elucidate the beta-tubulin binding site. A sequential Suzuki-aldol-Yamaguchi macrolactonization strategy was utilized employing a novel derivatized C1-C6 fragment. The C22-functionalized analog exhibited good activity in microtubule assembly assays, but cytotoxicity was significantly reduced. Molecular modeling simulations indicated that excessive steric bulk in the C22 position is accommodated by the large hydrophobic pocket of the binding site. Photoaffinity labeling studies were inconclusive suggesting non-specific labeling.

Regioselective Diels-Alder cycloadditions and other reactions of 4,5-, 5,6-, and 6,7-indole arynes.

The regioselectivity of Diels-Alder cycloadditions of indole arynes (indolynes) at all three benzenoid positions was examined. Cycloadditions with the 4,5-and 5,6-indolynes, derived via metal-halogen exchange from the corresponding o-dibromo indoles, showed essentially no selectivity with 2-t-butylfuran. In contrast, the 6,7-indolyne displayed virtually complete preference for the more sterically congested cycloadduct. This same cycloadduct undergoes a facile acid-catalyzed rearrangement to afford the annulated enone, or alternatively, undergoes hydrolysis and oxidation in the presence of air to give the indolobenzoquinone. The 5,6-difluoroindoles show anomolous behavior and give either 5-fluoro-6,7-indolynes with n-BuLi in ether, or 5,6-indolynes with n-BuLi in toluene. We have also demonstrated that benzenoid indolynes can be easily and conveniently generated by the fluoride-induced decomposition of o-trimethylsilyl triflates.

Synthetic studies on ezomycins: stereoselective route to a thymine octosyl nucleoside derivative.

The ezomycins are Streptomyces-derived antifungal natural products, belonging to the complex peptidyl nucleoside family of antibiotics. Employing D-serine as a chiral platform, we report herein a novel synthetic route to the bicyclic octosyl nucleoside core of the ezomycins. A key step in the sequence involved a stereoselective 6-exo-trig oxymercurationoxidation of a strategic delta-hydroxy alkene derivative, toward construction of the trans-fused furopyran ring system as present in the target products. In contrast to the known carbohydrate-based synthetic routes to the above furopyranyl fragment, the present amino acid chiral template approach is expected to offer a more flexible pathway toward potential SAR-targeted structural/stereochemical modifications of this central bicyclic nucleoside component of the ezomycins.

Synthesis of a natural product-inspired eight-membered ring lactam library via ring-closing metathesis.

We have prepared a novel speculative eight-membered lactam demonstration library based on the skeletal structure of the potent antitumor marine natural product octalactin A. The basic scaffold was readily constructed in a convergent fashion via ring-closing metathesis chemistry from the corresponding diene amides. A cursory examination of the biological properties of the library validates the relevance and significance of these structures.

Total synthesis and evaluation of C25-benzyloxyepothilone C for tubulin assembly and cytotoxicity against MCF-7 breast cancer cells.

The total synthesis of C25-benzyloxy epothilone C is described. A sequential Suzuki-Aldol-Yamaguchi macrolactonization strategy was utilized employing a novel derivatized C8-C12 fragment. The C25-benzyloxy analog exhibited significantly reduced biological activity in microtubule assembly and cytotoxicity assays. Molecular modeling simulations indicated that excessive steric bulk in the C25 position may reduce activity by disrupting key hydrogen bonds that are crucial for epothilone binding to beta-tubulin.

Indole-derived arynes and their Diels-Alder reactivity with furans.

Arynes derived from any position of the ubiquitous indole nucleus are unknown. We have now provided the first evidence for the formation and trapping of the 4,5-, 5,6-, and 6,7-indolynes. A series of o-dihalo indoles (Cl, Br, F) were synthesized and reacted under metal-halogen exchange conditions to give Diels-Alder cycloadducts in high yield with furan. The use of an excess of tert-butyllithium resulted in the rearrangement of the initially formed cycloadduct; however, employing only a slight excess of n-butyllithium cleanly gave cycloadducts with furan.