Postsynthetic Conjugation of RNA to Carboxylate and Dicarboxylate Molecules

Carboxylates and dicarboxylates are important phosphate mimics. Herein, we present a simple synthetic route for the preparation of RNA carboxylate/dicarboxylate conjugates, starting from suitably protected NH₂- and COOH-containing molecules that are coupled to the RNA on the solid support. The key point in our method was the use of trimethylsilylethanol (TMSE-OH) protecting group, which is removed simultaneously with the silyl protecting group on the 2′-OH of the RNA ribose (e.g. t-Butyldimethylsilyl) during the final RNA cleavage/deprotection steps. The usefulness of this method was demonstrated by preparing different RNA-phosphate mimics oligos.     

Interaction of purified alternative oxidase from thermogenic Arum maculatum with pyruvate

Plant alternative oxidase (AOX) activity in isolated mitochondria is regulated by carboxylic acids, but reaction and regulatory mechanisms remain unclear. We show that activity of AOX protein purified from thermogenic Arum maculatum spadices is sensitive to pyruvate and glyoxylate but not succinate. Rapid, irreversible AOX inactivation occurs in the absence of pyruvate, whether or not duroquinol oxidation has been initiated, and is insensitive to duroquinone. Our data indicate that pyruvate stabilises an active conformation of AOX, increasing the population of active protein in a manner independent of reducing substrate and product, and are thus consistent with an exclusive effect of pyruvate on the enzyme’s apparent V_max.     

Preparation, characterization and biological relevance of calcium(II)/diethylmalonate(-1,-2) complexes

Reactions of Ca(NO₃)₂·4H₂O and diethylmalonic acid (Et₂malH₂, its anions represent functional side-chain analogs of γ-carboxyglutamic acid residues which are implicated as essential Ca²⁺-binding ligands in a variety of proteins) in aqueous media have afforded compounds [Ca(Et₂malH)₂(H₂O)₃]_n (1) and [Ca(Et₂mal)(H₂O)]_n (2) at pH 4 and 8, respectively. The structure of 1 was determined by single-crystal, X-ray crystallography, which revealed an 1D coordination polymer. The diethylmalonate ligands exist in their monoanionic form and present two different coordination modes. The Ca^II ion is 7-coordinate with a pentagonal bipyramidal geometry. IR data are discussed in terms of the known (1) and proposed (2) structures of the complexes. The role of the carboxylate binding modes in determining the affinity of Ca²⁺ for the various metal binding sites in proteins containing the γ-carboxyglutamate residue is discussed in the light of our and previous results.     

A comparative study of ferrocenyl carboxylate cadmium(II) complexes prepared by two different synthetic methods

Reaction of ferrocenyl carboxylate H₂bfcs with Cd(Ac)₂ · 2H₂O (H₂bfcs = 1,1′-bis(3-carboxy-1-oxopropyl)ferrocene) gives the mononuclear tetrahydrate precursor Cd(Hbfcs)₂(H₂O)₄ (1). Investigation on the substitution reactions of 1 with imidazole or 2,2′-bpy afforded two one-dimensional (1D) complexes {[Cd₂(bfcs)₂(C₃H₄N₂)₆] · 4H₂O}_n (2) and {[Cd(bfcs)(2,2′-bpy)(H₂O)] · 2H₂O}_n (4) (2,2′-bpy = 2,2′-bipyridine), respectively. However, the one-step reactions of H₂bfcs, Cd(Ac)₂ · 2H₂O with imidazole or 2,2′-bpy result in the formation of two different 1D complexes {[Cd(bfcs)(C₃H₄N₂)₂] · CH₃OH · 2H₂O}_n (3) and [Cd(bfcs)(CH₃OH)]_n (5). It can be seen from the results that applying different synthetic routes produce dissimilar complexes from however the same materials and under the same reaction conditions. In addition, investigations of differential pulse voltammetry of these four 1D complexes indicate that their half-wave potentials are slightly higher than that of H₂bfcs.     

Synthesis and characterisation of dinuclear oxomolybdenum(V) complexes with thienyl carboxylate ligands

The first structurally characterised oxomolybdenum(V) complexes with thienyl carboxylate ligands were prepared by the reaction of [Mo₂O₃(C₅H₇O₂)₄] or (NH₄)₂[MoOCl₅] with the corresponding acid (2-thiophenecarboxylic, 5-methyl-2-thiophenecarboxylic or 3-(3-thienyl)acrylic acid). Complexes [Mo₂O₃(μ-OC₂H₅)(μ-O₂CR)(C₅H₇O₂)₂](R = -C₄H₃S (1), -C₄H₂S(CH₃) (2) or -CHCHC₄H₃S (3)) were obtained upon substitution of two acetylacetonate ligands from [Mo₂O₃(C₅H₇O₂)₄] with RCOO⁻ in dry ethanol. Reactions of (NH₄)₂[MoOCl₅] with the corresponding thienyl carboxylic acid in the presence of γ-picoline (C₆H₇N) yielded complexes (C₆H₇NH)[Mo₂O₄(μ-O₂CR)Cl₂(C₆H₇N)₂] (R = -C₄H₃S (4), -C₄H₂S(CH₃) (5) or -CHCHC₄H₃S (6)). All of the six new complexes were characterised as dinuclear. The molecular structures of 1, 3, 4·0.5CH₃CN and 5 were determined by the single crystal X-ray diffraction method. In the complexes the two molybdenum atoms are doubly bridged either by one oxygen and one ethoxy-oxygen, or alternatively by two oxo-oxygens, and are additionally bridged by the thienyl carboxylate ion in a didentate bridging manner. All complexes were further characterised by means of chemical analysis, IR spectroscopy, TG and in some cases by the one and two-dimensional NMR method.     

Synthesis and structure of a zinc(II)-carboxylate trimer containing the π···π stacking, 1,8-naphthalimide synthon: A supramolecular metal-organic framework

The reaction of the bifunctional ligand 3-(1,8-naphthalimido)propanoate (L_C2⁻), which combines a 1,8-naphthalimide strong π···π stacking synthon and a carboxylate donor group, with Zn(O₂CCH₃)₂(H₂O)₂ in methanol yields trimetallic Zn₃(L_C2)₆(MeOH)₄. The solid state structure has a central zinc(II) linked to two equivalent outer zinc(II) by both μ-κ¹ and μ-κ² carboxylate ligands. The two equivalent five-coordinate terminal zinc centers are also bonded to a third nonbridging κ²-carboxylate and to the oxygen atom of a methanol molecule. The central zinc(II) is six-coordinate with the four bridging carboxylate oxygen atoms forming a square planar arrangement and two trans oriented methanol molecules completing the coordination sphere. These trimers are organized into an extended structure exclusively by noncovalent interactions. Two types of strong π···π stacking interactions between sets of three stacked naphthalimide rings from three different trinuclear molecules organize the structure into two-dimensional thick sheets. The third dimension is organized by intermolecular hydrogen bonding interactions between the methanol molecules bonded to the terminal zinc(II) and the free oxygen of the μ-κ¹-carboxylates from adjacent trimeric units. This interaction is supported by weak π···π stacking. Overall the structure is a highly organized supramolecular metal-organic framework (SMOF) solid.     

Functional and molecular identification of sodium-coupled dicarboxylate transporters in rat primary cultured cerebrocortical astrocytes and neurons

Na+-coupled carboxylate transporters (NaCs) mediate the uptake of tricarboxylic acid cycle intermediates in mammalian tissues. Of these transporters, NaC3 (formerly known as Na+-coupled dicarboxylate transporter 3, NaDC3/SDCT2) and NaC2 (formerly known as Na+-coupled citrate transporter, NaCT) have been shown to be expressed in brain. There is, however, little information available on the precise distribution and function of both transporters in the CNS. In the present study, we investigated the functional characteristics of Na+-dependent succinate and citrate transport in primary cultures of astrocytes and neurons from rat cerebral cortex. Uptake of succinate was Na+ dependent, Li+ sensitive and saturable with a Michaelis constant (Kt) value of 28.4 microM in rat astrocytes. Na+ activation kinetics revealed that the Na+ to succinate stoichiometry was 3:1 and the concentration of Na+ necessary for half-maximal transport was 53 mM. Although uptake of citrate in astrocytes was also Na+ dependent and saturable, its Kt value was significantly higher (approximately 1.2 mM) than that of succinate. Unlabeled succinate (2 mM) inhibited Na+-dependent [14C]succinate (18 microM) and [14C]citrate (4.5 microM) transport completely, whereas unlabeled citrate inhibited Na+-dependent [14C]succinate uptake more weakly. Interestingly, N-acetyl-L-aspartate, which is the second most abundant amino acid in the nervous system, also completely inhibited Na+-dependent succinate transport in rat astrocytes. The inhibition constant (Ki) for the inhibition of [14C]succinate uptake by unlabeled succinate, N-acetyl-L-aspartate and citrate was 15.9, 155 and 764 microM respectively. In primary cultures of neurons, uptake of citrate was also Na+ dependent and saturable with a Kt value of 16.2 microM, which was different from that observed in astrocytes, suggesting that different Na+-dependent citrate transport systems are expressed in neurons and astrocytes. RT-PCR and immunocytochemistry revealed that NaC3 and NaC2 are expressed in cerebrocortical astrocytes and neurons respectively. These results are in good agreement with our previous reports on the brain distribution pattern of NaC2 and NaC3 mRNA using in situ hybridization. This is the first report of the differential expression of different NaCs in astrocytes and neurons. These transporters might play important roles in the trafficking of tricarboxylic acid cycle intermediates and related metabolites between glia and neurons.     

Metabolism of cyclohexane carboxylic acid by the photosynthetic bacteriumRhodopseudomonas palustris

Cyclohexane carboxylate supported relatively rapid growth (doubling times 7–8 h) of Rhodopseudomonas palustris under oxic or photosynthetic conditions, but did not serve as a substrate for either of the known aromatic CoA ligases. A CoA ligase that thioesterifies cyclohexane carboxylate was partially purified and did not cross react immunologically with the two CoA ligases purified previously from this bacterium. Crude extracts of R. palustris cells grown with a range of aromatic or alicyclic acids contained a dehydrogenase that reacted with cyclohexane carboxyl-CoA or cyclohex-1-ene carboxyl-CoA, using 2,6-dichlorophenolindophenol or ferricenium ion as electron carrier. This activity was not detected in extracts of adipate-, glutamate-, or succinate-grown cells. No oxidation or reduction of nonesterified cyclohexane carboxylate or cyclohexene carbocylate was detected in extracts of cells grown with aromatic or aliphatic substrates, neither aerobically nor anaerobically. A constitutively expressed thioesterase that hydrolyzed cyclohexane carboxyl-CoA and also some alicyclic and aliphatic CoA derivatives was purified and characterized. The enzyme had little or no activity on benzoyl-CoA or 4-hydroxybenzoyl-CoA. The presence of a thioesterase that effectively hydrolyzes cyclohexane carboxyl-CoA suggests that transient production of cyclohexane carboxylate is a physiological response to temporary excess of reductant during metabolism of aromatic compounds. Received: 22 May 1995 / Accepted: 13 September 1995     

Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations

There is a pressing need for accurate force fields to assist in metalloprotein analysis and design. Recent work on the design of mimics of dimetal proteins highlights the requirements for activity. DF1 is a de novo designed protein, which mimics the overall fold and active site geometry of a series of diiron and dimanganese proteins. Specifically, the dimanganese form of DF1 is a mimic of the natural enzyme manganese catalase, which catalyzes the dismutation reaction of hydrogen peroxide into water and oxygen. During catalytic turnover, the active site has to accommodate both the reduced and the oxidized state of the dimanganese core. The biomimetic protein DF1 is only stable in the reduced form and thus not active. Furthermore, the synthetic protein features an additional bridging glutamate sidechain, which occupies the substrate binding site. The goal of this study is to develop classical force fields appropriate for design of such important dimanganese proteins. To this aim, we use a nonbonded model to represent the metal-ligand interactions, which implicitly takes into account charge transfer and local polarization effects between the metal and its ligands. To calibrate this approach, we compare and contrast geometric and dynamical properties of manganese catalase and DF1. Having demonstrated a good correspondence with experimental structural data, we examine the effect of mutating the bridging glutamate to aspartate (M1) and serine (M2). Classical MD based on the refined forcefield shows that these point mutations affect not only the immediate coordination sphere of the manganese ions, but also the relative position of the helices, improving the similarity to Mn-catalase, especially in case of M2. On the basis of these findings, classical molecular dynamics calculations with the active site parameterization scheme introduced herein seem to be a promising addition to the protein design toolbox.