Hydrogen bonds and proton transfer in general-catalytic transition-state stabilization in enzyme catalysis.

The question of the nature of the proton bridge involved in general acid-base catalysis in both enzymic and non-enzymic systems is considered in the light of long-known but insufficiently appreciated work of Jencks and his coworkers and of more recent results from neutron-diffraction crystallography and NMR spectroscopic studies, as well as results from isotope-effect investigations. These lines of inquiry lead toward the view that the bridging proton, when between electronegative atoms, is in a stable potential at the transition state, not participating strongly in the reaction-coordinate motion. Furthermore they suggest that bond order is well-conserved at unity for bridging protons, and give rough estimates of the degree to which the proton will respond to structural changes in its bonding partners. Thus if a center involved in general-catalytic bridging becomes more basic, the proton is expected to move toward it while maintaining a unit total bond order. For a unit increase in the pK of a bridging partner, the other partner is expected to acquire about 0.06 units of negative charge. The implications are considered for charge distribution in enzymic transition states as the basicity of catalytic residues changes in the course of molecular evolution or during progress along a catalytic pathway.

Transition-state theoretical interpretation of the catalytic power of pyruvate decarboxylases: the roles of static and dynamical considerations.

The catalytic power of two thiamin diphosphate (ThDP)-dependent enzymes, yeast pyruvate decarboxylase (the hysteretically regulated enzyme from Saccharomyces cerevisiae, SCPDC) and bacterial pyruvate decarboxylase (the unregulated enzyme from Zymomonas mobilis, ZMPDC), are analyzed by thorough-going application of transition-state theory, i.e. by a static approach that emphasizes the state-function character of the free energy of activation and takes no explicit account of dynamical considerations. The overall catalytic reaction is resolved into manifolds for addition (conversion of free enzyme and substrate to the complex of enzyme with the pyruvate:ThDP adduct), decarboxylation, and elimination (conversion of the complex of enzyme with the acetaldehyde:ThDP adduct formed by decarboxylation into free product and free enzyme). For SCPDC, the addition manifold is most strongly catalyzed (3x1012-fold, corresponding to net transition-state stabilization of 72 kJ/mol, transition-state stabilization of 83 kJ/mol diminished by reactant-state stabilization of 11 kJ/mol), the decarboxylation manifold is least strongly catalyzed (5x107-fold, corresponding to net transition-state stabilization of 41 kJ/mol, transition-state stabilization of 68 kJ/mol diminished by reactant-state stabilization of 27 kJ/mol), and the elimination manifold is catalyzed to an intermediate degree (2x1010-fold, corresponding to net transition-state stabilization of 59 kJ/mol, transition-state stabilization of 76 kJ/mol diminished by reactant-state stabilization of 17 kJ/mol). A similar situation holds for ZMPDC. There is no need to make an explicit analysis of dynamical factors in order to describe the catalytic mechanism and catalytic power of these complex enzymes.

Ion channel properties of a protein complex with characteristics of a glutamate/N-methyl-D-aspartate receptor.

The functional reconstitution of glutamate receptor proteins purified from mammalian brain has been difficult to accomplish. However, channels activated by L-glutamate (L-Glu) and N-methyl-D-aspartate (NMDA) were detected in planar lipid bilayer membranes (PLMs) following the reconstitution of a complex of proteins with binding sites for NMDA receptor (NMDAR) ligands. The presence of glycine was necessary for optimal activation. A linear current-voltage relationship was observed with the reversal potential being zero. Channels activated by L-Glu had conductances of 23, 47 and 65 pS, and were suppressed partially by competitive and fully by noncompetitive inhibitors of NMDARs. Magnesium had little effect on the reconstituted channels.

Rapid chemical sampling of endogenous species from brain slice preparations.

A very simple method of chemical sampling from the surface of brain slices is described. This procedure utilizing micropipets involves no sample dilution, and thus has very high sensitivity. Basal and stimulated concentrations of neurotransmitters and their metabolites are sampled from a thin fluid layer on the slice surface and appear to be in mobile equilibrium with the brain slice extracellular fluid levels. Rapid sampling allows one to follow the time course of stimulated release and reuptake phenomena.

Secondary structure and protein deamidation.

The deamidation reactions of asparagine residues in alpha-helical and beta-turn secondary structural environments of peptides and proteins are reviewed. Both kinds of secondary structure tend to stabilize asparagine residues against deamidation, although the effects are not large. The effect of beta-sheet structures on asparagine stability is unclear, although simple considerations suggest a stabilization in this environment also.

Effect of 'pH' on the rate of asparagine deamidation in polymeric formulations: 'pH'-rate profile.

The rate of Asn deamidation of a model hexapeptide (L-Val-L-Tyr-L-Pro-L-Asn-Gly-L-Ala) was measured as a function of effective pH ('pH') in glassy and rubbery polymeric solids containing poly(vinyl pyrrolidone) (PVP) and in solution controls at 70 degrees C. The reaction exhibited pseudo-first-order kinetics in all samples over a wide 'pH' range (0.5 < 'pH' < 12); the formation of similar products suggests that the reaction mechanism is unaffected by matrix type. Rates of deamidation were comparable for the polymeric and solution samples in the acidic range ('pH' < 4). Solution-state rates were faster than those in polymeric solids at neutral 'pH' (6 < 'pH' < 8), increasing to a > 10,000-fold difference in the basic range ('pH' > 8). Specific base catalysis was observed in solution and in the polymeric solids under neutral conditions (6 < 'pH' < 8). In solution, the reaction exhibited general base catalysis for 'pH' > 8, whereas the reaction was 'pH'-independent in the polymeric solids in this range. The 'pH'-rate profile and supporting buffer catalysis data are consistent with a change in the rate-determining step in the basic range from 'pH'-dependent attack of the deprotonated backbone amide nitrogen on the Asn side chain in solution to 'pH'-independent ammonia expulsion in the polymeric solids. The results suggest that polymer matrix incorporation not only affects the magnitude of the deamidation rate constant but also the 'pH' dependency of the reaction and the rate-determining step in the basic 'pH' range.

Formaldehyde production by Tris buffer in peptide formulations at elevated temperature.

This technical note provides evidence for the degradation of Tris buffer in a peptide formulation stored at elevated temperature (70 degrees C). The buffer degrades to liberate formaldehyde, which is shown to react with the peptide tyrosine residue. Those involved in peptide/protein formulation should be aware of the possible instability in this common biological buffer.

On the mechanism of dehydration of a beta-hydroxycyclopentanone analogue of prostaglandin E1.

The dehydration of the beta-hydroxycyclopentanone, 11,16-dihydroxy-16-methyl-9-oxo-13-trans-protenoic acid methyl ester, an analogue of prostaglandin E1, proceeds with acid catalysis (pH less than 3), by uncatalyzed routes (pH congruent to 4 and congruent to 7), and with base catalysis (pH congruent to 5-6 and greater than 8). Deuterium from the solvent is not introduced alpha to the reactant keto function at 60% reaction at pH congruent to 1, but approximately 30% exchange has occurred at pH congruent to 5, 50% at pH congruent to 7, and 80% at pH congruent to 9. The data are consistent with a mechanism in which the substrate is initially enolized with catalysis by acid, base, and water to a 1,3-enediol, which looses water with catalysis by acid, base, and water. The first stage is rate determining in very acidic solution, while the second stage assumes the limitation of rate to an ever greater degree as the solution becomes more basic.

Chemical stability of peptides in polymers. 1. Effect of water on peptide deamidation in poly(vinyl alcohol) and poly(vinyl pyrrolidone) matrixes.

This paper examines the effect of water content, water activity, and glass transition temperature (T(g)) on the deamidation of an asparagine-containing hexapeptide (VYPNGA; Asn-hexapeptide) in lyophilized poly(vinyl alcohol) (PVA) and poly(vinyl pyrrolidone) (PVP) at 50 degrees C. The rate of Asn-hexapeptide deamidation increases with increasing water content or water activity and, hence, decreasing T(g). The rate of deamidation is more sensitive to changes in these parameters in PVA than in PVP. Deamidation is clearly evident in the glassy state in both formulations. In the glassy state, the peptide is more stable in PVA than in PVP formulations but is less stable in the rubbery state. No single variable (water content, water activity, or T(g)) could account for the variation in deamidation rates in PVA and PVP formulations. Deamidation rates were correlated with the degree of plasticization by water (distance of T(g) from the dry intrinsic glass transition temperature); coincident curves for the two polymers were obtained with this correlation. Deamidation in PVA and PVP was closely correlated with the extent of water-induced plasticization experienced by the formulation relative to its glass transition at 50 degrees C, suggesting that the physical state of formulations could be used to predict chemical stability.

Chemical stability of peptides in polymers. 2. Discriminating between solvent and plasticizing effects of water on peptide deamidation in poly(vinylpyrrolidone).

The mechanistic role of water in the deamidation of a model asparagine-containing hexapeptide (Val-Tyr-Pro-Asn-Gly-Ala) in lyophilized formulations containing poly(vinylpyrrolidone) (PVP) and glycerol was investigated. Glycerol was used as a plasticizer to vary formulation glass transition temperature (T(g)) without significantly changing water content or activity. Increases in moisture and glycerol contents increased the rate of peptide deamidation. This increase was strongly correlated with T(g) at constant water content and activity, suggesting that increased matrix mobility facilitates deamidation. In rubbery systems (T > T(g)), deamidation rates appeared to be independent of water content and activity in formulations with similar T(g)s. However, in glassy formulations with similar T(g)s, deamidation increased with water content, suggesting a solvent/medium effect of water on reactivity in this regime. An increase in water content also affected the degradation product distribution; less of the cyclic imide intermediate and more of the hydrolytic products, isoAsp- and Asp-hexapeptides, were observed as water content increased. Thus, residual water appears to facilitate deamidation in these solid PVP formulations both by enhancing molecular mobility and by solvent/medium effects, and also participates as a chemical reactant in the subsequent breakdown of the cyclic imide.

In vitro metabolism studies of the prodrug, 2',3',5'-triacetyl-6-azauridine, utilizing an automated analytical system.

The purpose was to study in vitro metabolism of 2',3',5'-triacetyl-6-azauridine (1) by porcine liver esterase (PLE) and in human plasma using an automated analytical system developed previously. A gradient-LC method was developed to study the concentration-time course of 1 and its metabolites. A fast-LC assay was used to study the temperature effect on the metabolism of 1 by the PLE. 1 and all of its proposed possible metabolites were separated by the gradient-LC method in less than 10 min. Two simplified kinetic schemes were developed to describe the time course of 1, the intermediates and final metabolites with only five rate constants for the metabolisms of 1 by PLE and four rate constants in human plasma. Both enthalpy and entropy of activation in the in vitro metabolism of 1 by PLE were obtained.

Degradation of dacarbazine in aqueous solution.

The effects of initial concentration (0.05-5.0 mg ml-1, 2.5 x 10(-4)-0.025 M) (pH 1-13), buffer concentration (0.01-0.075 M), light, antioxidants and co-solvents on the degradation of dacarbazine in aqueous solution were investigated at 37 degrees C. Liquid chromatography was used to monitor the degradation of dacarbazine as well as the appearance of degradation products. The kinetics of hydrolysis of dacarbazine in the dark were pseudo first-order and independent of the initial concentration of the drug. The degradation of dacarbazine was accelerated by light and at low concentration proceeded by pseudo zero-order kinetics. The pH-rate profiles showed that both the photolytic and the hydrolytic reactions were dependent on the ionization state of the molecule. The main degradation product of both hydrolysis and photolysis was detected by liquid chromatography and confirmed by mass spectrometry to be 2-azahypoxanthine.

Automated analytical systems for drug development studies. V. A system for enzyme kinetic studies.

Two similar automated analytical systems using liquid chromatography (LC) and microdialysis as an on-line sampling technique were applied to studies of enzyme kinetics. 2',3',5'-Triacetyl-6-azauridine (azaribine) with porcine liver esterase (PLE) and N-acetylphenylalanyl-3,5-diiodotyrosine (AcFY') with pepsin were used as model compounds. The microdialysis sampling technique permitted the rapid separation of low molecular weight analytes from macromolecules, thus simultaneously achieving clean-up of the samples and quenching of the reaction. The combination of rapid LC analysis and microdialysis sampling provided selectivity and automation. The systems are rugged and give reproducible results in agreement with those from manual sampling methods.

Automated analytical systems for drug development studies. I--A system for the determination of drug stability.

An automated system consisting of a pH-stat, microdialysis sampling and a liquid chromatograph was assembled to measure the rate of rapid chemical reactions. 2',3',5'-Triacetyl-6-azauridine was used as a model compound to validate the performance of the automated system. Buffer catalysis was minimized by using a non-catalytic concentration of borate buffer along with a pH-stat to maintain the pH during the kinetic run. The microdialysis sampling technique permitted sample quenching and buffering of the solutions to a pH compatible with the LC column materials. The combination of microdialysis sampling and rapid LC analysis allowed reactions with a half-life of approximately 1 min to be sampled every 30 s. The rates of hydrolysis of the drug, measured at different conditions of temperature (37-70 degrees C) and pH (9.0-10.5) using the automated system, compared well with the previously determined values.

Catalytic antibodies for complex reactions: hapten design and the importance of screening for catalysis in the generation of catalytic antibodies for the NDA/CN reaction.

Success in generating catalytic antibodies as enzyme mimics lies in the strategic design of the transition-state analog (TSA) for the reaction of interest, and careful development of screening processes for the selection of antibodies that are catalysts. Typically, the choice of TSA structure is straightforward, and the criterion for selection in screening is often binding of the TSA to the antibody in a microtiter-plate assay. This article emphasizes the problems of TSA design in complex reactions and the importance of selecting antibodies on the basis of catalysis as well as binding to the TSA. The target reaction is the derivatization of primary amines with naphthalene-2,3-dicarboxaldehyde (NDA) in the presence of cyanide ion. The desired outcome is selective catalysis of formation of the fluorescent derivative in preference to nonfluorescent side-products. In the study, TSA design was directed toward the reaction branch leading to the fluorescent product. Here, we describe a microtiter plate-based assay that is capable of detecting antibodies showing catalytic activity at an early stage. Of the antibodies selected, 36% showed no appreciable binding to any of the substrates tested, but did show catalytic activity in derivatizing one or more of the amino acids screened. In contrast, only two out of 77 clones that showed binding did not show catalysis. Thus, in this complex system, observation of binding is a good predictor of the presence of catalytic activity, and failure to observe binding is a poor predictor of the absence of catalytic activity.

Molecular interactions in intermediate and transition states in the self-stimulated inhibition of enzymes.

Di-isopropyl fluorophosphate (DFP) and other organophosphorus inhibitors recruit the catalytic power of their target enzymes: the enzyme catalyzes its own irreversible phosphorylation. The magnitude of the catalytic acceleration can approach the factor by which the enzyme catalyzes its own acylation by natural substrates. The reaction of DFP with five serine proteases [chymotrypsin, elastase, dipeptidyl peptidase IV (DP IV), subtilisin and thermitase] exhibits in all cases the same pH dependence as does enzyme acylation by natural substrates. Chymotrypsin and elastase form a "fast" class of enzymes which react about ten-fold faster than the other three "slow" enzymes. All enzymes show k(HOH)/k(DOD) of about 2 but the proton inventory indicates one-proton character for "slow" enzymes and multiproton character for "fast" enzymes. Enthalpies of activation are about 33 kJ/mol (subtilisin, "slow") and 10 kJ/mol (elastase, "fast"). Entropies of activation are about -120 J.T-1.mol-1 (subtilisin, "slow") and -175J.T-1.s-1 (elastase, "fast"; T = temperature in K).