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PubMed2002

Alkali metal mediated resorcarene capsules: an ESI-FTICRMS study on gas-phase structure and cation binding of tetraethyl resorcarene and its per-methylated derivative.

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) with additional ab initio calculations were used to examine the alkali metal cation binding selectivity (i.e., molecular recognition) and host properties of tetraethyl resorcarene (1) and its per-methylated derivative (2). The significance of intramolecular hydrogen bonding for the crown conformation was demonstrated. The presence of intramolecular flip-flop hydrogen bonding in 1 was confirmed both with calculations and in ND3-exchange experiments. All the alkali metal cations formed host-guest complexes by docking inside the cavity of the host. Complexation with the larger cations, especially Cs+, was favored. All the alkali metal cations also formed dimeric resorcarene capsules with 1. The capsules were directly H-bonded species, with no linking solvent molecules. ND3-exchange experiments and molecular modeling revealed the significance of direct intermolecular H-bonding for the crown conformation of 1 and stability of the capsule structure.

Alkalies↗
PubMed2003

Infrared multiphoton dissociation of alkali metal-coordinated oligosaccharides.

Infrared multiphoton dissociation (IRMPD) of alkali metal-coordinated oligosaccharides was obtained in a Fourier transform mass spectrometer. Fragmentation of the oligosaccharides was observed for Li+- and Na+-coordinated species. For larger alkali metal ions (K+, Rb+, and Cs+), the major products were the alkali metal ions. IRMPD experiments were performed on milk oligosaccharides, and the dissociation thresholds were determined. The threshold values were found to differ for the isomers. It is suggested that the threshold may be useful for differentiating isomeric compounds. Additionally, oligosaccharide alditols from biological samples were analyzed. Comparison of the collision-induced dissociation (CID) and IRMPD spectra of oligosaccharide alditols revealed that IRMPD could be used as a complementary method to obtain structural information.

Carbohydrate Sequence↗
PubMed1998

Coexisting kinetically distinguishable forms of dialkylglycine decarboxylase engendered by alkali metal ions.

The pyridoxal phosphate (PLP) dependent enzyme dialkylglycine decarboxylase (DGD) specifically binds alkali metal ions near the active site. Large ions (Rb+, K+) activate the enzyme while smaller ones (Na+, Li+) inhibit it. Crystallographic results have shown that DGD undergoes a metal ion size dependent structural switch [Hohenester, E., Keller, J. W., and Jansonius, J. N. (1994) Biochemistry 33, 13561], but no evidence for multiple conformations in crystalline DGD was obtained. Here, evidence is presented that DGD-K+ in solution exists in two conformations differing in catalytic competence. Initial rate traces for DGD-K+ exhibit a high degree of curvature due to decreasing activity over time. DGD remains tetrameric under the assay conditions as demonstrated by gel filtration experiments, arguing against the possibility of subunit dissociation as the source of activity loss. Likewise, the mass spectrum of DGD shows a single covalent form. A hysteretic model that assumes two slowly interconverting enzyme forms accounts well for the initial rate data when kinetic parameters from biphasic pre-steady-state kinetics are employed. The fit of the model to the data yields an estimate of 59 +/- 1% for the fast form. A cooperative model cannot account for the data. Double reciprocal plots for coenzyme binding to DGD exhibit two linear phases. Similarly, two kinetic phases are observed in PLP association kinetics. The substitution of Na+ or Rb+ for K+ alters the steady-state kinetic parameters of DGD. Preincubation of DGD-K+ with the competitive inhibitor 1-aminocyclopropane-1-carboxylate (ACC) lowers both kcat and KAIB apparently by drawing the enzyme toward the less active, tighter binding form observed in the pre-steady-state kinetics. These results suggest that the structure of the protein around the alkali metal ion determines the conformational distribution. The transamination reaction with l-alanine was coupled in the pre-steady-state to the LDH-catalyzed oxidation of NADH. This experiment yields an estimate of 68 +/- 4% for the fast form, in agreement with the hysteretic fit to the steady-state data. The reaction of DGD with dithiobis(nitrobenzoate) was used to probe the preexisting forms of DGD. Preincubation of DGD with ACC, like the exchange of Na+ for K+, shifts the conformational distribution, in agreement with the steady-state kinetics. These experiments clearly demonstrate that DGD is a hysteretic enzyme whose conformational distribution is controlled by the identity of the alkali metal ion bound near the active site, and that cooperativity does not play a role in catalysis or regulation.

Alanine↗
PubMed2006

Insight into indole interactions from alkali metal chloride effects on a tryptophan zipper beta-hairpin peptide.

Weakly solvated, low charge density, alkali metal cations (K+ and Rb+) destabilize tryptophan zipper (trpzip) peptides with an effectiveness (for Rb+) similar to that of the protein denaturant urea. An analysis of alkali metal cation effects on polypeptides stabilized predominantly either by hydrogen bonds or by the classical hydrophobic effect indicates that the alkali metals attenuate stabilizing interactions involving the tryptophan indole groups. Destabilization does not result from electrolyte screening of the electrostatic component of the indole-indole interaction, but is likely to involve direct interaction of the low charge density cation with the indole group in a cation-pi interaction. The observations highlight a general simplicity in the nature of molecular interactions in solution, in which stabilizing contributions to polypeptide and protein structures are attenuated by solutes of a complementary nature.

Amino Acid Sequence↗
PubMed2005

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes.

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

Cations↗
PubMed2001

Degradation of alkali-lignin residues from solid-state fermentation of wheat straw by streptomycetes.

The ability of three Streptomyces strains to degrade alkali-lignin, produced from the treatment of wheat straw by the same organisms, was examined. Decolourisation and loss of alkali-lignin was only detected in cultures supplemented with ammonium as an inorganic N source. The pH of cultures supplemented with inorganic N reached lower pH than in those supplemented with yeast extract. From FT-IR spectra corresponding to the alkalilignin obtained from the same cultures, a degradation of carbohydrate component concomitant with a modification in the aromatic moiety of lignin could be inferred. The results indicate that streptomycetes are suitable for use in the treatment of alkali-lignin effluents from the biological treatment of wheat straw by the same organisms and therefore support the role for these organisms in the development of clean technologies in pulp and paper industry.

Alkalies↗
PubMed2004

Effects of alkali pretreatment of silk fibroin on microstructure and properties of hydroxyapatite-silk fibroin nanocomposite.

Nanocomposites comprising hydroxyapatite (HAp) and silk fibroin (SF) were synthesized from Ca(OH)2 suspension co-dispersed with SF fine particles and H3PO4 solution via a wet-mechanochemical route. The SF particles were modified with an alkali solution to increase contact points between HAp phase and SF matrix. HAp crystallites grow more preferentially along c-axis on alkali pretreated SF substrates. The composites exhibit porous microstructure with 70% of open porosity and about 70% of the interpores ranging from 40 to 115 microm in diameter. The peak shifts in amide II band of SF indicate that the chemical interactions between HAp crystals and SF matrix are intensified by the alkali pretreatment of SF. The stronger inorganic-organic interactions promote the formation of three-dimensional network extending throughout the composites, bringing about an increase of 63% in the Vickers hardness to the composite.

Alkalies↗
PubMed2006

Mesenchymal stem cell transplantation in a rabbit corneal alkali burn model: engraftment and involvement in wound healing.

PURPOSE: To investigate whether systemically transplanted mesenchymal stem cells (MSCs) can home and engraft in tissue to promote cornea wound healing after alkali burn, as a new source for treatment. METHODS: Corneal alkali burn was created in four group rabbits: Group I, normal bone marrow function, without MSCs transplantation; Group II, normal bone marrow function, with MSCs transplantation; Group III, bone marrow suppressed by cyclophosphamide, without MSCs; Group IV, bone marrow suppressed by cyclophosphamide, with MSCs. Clinical outcome was evaluated by cornea re-epithelization, cornea opacity, and neovascularization. Cell engraftment into bone marrow, circulation, and cornea was monitored. Immunohistochemistry, using proliferating cell nuclear antigen (PCNA), P63, vimentin, and alpha-smooth muscle actin (alpha-SMA) was carried out to assess the cell proliferative and differentiative ability. RESULTS: At the time of 1-month follow-up, Group II rabbits showed the best clinical results with a clearer healed cornea compared with other groups. Well-formed neovascularization appeared on day 14 after alkali burn in Group II, that coincided with the maximum engraftment of MSCs. PCNA, P63, vimentin were more strongly expressed in Group II at multiple time points. DiI-labelled MSCs were differentiated into myofibroblast by the expression of alpha-SMA. Delayed and insufficient cell engraftment, with malformed neovascularization and retarded corneal wound healing was found in Groups III and IV. CONCLUSIONS: Systemically transplanted MSCs can engraft to injured cornea to promote wound healing, by differentiation, proliferation, and synergizing with haemotopoietic stem cells.

Alkalies↗
PubMed2005

Catalysis of the ethanolysis of aryl methyl phenyl phosphinate esters by alkali metal ions: transition state structures for uncatalyzed and metal ion-catalyzed reactions.

This paper reports on a spectrophotometric kinetic study of the effects of the alkali metal ions Li+ and K+ on the ethanolysis of the aryl methyl phenyl phosphinate esters 3a-f in anhydrous ethanol at 25 degrees C. Rate data obtained in the absence and presence of complexing agents afford the second-order rate constants for the reaction of free ethoxide (k(EtO-)) and metal ion-ethoxide ion pairs (k(MOEt)). The sequence k(EtO-) < k(MOEt) is established for all the substrates, contrary to the generally observed reactivity order in nucleophilic substitution processes. The quantities deltaG(ip), deltaG(ts) and DeltaG(cat), which quantify the observed alkali metal ion effect in terms of transition state stabilization through chelation of the metal ion, give the order deltaG(ts) > deltaG(ip) for Li+ and K+. Hammett plots show significantly better correlation of rates with sigma and sigma(o) substituent constants than with sigma-, yielding moderately large rho(rho(o)) values that are consistent with a stepwise mechanism in which formation of a pentacoordinate (phosphorane) intermediate is the rate-limiting step. The range of the values of the selectivity parameter, rho(n) (= rho]/rho(eq)), 1.3-1.6, obtained for the uncatalyzed and alkali metal ion catalyzed reactions indicates that there is no significant perturbation of the transition state (TS) structure upon chelation of the metal ions. This finding is relevant to the mechanism of enzymatic phosphoryl transfer involving metal ion co-factors. The present results enable one to compare structural effects for nucleophilic reactions of several series of organophosphorus substrates. It is shown that the order of reactivity of the substrates: 4-nitrophenyl dimethyl phosphinate (2) > 3a > 4-nitrophenyl diphenyl phosphinate (1) is determined mainly by the steric effects of the alkyl/aryl substituents around the central P atom in the TS of the reaction.

Catalysis↗
PubMed1970

Preparation, purification and analyses of thirteen alkali-stable dinucleotides from yeast ribonucleic acid.

Of the 16 alkali-stable dinucleotides known to be obtained by hydrolysis of commercial yeast RNA with alkali, 13 were prepared in quantities of the order of 10mg or more. The samples, with only one exception, contain at least 90% of dinucleotide, and spectroscopic constants and nucleotide-sequence determinations, although not conclusive, indicate a high degree of purity of these products. The small dinucleotide fraction in 150g of RNA hydrolysed with alkali (1-2% of the total nucleotides) was separated from the mononucleotides by stepwise ion-exchange chromatography on DEAE-cellulose columns and resolved into seven fractions containing from one to four different dinucleotides by electrophoresis on paper at pH3.0. These fractions were resolved into their constituent dinucleotides by chromatography in ammonium sulphate. Contamination of the products by impurities from the paper was minimized by washing it before using it for chromatography or electrophoresis and, by using a thick grade of paper (Whatman no. 17), it was possible to handle and purify relatively large quantities of nucleotides.

Alkalies↗
PubMed1991

Proton and multinuclear N.M.R. studies of cyclogentiotetraose peracetate-alkali cation complexation.

Complexation of alkali cation picrates with cyclogentiotetraose peracetate (CGD4Ac) have been studied by 1H-N.M.R. spectroscopy in acetone d6 and nitromethane d3. We determined the stability constants directly from the observed change of the chemical shifts of H-4 and H-6 pro S protons of CGD4Ac at constant ligand concentration with increasing amounts of alkali salt. The stability constants have also been determined by multinuclear n.m.r. spectroscopies, from the observed change of the chemical shifts of Lithium-7, Sodium-23, Potassium-39, Rubidium-87 and Cesium-133 at constant alkali salt concentration with increasing amount of CGD4Ac. The stabilities of the complexes varied in the order Cs+ greater than Rb+ greater than K+ greater than Na+ greater than Li+. The complexation of CGD4Ac with Cs+ induced conformational change, the gg conformer being predominant at the complexed state. In most cases the cationic exchanges between the free and complexed sites were rapid. However in the CsPic-CGD4Ac-Acetone system the exchange was slow enough to observe below 288 K two 133Cs+ resonances.

Carbohydrates↗
PubMed1979

Alkali-labile sites and post-irradiation effects in gamma-irradiated biologically active double-stranded DNA in aqueous solution.

Gamma-irradiation of double-stranded RF-DNA of bacteriophage phi X174 in aqueous solution in the presence of oxygen produces at least one type of alkali-labile site. It is lethal and gives rise to breaks by alkali and is identical with the damage which becomes manifest by post-irradiation heat treatment. The effect of alkali is dependent on temperature. Furthermore, the excision repair system is not involved in eliminating lethal nucleotide damage in RFI-DNA.

Alkalies↗
PubMed1981

Alkali-labile sites in biologically active DNA: comparison of radiation induced potential breaks and apurinic sites.

Gamma-ray induced alkali-labile sites, which are converted into breaks by alkali or heat, are compared with apurinic sites in both single-stranded and phi X174RF-DNA. It is shown that the kinetics of the conversion into breaks are completely different for both sites. The conclusion is: the gamma-ray induced alkali-labile sites are not identical with apurinic or/and apyrimidinic sites.

Alkalies↗
PubMed1961

Graded and all-or-none electrogenesis in arthropod muscle. I. The effects of alkali-earth cations on the neuromuscular system of Romalea microptera.

Graded electrically excited responsiveness of Romalea muscle fibers is converted to all-or-none activity by Ba(++), Sr(++), or Ca(++), the two former being much the more effective in this action. The change occurs with as little as 7 to 10 per cent of Na(+) substituted by Ba(++). The spikes now produced have overshoots and may be extremely prolonged, lasting many seconds. During the spike the membrane resistance is lower than in the resting fiber, but the resting resistance and time constant are considerably increased by the alkali-earth ions. The excitability is also increased, spikes arising neurogenically from spontaneous repetitive discharges in the axon as well as myogenically from spontaneous activity in the muscle fibers. Repetitive responses frequently occur on intracellular stimulation with a brief pulse. The data indicate that the alkali-earth ions exert a complex of effects on the different action components of electrically excitable membrane. They may be described in terms of the ionic theory as follows: The resting K(+) conductance is diminished. The sodium inactivation process is also diminished, and sodium activation may be increased. Together these changes can act to convert graded responsiveness to the all-or-none variety. The alkali-earth ions can also to some degree carry inward positive charge during activity, since spikes are produced when Na(+) is fully replaced with the divalent ions.

Alkalies↗
PubMed1982

Alkali-sensitive sites in DNA from human cells treated with ultraviolet light, 1'-acetoxysafrole or 1'-acetoxyestragole.

The formation and repair of alkali-labile sites in the DNA of human cells treated with 254 nm u.v. light, 1'-acetoxyestragole (1'-AcO-E) or 1'-acetoxysafrole (1'-AcO-S) have been studied. DNA was analysed by sedimentation in alkaline sucrose gradients after the cells had been layered on the gradients in lysis solution for 15 h (long lysis) or for only 0.75 h (short lysis). With the long lysis technique, a dose of 20 J/m2 resulted in 0.2-0.4 strand breaks/10(8) daltons while treatment of cells with 0.5 mM 1'-AcO-E or 1'-AcO-S caused 0.1-0.3 strand breaks/10(8) daltons. In excision repair proficient T98G cells, one third to two thirds of these strand breaks disappeared upon 4 h incubation after exposure to each of the three agents. In excision repair deficient xeroderma pigmentosum fibroblasts (XPA), the alkali-labile sites produced by 1'-AcO-E or 1'-AcO-S were still repaired, although those resulting from u.v.-irradiation were not. Similar characteristics were observed after the short lysis period. The sedimentation velocities of nucleoids, prepared from treated XPA cells, in neutral sucrose gradients containing ethidium bromide, did not reveal the presence of overt strand breaks in the DNA, suggesting that the lesions were of a type in which the sugar-phosphate backbone was intact but sensitive to hydrolysis by alkali. The contribution of this type of damage to the total DNA damage produced by the agents was estimated to be less than 1% for u.v., and less than 2.5% for 1'-AcO-E and 1'-AcO-S.

Alkalies↗
PubMed1984

Analysis of the induction of alkali sensitive sites in the DNA by chromate and other agents that induce single strand breaks.

CaCrO4 was shown to induce alkali labile sites in the DNA of Chinese hamster ovary cells by analysis of the lack of linearity in the alkaline elution curves, and by a study of the dependence upon pH in the elution of DNA from filters. The effect of CaCrO4 on these parameters was compared with N-methyl-N-nitrosourea, an agent known to produce alkali labile sites. Based upon the aforementioned parameters HgCl2, formaldehyde and X-rays caused the formation of frank single strand breaks with little or no induction of alkaline labile sites. These findings demonstrate differences in the production of alkali sensitive sites by agents that cause DNA single strand breaks.

Alkalies↗
PubMed1999

Krill protease effects on wound healing after corneal alkali burn.

PURPOSE: To study the effect of a novel protease in the development and progression of corneal ulceration secondary to alkali burning. METHODS: By using a 4N alkali burn model of corneal ulceration in rabbits, the effects and efficacy of topical application of a novel protease (PHM-101) capable of degrading metalloproteinases was studied for 28 days of treatment and 7 days off treatment for its effect on corneal ulceration and recurrent erosion. RESULTS: At day 28, both the protease- and placebo-treated groups had different numbers of eyes showing reepithelialization (nine (45%) of 20 and six (33%) of 18, respectively]. By day 35 the protease-treated group had significantly fewer recurrent epithelial defects [two (13%) of 15 vs. eight (61%) of 13; p = 0.02]. Similarly, at day 35 the protease-treated group showed significantly less corneal ulceration [two (13%) of 15 vs. six (46%) of 13; p = 0.02], and those ulcers were of a lesser severity (three units vs. 17.76 units). No difference was found in the degree of stromal edema or neovascularization, nor was there any difference in histopathologic characteristics of inflammatory cell infiltration and corneal scarring. CONCLUSION: We conclude that this novel protease is efficient in reducing recurrent corneal epithelial defects and stromal ulceration after alkali burning.

Alkalies↗
PubMed1983

Retrospective study of alkali burns of the eye.

This report examines the epidemiology, management and morbidity of 159 cases of alkali burns of the eye admitted to The Royal Victorian Eye and Ear Hospital from 1972 to 1981. It was intended to use this as a basis for future accurate assessment and management of this problem. Grading of burns on information provided within the histories was according to Hughes' classification as modified by Ballen. Aspects examined were type of alkali, nature of accident, treatment, complications and follow-up. Results showed that the majority of burns were grade 1 or 2; only a few grade 1 and slightly more grade 2 burn patients suffered any complications, and none of these resulted in loss of vision. All patients with grade 3 and 4 burns suffered severe complications. It would appear that grade 3 and 4 burns need a more specific and energetic plan of treatment. Lime was the most common agent, and the largest group involved comprised male workers who suffered injuries at work. On the basis of the findings of the study the following points are raised: (i) a protocol for future study is suggested; (ii) there is a need for a more discriminate use of EDTA; (iii) do grade 1 burns require hospital admission?; (iv) treatment of grade 3 and 4 burns is still unsatisfactory; (v) the public must be made aware of the existing dangers of alkali burns and their prevention.

Adolescent↗