Reactivity of plasmalogens: kinetics of acid-catalyzed hydrolysis

The acid-catalyzed hydrolysis of the alpha,-unsaturated ether group of two plasmalogens, lysophosphatidal choline and lysophosphatidal ethanolamine, and several model compounds (isobutyl vinyl ether, 1-butenyl ethyl ether, and dihydropyran) was studied by determining the true second-order rate constants. The results indicate that the chemical reactivity of the substituted vinyl ether group in plasmalogens is not appreciably affected by the presence of a bulky substituent on the -carbon. Activation energies, enthalpies, and entropies were also determined (from measurements of the rate constants at different temperatures).     

Kinetic modeling analysis of maleic acid-catalyzed hemicellulose hydrolysis in corn stover

Maleic acid-catalyzed hemicellulose hydrolysis reaction in corn stover was analyzed by kinetic modeling. Kinetic constants for Saeman and biphasic hydrolysis models were analyzed by an Arrhenius-type expansion which include activation energy and catalyst concentration factors. The activation energy for hemicellulose hydrolysis by maleic acid was determined to be 83.3 +/- 10.3 kJ/mol, which is significantly lower than the reported E(a) values for sulfuric acid catalyzed hemicellulose hydrolysis reaction. Model analysis suggest that increasing maleic acid concentrations from 0.05 to 0.2 M facilitate improvement in xylose yields from 40% to 85%, while the extent of improvement flattens to near-quantitative by increasing catalyst loading from 0.2 to 1 M. The model was confirmed for the hydrolysis of corn stover at 1 M maleic acid concentrations at 150 degrees C, resulting in a xylose yield of 96% of theoretical. The refined Saeman model was used to evaluate the optimal condition for monomeric xylose yield in the maleic acid-catalyzed reaction: low temperature reaction conditions were suggested, however, experimental results indicated that bi-phasic behavior dominated at low temperatures, which may be due to the insufficient removal of acetyl groups. A combination of experimental data and model analysis suggests that around 80-90% xylose yields can be achieved at reaction temperatures between 100 and 150 degrees C with 0.2 M maleic acid.     

Kinetics and mechanism of the acid-catalyzed hydrolysis of a hypermodified nucleoside wyosine and its 5''-monophosphate.

The rates of acid-catalyzed hydrolysis of a hypermodified nucleoside, wyosine and its 5'-monophosphate were determined at various pH, temperature and buffer concentrations. The results show that despite distinct differences in structure and the glycosyl bond stability, the hydrolysis of wyosine proceeds via cleavage of the C-N bond by A-1 mechanism, analogously to simple nucleosides. Unlike majority of other monophosphates studied so far, wyosine 5'-monophosphate is not more stable than respective nucleoside.     

Preferential conformation of substance P in solution

The three-dimensional structure of substance P has been studied by 1H-NMR, (500 MHz), and by circular dichroism (CD) in different solvents. The analysis of the different NMR parameters suggest that substance P adopts a rather extended structure in dimethylsulfoxide and pyridine. In water, besides the aggregation phenomenon, the monomeric substance P presents a complex conformational equilibrium. The addition of sodium dodecylsulfate to the aqueous solution induces, as shown by CD spectroscopy, a preferential alpha-helical conformation. And in methanol three structural conclusions may be drawn: the flexibility of the N-terminal Arg-Pro-Lys, the alpha-helical structure of Pro4-Gln5-Gln6-Phe7-Phe8 and the interaction of the C-terminal carboxamide with the primary amides from both glutamines.     

Structural analysis of the peptides derived from specific acid-catalyzed hydrolysis at aspartylprolyl peptide bonds in human J chain.

Human J chain from IgM has been selectively cleaved at three aspartylprolyl peptide bonds to yield four fragments containing 62, 20, 25, and 22 amino acids, respectively. The amino acid sequence of each peptide has been partially determined, (59 of a total of 129 residues) and its position in the J chain ascertained. There were no obvious similarities to known sequences in other immunoglobulin polypeptide chains.     

On the mechanism of the acid-catalyzed hydrolysis of uridine to uracil. Evidence for 6-hydroxy-5,6-dihydrouridine intermediates

In acidic media, the 5,6-double bond of uridine is rapidly hydrated to give a small amount of 6-hydroxy-5,6-dihydrouridine (Urd-H2O), the mechanism of which is known from studies of the acid-catalyzed dehydration of Urd-H2O (Prior, J. J., Maley, J., and Santi, D. V. (1984) J. Biol. Chem. 258, 2422-2428). In addition to dehydration, Urd-H2O also undergoes direct hydrolysis of the N-glycosidic bond in acidic solution. The kinetics of the above reaction demonstrates that Urd-H2O, or an intermediate in the pathway leading from Urd to Urd-H2O, is kinetically competent to account for the hydrolysis of the N-glycosidic bond of Urd. The hydrolysis of (1'-2H)Urd proceeds with an alpha-secondary deuterium isotope effect of kH/kD of 1.11 at 25 degrees C. This isotope effect is sufficiently large to implicate carbonium ion character at the 1'-carbon during hydrolysis but, since it is not the maximal value expected, suggests that N-glycoside cleavage is rate-determining with a transition state intermediate between reactant and products. Importantly, the hydrolysis of [6-3H]Urd proceeds with a substantial inverse secondary isotope effect of kT/kH = 1.15 at 25 degrees C which indicates some degree of sp2 to sp3 rehybridization of C-6 of the pyrimidine moiety during hydrolysis. From the data available, it appears that an important pathway in the hydrolysis of the N-glycoside bond of Urd involves either spontaneous cleavage of Urd which is protonated at the 5-carbon or a protonated species of Urd-H2O. The studies described here, together with the known susceptibility of the 6-position of pyrimidine heterocycles toward nucleophiles, permits the proposal of chemically reasonable mechanisms for enzyme-catalyzed cleavage of N-glycosidic bonds of pyrimidines.     

Preferential hydrolysis of peroxidized phospholipid by lysosomal phospholipase C

The susceptibility of partially peroxidized liposomes of 2-[1-14C] linoleoylphosphatidylethanolamine ([14C]PE) to hydrolysis by cellular phospholipases was examined. [14C]PE was peroxidized by exposure to air at 37 degrees C, resulting in the formation of more polar derivatives, as determined by thin-layer chromatographic analysis. Hydrolysis of these partially peroxidized liposomes by lysosomal phospholipase C associated with cardiac sarcoplasmic reticulum, and by rat liver lysosomal phospholipase C, was greater than hydrolysis of non-peroxidized liposomes. By contrast, hydrolysis of liposomes by purified human synovial fluid phospholipase A2 or bacterial phospholipase C was almost completely inhibited by partial peroxidation of PE. Lysosomal phospholipase C preferentially hydrolyzed the peroxidized component of the lipid substrate which had accumulated during autoxidation. The major product recovered under these conditions was 2-monoacylglycerol, indicating sequential degradation by phospholipase C and diacylglycerol lipase. Liposomes peroxidized at pH 7.0 were more susceptible to hydrolysis by lysosomal phospholipases C than were liposomes peroxidized at pH 5.0, in spite of greater production of polar lipid after peroxidation at pH 5.0. Sodium bisulfite, an antioxidant and an inhibitor of lysosomal phospholipases, prevented: (1) lipid autoxidation, (2) hydrolysis of both non-peroxidized and peroxidized liposomes by sarcoplasmic reticulum and (3) loss of lipid phosphorus from endogenous lipids when sarcoplasmic reticulum was incubated at pH 5.0. These studies show that lipid peroxidation may modulate the susceptibility of phospholipid to attack by specific phospholipases, and may therefore be an important determinant in membrane dysfunction during injury. Preservation of membrane structural and functional integrity by antioxidants may result from inhibition of lipid peroxidation, which in turn may modulate cellular phospholipase activity.     

Preferential coupling of cell surface muscarinic receptors to phosphoinositide hydrolysis in human neuroblastoma cells.

The ability of muscarinic receptors, present in either the cell surface or sequestered compartments of intact human SK-N-SH neuroblastoma cells, to stimulate phosphoinositide hydrolysis has been examined. When cells were first exposed to carbachol for 1 h at 37 degrees C, approximately 50% of the cell surface receptors became sequestered, and this was accompanied by a comparable reduction in the subsequent ability of muscarinic agonists to stimulate phosphoinositide turnover, as monitored by the release of labeled inositol phosphates at 10 degrees C. At this temperature, muscarinic receptor cycling between the two cell compartments is prevented. Upon warming the carbachol-pretreated cells to 37 degrees C, receptor cycling is reinitiated and stimulated phosphoinositide turnover is fully restored within 5-8 min. When measured at 10 degrees C, the reduction of stimulated phosphoinositide turnover observed following carbachol pretreatment was similar in magnitude for both hydrophilic (carbachol, oxotremorine-M) and lipophilic (arecoline, oxotremorine-2, and L-670,548) agonists. The loss of response for both groups of agonists could be prevented if the incubation temperature was maintained at 37 degrees C, rather than at 10 degrees C. At the latter temperature carbachol pretreatment of SK-N-SH cells reduced the maximum release of inositol phosphates elicited by either carbachol or L-670,548 but not the agonist concentrations required for half-maximal stimulation. Radioligand binding studies, carried out at 10 degrees C, indicate that following receptor sequestration, significantly higher concentrations of carbachol were required to occupy the available muscarinic receptor sites. In contrast the lipophilic full agonist L-670,548 recognized receptors present in control and carbachol-pretreated cells with comparable affinities. Analysis of the inositol lipids present after carbachol pretreatment indicate that only a minimal depletion of the substrates necessary for phospholipase C activation had occurred. The results indicate that the agonist-induced sequestration of muscarinic receptors from the cell surface results in a loss of stimulated phosphoinositide hydrolysis when measured under conditions in which the return of the sequestered receptors to the cell surface is prevented. Thus, only those receptors present at the cell surface are linked to phospholipase C activation.     

Dielectric behaviour of frozen DNA in solution

In this article, measurements are reported on ice and frozen DNA solutions between 100 Hz–10 MHz. Pure ice is shown to exhibit single relaxation behaviour, which confirms previous work taken over a more restricted frequency range. The frozen DNA solution displays double‐dispersion behaviour. One dispersion centred around 3 kHz is due to a defect mechanism while the other, centred around 2 MHz, may be attributed to counterion flow through the water immediately adjacent to the DNA molecule. Bioelectromagnetics 20:40–45, 1999. © 1999 Wiley‐Liss, Inc.     

Conversion of bark-rich biomass mixture into fermentable sugar by two-stage dilute acid-catalyzed hydrolysis

Despite high availability and low cost, bark has not actively been considered as a biomass feedstock for producing bio-based products due to its high content of extractives and lignin. In this study, to investigate the feasibility of utilizing bark-rich sawmill residues for producing value-added materials, the mixed Hemlock hog fuel/pin chips (85:15 by dry weight) from a local sawmill were converted into fermentable sugar by two-stage dilute sulfuric acid-catalyzed hydrolysis. Combining the sugar yields from the first-stage (190 degrees C for 150 s with 1.1% acid) and second-stage (210 degrees C for 115 s with 2.5% acid) hydrolyses, which aimed to maximize the recovery of mannose/galactose and glucose, respectively, 13.6 g of glucose (46% theoretical maximum), 10.5 g of mannose and galactose (98% theoretical maximum), and 2.8 g of xylose (85% theoretical maximum) were obtained per 100 g of the original dry feedstock.     

On the hydration of DNA. I. Preferential hydration and stability of DNA in concentrated trifluoroacetate solution

The hydration of DNA is an important factor in the stability of its secondary structure. Methods for measuring the hydration of DNA in solution and the results of various techniques are compared and discussed critically. The buoyant density of native and denatured T-7 bacteriophage DNA in potassium trifluoroacetate (KTFA) solution has been measured as a function of temperature between 5 and 50°C. The buoyant density of native DNA increased linearly with temperature, with a dependence of (2.3 ± 0.5) × 10^?4 g/cc-°C. DNA which has been heat denatured and quenched at 0°C in the salt solution shows a similar dependence of buoyant density on temperature at temperatures far below the T_m, and above the T_m. However, there is an inflection region in the buoyant density versus T curve over a wide range of temperatures below the T_m. Optical density versus temperature studies showed that this is due to the. inhibition by KTFA of recovery of secondary structure on quenching. If the partial specific volume is assumed to be the same for native and denatured DNA, the loss of water of hydration on denaturation is calculated to be about 20% in KTFA at a water activity of 0.7 at 25°C. By treating the denaturation of DNA as a phase transition, an equation has immmi derived relating the destabilizing effect of trifluoroacetate to the loss of hydration on denaturation. The hydration of native DNA is abnormally high in the presence of this anion, and the loss of hydration on denaturation is greater than in CsCl. In addition, trifluoroacetate appears to decrease the ΔHof denaturation.     

Spontaneous hydrolysis of heroin in buffered solution

Electron-capture gas-liquid chromatography was used to study the spontaneous hydrolysis of heroin in phosphate buffer (pH 6.4 and pH 7.4) at 23 degrees C. Aliquots of solution were taken over a 24-h period. After extraction at pH 8.9 into propan-2-ol (10%)-ethyl acetate, deacetylated products were made into hepafluorobutyrate derivatives which were analyzed quantitatively using nalorphine as the internal standard. Heroin decomposes to 06-monoacetylmorphine (06-MAM) under these conditions. Further decomposition to morphine was not observed. Spontaneous hydrolysis was faster at pH 7.4 (first-order rate constant, 9.6 x 10-5 min-1) than at pH 6.4 (first-order rate constant, 3.0 x 10-5 min-1). In 24 h, the decomposition to 06-MAM was 13 and 4%, respectively.     

Fluctuation and linkage relations in macromolecular solution

It is shown in the appendix that the derivatives of the excess free energy of a macromolecule in solution, with respect to the activities of other solution components, lead to fluctuation and linkage relations among these other components. Solution fluctuation theory is used, but it is specialized to the fluctuations and correlations associated with the presence of a macromolecule, and is developed with a modified ensemble. The relations of the appendix are used to analyze the interaction of two solution components, A and B, with the macromolecule and with one another. Three cases are considered: (1) A and B are ligands that bind stoichiometrically to the macromolecule. This case reduces to Wyman's binding polynomial analysis. (2) A and B are two substances at high concentration that interact selectively with the macromolecule. (3) A is a species that binds stoichiometrically to the macromolecule, while B is a component at high concentration that interacts weakly with the macromolecule.     

Prebiotic phosphorylation of nucleosides in formamide.

A possible prebiotic phosphorylation method has been investigated in which formamide served as the reaction medium. Nucleotides and nucleotide derivatives were formed when nucleosides were allowed to react with different orthophosphate, hydrogen phosphate or dihydrogen phosphate salts or with different condensed phosphate salts. The reaction products obtained from the phosphorylation of adenosine were 2'3' and 5'-AMPs, 2',5' and 3',5'-ADPs and 2',3'-cyclic AMP. The extent of phosphorylation in formamide exceeded 50% under favorable conditions after 15 days at 70 degrees. The acidic dihydrogen phosphates and condensed hydrogen phosphates proved to be the best phosphorylating agents. The presence of water in the medium decreased the yield of nucleotide derivatives, but some phosphorylation of adenosine was detected using dihydrogen phosphate in formamide containing water. The phosphorylation reactions were also observed for deoxynucleosides. Little decompression of the nucleosides was detected during the reaction time needed to form nucleotide derivatives. The facility with which phosphorylation takes place in formamide under very mild conditions may justify further studies both of prebiotic phosphorylation and synthetic phosphorylation using this solvent.     

Preferential interactions of urea with lysozyme and their linkage to protein denaturation

The interactions involved in the denaturation of lysozyme in the presence of urea were examined by thermal transition studies and measurements of preferential interactions of urea with the protein at pH 7.0, where it remains native up to 9.3 M urea, and at pH 2.0, where it undergoes a transition between 2.5 and 5.0 M urea. The destabilization of lysozyme by urea was found to follow the linear dependence on urea molar concentration, M(u), DeltaG(u)(o)=DeltaG(w)(o)-2.1 M(u), over the combined data, where DeltaG(u)(o) and DeltaG(w)(o) are the standard free energy changes of the N right harpoon over left harpoon D reaction in urea and water, respectively. Combination with the measured preferential binding gave the result that the increment of preferential binding, deltaGamma(23)=Gamma(23)(D)-Gamma(23)(N), is also linear in M(u). A temperature dependence study of preferential interactions permitted the evaluation of the transfer enthalpy, DeltaHmacr;(2,tr)(o), and entropy, DeltaSmacr;(2,tr)(o) of lysozyme from water into urea in both the native and denatured states. These values were found to be consistent with the enthalpy and entropy of formation of inter urea hydrogen bonds (Schellman, 1955; Kauzmann, 1959), with estimated values of DeltaHmacr;(2,tr)(o)=ca. -2.5 kcal mol(-1) and DeltaSmacr;(2,tr)(o)=ca. -7.0 e.u. per site. Analysis of the results led to the conclusion that the stabilization of the denatured form was predominantly by preferential binding to newly exposed peptide groups. Combination with the knowledge that stabilizing osmolytes act by preferential exclusion from peptide groups (Liu and Bolen, 1995) has led to the general conclusion that both the stabilization and destabilization of proteins by co-solvents are controlled predominantly by preferential interactions with peptide groups newly exposed on denaturation.