Regioselectivity in the homolytic cleavage of S-adenosylmethionine

The observed regioselectivity of the homolytic cleavage of S-adenosylmethionine (SAM) by the radical SAM enzymes is modeled by free radical displacement reactions at sulfoxide centers. These displacements are also regioselective, in direct consequence of the reaction mechanism. The selectivity in the radical SAM reactions is explained by the geometry of the free radical displacement mechanism, required by the chemical reaction and arranged in the active site by the radical SAM proteins.     

Effects of vitamins, coenzymes and amino acids on reactions of homolytic cleavage of the O-glycoside bond in carbohydrates

It has been established that vitamins B1, K3 and C, coenzyme Q0 and amino acids cysteine and histidine effectively inhibit reactions of homolytic cleavage of the O-glycoside bond, which are responsible for the destruction of di- and polysaccharides on gamma-irradiation or the action of other reactive radical initiators. This effect was shown to originate from either oxidation or reduction of the radicals of carbohydrates undergoing destruction.     

Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase

The reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O2 in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing.     

Cell shrinkage and apoptosis: a role for potassium and sodium ion efflux

In this study we have shown that redistribution of the lipid composition of the external and internal leaflets of the PM during apoptosis results in two main alterations in the cell surface, externalisation of PS, and a looser packing of the lipid hydrophobic head groups in the external leaflet. Significantly, neither of these alterations can be directly implicated in the mechanism of apoptotic cell shrinkage, however they do have functions in other phases of the apoptotic process. Progressional studies involving morphological and flow cytometric evaluation, and DNA gel electrophoresis revealed that apoptotic cell shrinkage is associated with a decrease in [Na+]i and [K+]i which occurs after visualisation of chromatin condensation and internucleosomal DNA fragmentation, and prior to apoptotic body formation. When apoptotic cultures were supplemented with inhibitors of the Na+, K+-ATPase pump or the Ca2+-dependent K+ channel, essentially all of the respective Na+ or K+ efflux during apoptosis can be inhibited, suggesting that essentially all of the Na+ and K+ efflux can be ascribed to active pumping via the Na+, K+-ATPase pump and the Ca2+-dependent K+ channel.     

Nickel in higher plants: further evidence for an essential role

Soybeans (Glycine max [L.] Merr.) grown in Ni-deficient nutrient solutions accumulated toxic urea concentrations which resulted in necrosis of their leaflet tips, a characteristic of Ni deficiency. Estimates of the Ni requirement of a plant were made by using seeds produced with different initial Ni contents. When compared to soybeans grown from seeds containing 2.5 nanograms Ni, plants grown from seeds containing 13 nanograms Ni had a significantly reduced incidence of leaflet tip necrosis. Plants grown from seeds containing 160 nanograms Ni produced leaves with almost no leaflet tip necrosis symptoms. Neither Al, Cd, Sn, nor V were able to substitute for Ni.

In other experiments, a small excess of EDTA was included in the nutrient solution in addition to that needed to chelate micronutrient metals. Under these conditions, nodulated nitrogen-fixing soybeans had a high incidence of leaflet tip necrosis, even when 1 micromolar NiEDTA was supplied. However, in nutrient solutions containing inorganic sources of N, 1 micromolar NiEDTA almost completely prevented leaflet tip necrosis, although no significant increase in leaf urease activity was observed. Cowpeas (Vigna unguiculata [L.] Walp) grown in Ni-deficient nutrient solutions containing NO₃ and NH₄ also developed leaflet tip necrosis, which was analogous to that produced in soybeans, and 1 micromolar NiEDTA additions prevented these symptoms.

These findings further support our contention that Ni is an essential element for higher plants.

     

Conserved cysteines in the sialyltransferase sialylmotifs form an essential disulfide bond

The sialyltransferase gene family is comprised of 16 cloned enzymes. All members contain two conserved protein domains, termed the S- and L-sialylmotifs, that participate in substrate binding. Of only six invariant amino acids, two are cysteines, with one found in each sialylmotif. Although the recombinant soluble form of ST6Gal I has six cysteines, quantitative analysis indicated the presence of only one disulfide linkage, and thiol reducing agents dithiothreitol and beta-mercaptoethanol inactivated the enzyme. Analysis of site-directed mutants showed that alanine or serine mutants of invariant Cys(181) or Cys(332) exhibit no detectable activity, either by direct assay or by staining of the transfected cells with Sambucus nigra agglutinin, which recognizes the product NeuAcalpha2,6Galbeta1,4GlcNAc on glycoproteins. In contrast, alanine mutations of charged residues adjacent to either cysteine showed little or no effect on enzyme activity. Immunofluorescence microscopy showed that although the wild type sialyltransferase is properly localized in the Golgi apparatus, the inactive cysteine mutants are retained in the endoplasmic reticulum. The results suggest that the invariant cysteine residues in the L- and S-sialylmotifs participate in the formation of an intradisulfide linkage that is essential for proper conformation and activity of ST6Gal I.     

Inspired by nature: an exploration of biocatalyzed siloxane bond formation and cleavage

The intricate siliceous architectures of diatom species have inspired our exploration of biosilicification. In vitro studies of natural systems within the area of silica biosynthesis are complicated. Previous studies, which included biomimetic approaches, often failed to recognize the chemistry of silicic acid and its analogues. To better understand the role of various proteins in the biosilicification process, recent studies have been conducted to test the ability of enzymes to catalyze the formation and cleavage of siloxane bonds. Notably, biocatalysis at silicon was observed. Further understanding of the biotransformation strategy in the design and synthesis of structurally complex materials would be beneficial.     

The catalytic serine of meta-cleavage product hydrolases is activated differently for C-O bond cleavage than for C-C bond cleavage

meta-Cleavage product (MCP) hydrolases catalyze C-C bond fission in the aerobic catabolism of aromatic compounds by bacteria. These enzymes utilize a Ser-His-Asp triad to catalyze hydrolysis via an acyl-enzyme intermediate. BphD, which catalyzes the hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) in biphenyl degradation, catalyzed the hydrolysis of an ester analogue, p-nitrophenyl benzoate (pNPB), with a k(cat) value (6.3 ± 0.5 s(-1)) similar to that of HOPDA (6.5 ± 0.5 s(-1)). Consistent with the breakdown of a shared intermediate, product analyses revealed that BphD catalyzed the methanolysis of both HOPDA and pNPB, partitioning the products to benzoic acid and methyl benzoate in similar ratios. Turnover of HOPDA was accelerated up to 4-fold in the presence of short, primary alcohols (methanol > ethanol > n-propanol), suggesting that deacylation is rate-limiting during catalysis. In the steady-state hydrolysis of HOPDA, k(cat)/K(m) values were independent of methanol concentration, while both k(cat) and K(m) values increased with methanol concentration. This result was consistent with a simple model of nucleophilic catalysis. Although the enzyme could not be saturated with pNPB at methanol concentrations of >250 mM, k(obs) values from the steady-state turnover of pNPB at low methanol concentrations were also consistent with a nucleophilic mechanism of catalysis. Finally, transient-state kinetic analysis of pNPB hydrolysis by BphD variants established that substitution of the catalytic His reduced the rate of acylation by more than 3 orders of magnitude. This suggests that for pNPB hydrolysis, the serine nucleophile is activated by the His-Asp dyad. In contrast, rapid acylation of the H265Q variant during C-C bond cleavage suggests that the serinate forms via a substrate-assisted mechanism. Overall, the data indicate that ester hydrolysis proceeds via the same acyl-enzyme intermediate as that of the physiological substrate but that the serine nucleophile is activated via a different mechanism.     

Ferric bleomycin catalyzed reduction of 10-hydroperoxy-8,12-octadecadienoic acid: evidence for homolytic O-O bond scission

10-Hydroperoxy-8,12-octadecadienoic acid (1) is reduced by ferric bleomycin in aqueous and methanol solutions to yield 10-oxo-8-decenoic acid (2) as the major product (80-90%). Trace amounts of 10-oxo-8,12-octadecadienoic acid (3) (5-10%) and 10-hydroxy-8,12-octadecadienoic acid (4) (5-10%) were also detected. The reduction product ratios remained relatively constant in the presence or absence of the reducing substrate phenol, over the pH range 6.5-8.5, in incubations from 30 s to 1 h, and over a series of ferric drug concentrations. In the presence of phenol, incubations of ferric bleomycin and 1 yielded 2,2'-biphenol and 4,4'-biphenol as oxidation products. In reactions where phenol was replaced with the drug's biological substrate DNA, 1 was found to support ferric bleomycin mediated DNA degradation. Extracts from these assays also found 2 to be the major reduction product derived from the oxidant, with trace quantities of 3 and 4 present. Control experiments demonstrated the reactions to be dependent on both 1 and ferric bleomycin. The reduction products 2 and 3 have previously been shown to originate from transient alkoxyl radicals formed by homolysis of the peroxy O-O bond. Product 4 results from heterolysis of the peroxy O-O bond [Labeque, R., & Marnett, L. J. (1987) J. Am. Chem. Soc. 109, 2828-2829]. The results of this investigation indicate that ferric bleomycin catalyzes the homolytic cleavage of the O-O bond of 1 almost exclusively while supporting various oxidative reactions.     

Dermal connective tissue development in mice: an essential role for tenascin-X

Deficiency of the extracellular matrix protein tenascin-X (TNX) causes a recessive form of Ehlers‐Danlos syndrome (EDS) characterized by hyperextensible skin and hypermobile joints. It is not known whether the observed alterations of dermal collagen fibrils and elastic fibers in these patients are caused by disturbed assembly and deposition or by altered stability and turnover. We used biophysical measurements and immunofluorescence to study connective tissue properties in TNX knockout and wild-type mice. We found that TNX knockout mice, even at a young age, have greatly disturbed biomechanical properties of the skin. No joint abnormalities were noted at any age. The spatio-temporal expression of TNX during normal mouse skin development, during embryonic days 13–19 (E13–E19), was distinct from tropoelastin and the dermal fibrillar collagens type I, III, and V. Our data show that TNX is not involved in the earliest phase (E10–E14) of the deposition of collagen fibrils and elastic fibers during fetal development. From E15 to E19, TNX starts partially to colocalize with the dermal collagens and elastin, and in adult mice, TNX is present in the entire dermis. In adult TNX knockout mice, we observed an apparent increase of elastin. We conclude that TNX knockout mice only partially recapitulate the phenotype of TNX-deficient EDS patients, and that TNX could potentially be involved in maturation and/or maintenance of the dermal collagen and elastin network.     

Selective disulfide bond cleavage in gold(I) cationized polypeptide ions formed via gas-phase ion/ion cation switching

Gaseous multiply protonated disulfide-linked peptides have been subjected to reactions with AuCl2(-) ions to explore the possibility of effecting cation switching of Au+ for two protons and to determine whether cationization by Au+ ions affords selective dissociation of disulfide linkages. The incorporation of Au+ into several model disulfide-linked peptides proved to be straightforward. The primary ion/ion reaction channels were proton transfer, which does not lead to Au+ incorporation, and attachment of AuCl2(-) ions to the polypeptide cation, which does incorporate Au+. Fragmentation of the attachment product, the extent of which varied with peptide and charge state, led to losses of one or more molecules of HCl and, to some extent, cleavage of polypeptides at the disulfide linkage into its two constituent chains. Collisional activation of the intact metal-ion-incorporated peptides showed cleavage of the disulfide linkage to be a major, and in some cases exclusive, process. Cations with protons as the only cationizing agents showed only small contributions from cleavage of the disulfide linkage. These results indicate that Au+ incorporation into a disulfide-linked polypeptide ion is a promising way to effect selective dissociation of disulfide bonds. Cation switching via ion/ion reactions is a convenient means for incorporating gold and is attractive because it avoids the requirement of adding metal salts to the analyte solution.     

Phenylene-ethynylene trication as an efficient fluorescent signal transducer in an aptasensor for potassium ion

A tricationic phenylene-ethynylene (N(3+)) fluorophore is investigated as a fluorescent transducer in homogeneous aptasensing system for potassium ion (K(+)) assay in aqueous media. The enhancement of the fluorescent signal of N(3+) by three K(+) aptamers consisting of 12, 15, and 21 nucleotides are observed and used for the determination of N(3+)-aptamer binding affinities. The binding affinities increase with the length of the aptameric oligonucleotides and are proven to be important to the sensitivity and selectivity of the aptasensors. The enhanced fluorescent signal of each N(3+)-aptamer solution is selectively quenched by K(+) due to the ability of K(+) in stabilizing the G-quadruplex structure of the aptamer. Among three aptamers, the 15-base aptamer provides optimal sensitivity and selectivity over other ions such as Li(+), Na(+), NH(4)(+), Mg(2+), Ca(2+) and Sr(2+). The sensing system shows the detection limit of 1 μM of K(+) in clean buffered solution and 30 μM of K(+) in the solution containing 4800-fold excess of Na(+), with wide linear dynamic ranges of micro- to millimolar concentration. This label-free fluorescence aptasensor is conveniently and effectively applicable for analysis of K(+) in urine samples.     

Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage

Phosphonatase functions in the 2-aminoethylphosphonate (AEP) degradation pathway of bacteria, catalyzing the hydrolysis of the C-P bond in phosphonoacetaldehyde (Pald) via formation of a bi-covalent Lys53ethylenamine/Asp12 aspartylphosphate intermediate. Because phosphonatase is a member of the haloacid dehalogenase superfamily, a family predominantly comprised of phosphatases, the question arises as to how this new catalytic activity evolved. The source of general acid-base catalysis for Schiff-base formation and aspartylphosphate hydrolysis was probed using pH-rate profile analysis of active-site mutants and X-ray crystallographic analysis of modified forms of the enzyme. The 2.9 A X-ray crystal structure of the mutant Lys53Arg complexed with Mg2+ and phosphate shows that the equilibrium between the open and the closed conformation is disrupted, favoring the open conformation. Thus, proton dissociation from the cap domain Lys53 is required for cap domain-core domain closure. The likely recipient of the Lys53 proton is a water-His56 pair that serves to relay the proton to the carbonyl oxygen of the phosphonoacetaldehyde (Pald) substrate upon addition of the Lys53. The pH-rate profile analysis of active-site mutants was carried out to test this proposal. The proximal core domain residues Cys22 and Tyr128 were ruled out, and the role of cap domain His56 was supported by the results. The X-ray crystallographic structure of wild-type phosphonatase reduced with NaBH4 in the presence of Pald was determined at 2.4A resolution to reveal N epsilon-ethyl-Lys53 juxtaposed with a sulfate ligand bound in the phosphate site. The position of the C2 of the N-ethyl group in this structure is consistent with the hypothesis that the cap domain N epsilon-ethylenamine-Lys53 functions as a general base in the hydrolysis of the aspartylphosphate bi-covalent enzyme intermediate. Because the enzyme residues proposed to play a key role in P-C bond cleavage are localized on the cap domain, this domain appears to have evolved to support the diversification of the HAD phosphatase core domain for catalysis of hydrolytic P-C bond cleavage.     

Neuronal life and death: an essential role for the p53 family

Recent evidence indicates that the p53 tumor suppressor protein, and its related family member, p73, play an essential role in regulating neuronal apoptosis in both the developing and injured, mature nervous system. In the developing nervous system, they do so by regulating naturally-occurring cell death in neural progenitor cells and in postmitotic neurons, acting to ensure the apoptosis of cells that either do not appropriately undergo the progenitor to postmitotic neuron transition, or that fail to compete for sufficient quantities of trophic support. Somewhat surprisingly, in developing postmitotic neurons, p53 plays a proapoptotic role, while a naturally-occurring, truncated form of p73, DeltaNp73, antagonizes p53 and plays an anti-apoptotic role. In the mature nervous system, numerous studies indicate that p53 is essential for the neuronal death in response to a variety of insults, including DNA damage, ischemia and excitotoxicity. It is likely that all of these insults culminate in DNA damage, which may well be a common trigger for neuronal apoptosis. In this regard, the signaling pathways that are responsible for triggering p53-dependent neuronal apoptosis are starting to be elucidated, and involve cell cycle deregulation and activation of the JNK pathway. Finally, accumulating evidence indicates that p53 is perturbed in the CNS in a number of neurodegenerative disorders, leading to the hypothesis that longterm oxidative damage and/or excitotoxicity ultimately trigger p53-dependent apoptosis in the chronically degenerating nervous system.     

Reversible cleavage of the cobalt-carbon bond to coenzyme B12 catalysed by methylmalonyl-CoA mutase from Propionibacterium shermanii. The use of coenzyme B12 stereospecifically deuterated in position 5'

1. (5'R)-(5'-2H1)Adenosine [(5'R):(5'S) = 85:15] was prepared by a procedure which involved inter alia the reduction of 6-N-benzoyl-2',3'-O-isopropylidene-5'-oxoadenosine with a reagent obtained from LiAl2H4 and (-)-isoborneol. 2. (5'S)-(5'-2H1)AdoCbl [(5'S):(5'R) = 74:26] (AdoCbl = 5'-deoxyadenosylcobalamin) was synthesized by reacting cobal(I)amin with (5'R)-2'-3'-O-isopropylidene-5'-tosyl-(5'-2H1) adenosine followed by acid hydrolysis to remove the isopropylidene protective group. 3. (5'R)-(5'-2H1)AdoCbl [(5'R):(5'S) = 77:23] was prepared by reacting cobalt(I)amin with (5'S)-5'-chloro-5'-(5'-2H1)deoxyadenosine [(5'S):(5'R) = 80:20] obtained in turn from (5'R)-(5'-2H1)adenosine. The reaction sequence involved two consecutive inversions at the C-5' atom of adenosine 4. Comparison of the 500-MHz 1H-NMR spectra of unlabelled, (5'S)- and (5'R)-(5'-2H1)AdoCbl allowed assignment of the triplet at 0.58 ppm and the doublet at 1.525 ppm to the diastereotopic 5'-HRe and 5'-HSi atoms, respectively. On acidification, these two protons gave rise to two triplets at 0.11 ppm and 1.78 ppm indicating that torsion had occurred around the C-4'--C-5' bond. 5. Samples of (5'R)- and (5'S)-(5'-2H1)AdoCbl were incubated with methylmalonyl-CoA mutase from Propionibacterium shermanii. Examination by 1H-NMR spectroscopy at 500 MHz revealed partial loss and stereochemical scrambling of the deuterium at the 5' position. This indicates transient conversion of the C-5' atom into a torsiosymmetric group and hence cleavage of the cobalt-carbon bond during interaction with the enzyme. The mechanism by which deuterium is lost remains to be elucidated.