Theoretical conformational analysis in the determination of productive conformations of substrates for acetylcholinesterase and butyrylcholinesterase

All the equilibrium conformations of 34 analogues of acetylcholine (ACh) with the general formula R-C(O)O-Alk-N+(CH3)3 are calculated by the method of molecular mechanics. In the series R-C(O)O-(CH2)2-N+(CH3)3, a reliable correlation is found between the molecular volume of the substrate and the rate of its hydrolysis by acetylcholinesterase (AChE); the absence of such a correlation is demonstrated for butyrylcholinesterase (BChE). Theoretical conformational analysis confirms that the completely extended tt conformation of ACh is productive for the hydrolysis by AChE, which agrees with the results of X-ray analysis of AChE. AChE is shown to hydrolyze only those substrates that form equilibrium conformers compatible in the mutual arrangement of trimethylammonium group, carbonyl carbon, and carbonyl oxygen with the tt conformation of ACh; in this case, the rate of substrate hydrolysis depends on the total population of these conformers. A reliable correlation was found between the population of the semifolded (tg-) conformation of the choline moiety of substrate molecules and the rate of their BChE hydrolysis. In a series of CH3-C(O)O-Alk-N+(CH3)3, the rate of BChE hydrolysis is demonstrated to depend on the total population of conformations compatible in the mutual arrangement of functionally important atoms with the tg- conformation of ACh. The tg- conformation of ACh is concluded to be productive for BChE hydrolysis. Similar orientations of the substrate molecules relative to the catalytic triads of both AChE and BChE are proven to coincide upon the substrate productive sorption in their active sites. It is hypothesized that the sorption stage is rate-limiting in cholinesterase hydrolysis and the enzyme hydrolyzes the ACh molecule in its energetically favorable conformation.     

Steady-state kinetic analysis of human cholinesterases over wide concentration ranges of competing substrates

Substrate competition for human acetylcholinesterase (AChE) and human butyrylcholinesterase (BChE) was studies under steady-state conditions using wide range of substrate concentrations. Competing couples of substates were acetyl-(thio)esters. Phenyl acetate (PhA) was the reporter substrate and competitor were either acetylcholine (ACh) or acetylthiocholine (ATC). The common point between investigated substrates is that the acyl moiety is acetate, i.e. same deacylation rate constant for reporter and competitor substrate.Steady-state kinetics of cholinesterase-catalyzed hydrolysis of PhA in the presence of ACh or ATC revealed 3 phases of inhibition as concentration of competitor increased: a) competitive inhibition, b) partially mixed inhibition, c) partially uncompetitive inhibition for AChE and partially uncompetitive activation for BChE. This sequence reflects binding of competitor in the active centrer at low concentration and on the peripheral anionic site (PAS) at high concentration. In particular, it showed that binding of a competing ligand on PAS may affect the catalytic behavior of AChE and BChE in an opposite way, i.e. inhibition of AChE and activation of BChE, regardless the nature of the reporter substrate.For both enzymes, progress curves for hydrolysis of PhA at very low concentration (?K_m) in the presence of increasing concentration of ATC showed that: a) the competing substrate and the reporter substrate are hydrolyzed at the same time, b) complete hydrolysis of PhA cannot be reached above 1 mM competing substrate. This likely results from accumulation of hydrolysis products (P) of competing substrate and/or accumulation of acetylated enzyme·P complex that inhibit hydrolysis of the reporter substrate.     

Enantioconvergent hydrolysis of racemic styrene oxide at high concentration by a pair of novel epoxide hydrolases into (<Emphasis Type="Italic">R</Emphasis>)-phenyl-1,2-ethanediol

Objectives

To prepare (R)-phenyl-1,2-ethanediol ((R)-PED) with high enantiomeric excess (ee _p) and yield from racemic styrene oxide (rac-SO) at high concentration by bi-enzymatic catalysis.

Results

The bi-enzymatic catalysis was designed for enantioconvergent hydrolysis of rac-SO by a pair of novel epoxide hydrolases (EHs), a Vigna radiata EH3 (VrEH3) and a variant (AuEH2^A250I) of Aspergillus usamii EH2. The simultaneous addition mode of VrEH3 and AuEH2^A250I, exhibiting the highest average turnover frequency (aTOF) of 0.12 g h^?1 g^?1, was selected, by which rac-SO (10 mM) was converted into (R)-PED with 92.6% ee _p and 96.3% yield. Under the optimized reaction conditions: dry weight ratio 14:1 of VrEH3-expressing E. coli/vreh3 to AuEH2^A250I-expressing E. coli/Aueh2 ^A250I and reaction at 20 °C, rac-SO (10 mM) was completely hydrolyzed in 2.3 h, affording (R)-PED with 98% ee _p. At the weight ratio 0.8:1 of rac-SO to two mixed dry cells, (R)-PED with 97.4% ee _p and 98.7% yield was produced from 200 mM (24 mg/ml) rac-SO in 10.5 h.

Conclusions

Enantioconvergent hydrolysis of rac-SO at high concentration catalyzed by both VrEH3 and AuEH2^A250I is an effective method for preparing (R)-PED with high ee _p and yield.

     

Conjugates of Tacrine and Its Cyclic Homologues with <Emphasis Type="Italic">p</Emphasis>-Toluenesulfonamide as Novel Acetylcholinesterase and Butyrylcholinesterase Inhibitors

Using the acylation reaction with tosyl chloride of N-aminopropyl analogues of tacrine and its cyclic homologues with different size of the aliphatic cycle (5–8), we synthesized a number of new derivatives of p-toluenesulfonamide. It is shown that the synthesized hybrid compounds of tacrine and p-toluenesulfonamide are effective inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with the preferential inhibition of BChE. They also displace propidium from the peripheral anionic site of the electric eel AChE (Electrophorus electricus). The characteristics of the efficiency and selectivity of cholinesterase inhibition by the test compounds were confirmed by the results of molecular docking.     

Design and synthesis of cholecystokinin-4 dipeptide analogues with anxiolytic and anxiogenic activities

A new series of dipeptide analogues of the general formula Ph(CH₂) _n CO-NH(CH₂) _m CO-Trp-NH₂ (n = 1, 3–5; m = 1–3) was designed based on the structure of the endogenous tetrapeptide cholescystokinin-4 (CCK-4) and the topochemical Shemyakin-Ovchinnikov-Ivanov principle. The L-tryptophan derivatives exhibited anxiolytic properties and the D-tryptophan derivatives, anxiogenic properties. The dipeptide Ph(CH₂)₅CO-Gly-L-Trp-NH₂ (GB-115) with the activity in rats of 0.05–0.2 mg/kg after oral and intraperitoneal administration was chosen for further studies as a promising anxiolytic agent.     

Complex invader-ecosystem interactions and seasonality mediate the impact of non-native <Emphasis Type="Italic">Phragmites</Emphasis> on CH<Subscript>4</Subscript> emissions

Invasive plants can influence ecosystem processes such as greenhouse gas (GHG) emissions from wetland systems directly through plant-mediated transfer of GHGs to the atmosphere or through indirect modification of the environment. However, patterns of plant invasion often co-vary with other environmental gradients, so attributing ecosystem effects to invasion can be difficult in observational studies. Here, we assessed the impact of Phragmites australis invasion into native shortgrass communities on methane (CH₄) emissions by conducting field measurements of CH₄ emissions along transects of invasion by Phragmites in two neighboring brackish marsh sites and compared these findings to those from a field-based mesocosm experiment. We found remarkable differences in CH₄ emissions and the influence of Phragmites on CH₄ emissions between the two neighboring marsh sites. While Phragmites consistently increased CH₄ emissions dramatically by 10.4 ± 3.7 µmol m^?2 min^?1 (mean ± SE) in our high-porewater CH₄ site, increases in CH₄ emissions were much smaller (1.4 ± 0.5 µmol m^?2 min^?1) and rarely significant in our low-porewater CH₄ site. While CH₄ emissions in Phragmites-invaded zones of both marsh sites increased significantly, the presence of Phragmites did not alter emissions in a complementary mesocosm experiment. Seasonality and changes in temperature and light availability caused contrasting responses of CH₄ emissions from Phragmites- versus native zones. Our data suggest that Phragmites-mediated CH₄ emissions are particularly profound in soils with innately high rates of CH₄ production. We demonstrate that the effects of invasive species on ecosystem processes such as GHG emissions may be predictable qualitatively but highly variable quantitatively. Therefore, generalizations cannot be made with respect to invader-ecosystem processes, as interactions between the invader and local abiotic conditions that vary both spatially and temporally on the order of meters and hours, respectively, can have a stronger impact on GHG emissions than the invader itself.     

Carbon Dioxide and Methane Fluxes From Tree Stems,Coarse Woody Debris,and Soils in an Upland Temperate Forest

Forest soils and canopies are major components of ecosystem CO₂ and CH₄ fluxes. In contrast, less is known about coarse woody debris and living tree stems, both of which function as active surfaces for CO₂ and CH₄ fluxes. We measured CO₂ and CH₄ fluxes from soils, coarse woody debris, and tree stems over the growing season in an upland temperate forest. Soils were CO₂ sources (4.58 ± 2.46 µmol m^?2 s^?1, mean ± 1 SD) and net sinks of CH₄ (?2.17 ± 1.60 nmol m^?2 s^?1). Coarse woody debris was a CO₂ source (4.23 ± 3.42 µmol m^?2 s^?1) and net CH₄ sink, but with large uncertainty (?0.27 ± 1.04 nmol m^?2 s^?1) and with substantial differences depending on wood decay status. Stems were CO₂ sources (1.93 ± 1.63 µmol m^?2 s^?1), but also net CH₄ sources (up to 0.98 nmol m^?2 s^?1), with a mean of 0.11 ± 0.21 nmol m^?2 s^?1 and significant differences depending on tree species. Stems of N. sylvatica, F. grandifolia, and L. tulipifera consistently emitted CH₄, whereas stems of A. rubrum, B. lenta, and Q. spp. were intermittent sources. Coarse woody debris and stems accounted for 35% of total measured CO₂ fluxes, whereas CH₄ emissions from living stems offset net soil and CWD CH₄ uptake by 3.5%. Our results demonstrate the importance of CH₄ emissions from living stems in upland forests and the need to consider multiple forest components to understand and interpret ecosystem CO₂ and CH₄ dynamics.     

A comparative spin trapping study of the interaction of hypobromous and hypochlorous acids with <Emphasis Type="Italic">tert</Emphasis>-butyl hydroperoxide

Hypochlorite (HOCl/OCl^?) and hypobromite (HOBr/OBr^?) are shown to react with tert-butyl hydroperoxide with close rate constants (10.8 and 8.9 M^?1 s^?1, respectively). Using a spin trap α-(4-pyridyl-1-oxide)-N-tert-butyl nitrone, both reactions are shown to proceed through decomposition of the hydroperoxide yielding butylperoxyl [˙OOC(CH₃)₃] and butoxyl [˙OC(CH₃)₃] radicals in a ratio depending on the hydroperoxide concentration. Thus, like hypochlorite, hypobromite can generate free radicals in reactions with organic hydroperoxides, which can be important for intensification of free-radical processes, e.g., lipid peroxidation at the chain branching stage.     

Use of chemical ionization for GC–MS metabolite profiling

Metabolite profiling is commonly performed by GC–MS of methoximated trimethylsilyl derivatives. The popularity of this technique owes much to the robust, library searchable spectra produced by electron ionization (EI). However, due to extensive fragmentation, EI spectra of trimethylsilyl derivatives are commonly dominated by trimethylsilyl fragments (e.g. m/z 73 and 147) and higher m/z fragment ions with structural information are at low abundance. Consequently different metabolites can have similar EI spectra, and this presents problems for identification of “unknowns” and the detection and deconvolution of overlapping peaks. The aim of this work is to explore use of positive chemical ionization (CI) as an adjunct to EI for GC–MS metabolite profiling. Two reagent gases differing in proton affinity (CH₄ and NH₃) were used to analyse 111 metabolite standards and extracts from plant samples. NH₃-CI mass spectra were simple and generally dominated by [MH]⁺ and/or the adduct [M+NH₄]⁺. For the 111 metabolite standards, m/z 73 and 147 were less than 3% of basepeak in NH₃-CI and less than 30% of basepeak in CH₄-CI. With CH₄-CI, [MH]⁺ was generally present but at lower relative abundance than for NH₃-CI. CH₄-CI spectra were commonly dominated by losses of CH₄ [M+1-16]⁺, 1–3 TMSOH [M+1-nx90]⁺, and combinations of CH₄ and TMSOH losses [M+1-nx90-16]⁺. CH₄-CI and NH₃-CI mass spectra are presented for 111 common metabolites, and CI is used with real samples to help identify overlapping peaks and aid identification via determination of the pseudomolecular ion with NH₃-CI and structural information with CH₄-CI.     

Conformational Flexibility of Choline Derivatives

CHOLINERGIC substrates have been found in a gauche conformation (G), skewed about the C_α–C_β bond of the (CH₃)₃N⁺–CH₂–CH₂–O cholinic fragment in a number of crystal structures^1–11. Sulphur and selenium isologues, on the other hand, with the (CH₃)₃N–CH₂–CH₂–(S,Se) group, are normally in the extended trans conformations (T)^10,12,13. In agreement with the assumption that the reduced spectrum of biological activity of many rigid analogues and C_α or C_β substituted derivatives of acetylcholine can be partially ascribed to the reduction in conformational flexibility^14–17, a theoretical investigation¹⁸ predicted the existence of four almost isoenergetic conformations TTTT, TGTT, TTGT and TGGT about the ψ₀, ψ₁, ψ₂ and ψ₃ internal rotation angles schematically represented in Fig. 1.     

Growth and photosynthetic response of two larches exposed to O<Subscript>3</Subscript> mixing ratios ranging from preindustrial to near future

In this study, we questioned whether ground-level ozone (O₃) induces hormesis in Japanese larch (Larix kaempferi) and its hybrid F₁ (L. gmelinii var. japonica × L. kaempferi). In order to answer the question, we exposed seedlings of both taxa to four O₃ treatments [ranging from ≈10 to 60 nmol(O₃) mol^–1] in open-top chambers for two consecutive growing seasons. We found a hormetic response in maximum photosynthetic rate (P_Nmax) at 1700 μmol(CO₂) mol^–1 and maximum rates of carboxylation (V_cmax) and electron transport (J_max) in both larches. Stimulation of P_Nmax, V_cmax, and J_max did not lead to suppressed plant productivity in Japanese larch, which followed a stress-tolerant strategy, but it did lead to suppressed plant productivity in hybrid larch which followed a competitive strategy. These findings are the first to suggest that stimulation of physiological functions by low O₃ exposures may have negative consequences for larch reproduction.     

Asymmetric reduction of ketopantolactone using a strictly (<Emphasis Type="Italic">R</Emphasis>)-stereoselective carbonyl reductase through efficient NADPH regeneration and the substrate constant-feeding strategy

Objectives

To characterize a recombinant carbonyl reductase from Saccharomyces cerevisiae (SceCPR1) and explore its use in asymmetric synthesis of (R)-pantolactone [(R)-PL].

Results

The NADPH-dependent SceCPR1 exhibited strict (R)-enantioselectivity and high activity in the asymmetric reduction of ketopantolactone (KPL) to (R)-PL. Escherichia coli, coexpressing SceCPR1 and glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH), was constructed to fulfill efficient NADPH regeneration. During the whole-cell catalyzed asymmetric reduction of KPL, the spontaneous hydrolysis of KPL significantly affected the yield of (R)-PL, which was effectively alleviated by the employment of the substrate constant-feeding strategy. The established whole-cell bioreduction for 6 h afforded 458 mM (R)-PL with the enantiomeric excess value of >99.9% and the yield of 91.6%.

Conclusions

Escherichia coli coexpressing SceCPR1 and EsGDH efficiently catalyzed the asymmetric synthesis of (R)-PL through the substrate constant-feeding strategy.

     

Carbenicillin as Inhibitor of β-Lactamase from <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>

CARBENICILLIN was produced as a new, semi-synthetic penicillin with antibacterial activity against Pseudomonas aeruginosa and some other microorganisms¹, but this compound was known to be destroyed by staphylococcal penicillinase². Newsom et al.³ described the substrate profile of a constitutive β-lactamase from one strain of Pseudomonas aeruginosa and reported the hydrolysis of carbenicillin at a rate higher than benzylpenicillin. When compared with the inducible enzyme described by Sabath et al.⁴, it differed both in the substrate profile and the ability to hydrolyse carbenicillin. Lack of activity of the inducible enzyme on carbenicillin was also reported by Garber and Friedman⁵ when studying eight strains of Pseudomonas aeruginosa. Sykes and Richmond⁶ were able to identify three types of β-lactamases among fifty-six strains of Pseudomonas aeruginosa according to induci-bility, substrate profile and activity on carbenicillin. Type I (Sabath et al.⁴) was inducible, highly active on cephaloridine and showed no activity on carbenicillin. Types II (Sykes and Richmond⁷) and III (Newsom et al.³) were constitutive and inactivated carbenicillin at different rates. Only the constitutive enzymes conferred resistance towards carbenicillin. We have investigated the activity on carbenicillin of β-lactamases from strains of Pseudomonas aeruginosa isolated from clinical specimens. Activity on benzylpenicillin and cephaloridine was also studied.     

Purification of recombinant extracellular proteases from <Emphasis Type="Italic">Bacillus pumilus</Emphasis> for ß-amyloid peptide cleavage

Using the expression vector pGP382 containing a constitutive promoter (P _degQ36 ) and an affinity tag (Strep-tag), we have obtained highly purified recombinant Bacillus pumilus 3-19 proteinases with different substrate specificities: glutamylendopeptidase (GseBp), subtilisin-like protease (AprBp), and metalloendopeptidase (MprBp). The products of the hydrolysis of the ß-amyloid peptide by the bacterial proteases from B. pumilus have been studied. The findings on the potential of the practical application of these bacterial enzymes as the agents preventing the development of the Alzheimer’s disease are presented.     

Kinetic Analyses of the Substrate Inhibition of <Emphasis Type="Italic">Paramecium</Emphasis> Arginine Kinase

Paramecium tetraurelia expresses four types of arginine kinase (AK1–AK4). In a previous study, we showed that AK3 is characterized by typical arginine substrate inhibition, where enzymatic activity markedly decreases near a concentration of 1 mM of arginine substrate. This is in sharp contrast to the three other AK types, which obey the Michaelis–Menten reaction curve. Since cellular arginine concentration in another ciliate Tetrahymena is estimated to be 3–15 mM in vivo, Paramecium AK3 likely functions in conditions that are strongly affected by substrate inhibition. The purpose of this work is to find some novel aspect on the kinetic mechanism of the substrate inhibition of Paramecium AK3 enzyme. Substrate inhibition kinetics for AK3 were analyzed using three models and their validity were evaluated with three static parameters (R², AICc, and Sy.x). The most accurate model indicated that not only ES but also the SES complex reacts to form products, the latter being the complex with two substrates in the active center. The maximum reaction rate for the SES complex, V_max^SES?=?30.4 µmol Pi/min/mg protein, was one-eighth of the ES complex, V_max^ES?=?241.7. The dissociation constant for the SES complex (K_i^SES: 0.34 mM) was two times smaller than that of the ES complex (K_s^ES: 0.61 mM), suggesting that after the primary binding of the arginine substrate (ES complex formation), the binding of a second arginine to the secondarily induced inhibitory site is accelerated to form an SES complex with a lower V_max^SES. The same kinetics were used for the S79A, S80A, and V81A mutants. The results indicate that the S79 residue is significantly involved in the process of binding the second arginine substrate. Herein, the K_i^SES value was ten times (3.62 mM) the value for the wild-type (0.34 mM), weakening substrate inhibition. In contrast, V_max^ES and V_max^SES values for the mutants decreased by one-third, except for the V_max^SES of the S79A mutant, which had a value that was comparable with the value for the wild-type.     

Assessment of photosynthetic potential of indoor plants under cold stress

Photosynthetic parameters including net photosynthetic rate (P_N), transpiration rate (E), water-use efficiency (WUE), and stomatal conductance (g_s) were studied in indoor C₃ plants Philodendron domesticum (Pd), Dracaena fragans (Df), Peperomia obtussifolia (Po), Chlorophytum comosum (Cc), and in a CAM plant, Sansevieria trifasciata (St), exposed to various low temperatures (0, 5, 10, 15, 20, and 25°C). All studied plants survived up to 0°C, but only St and Cc endured, while other plants wilted, when the temperature increased back to room temperature (25°C). The P_N declined rapidly with the decrease of temperature in all studied plants. St showed the maximum P_N of 11.9 μmol m^?2 s^?1 at 25°C followed by Cc, Po, Pd, and Df. E also followed a trend almost similar to that of P_N. St showed minimum E (0.1 mmol m^?2 s^?1) as compared to other studied C₃ plants at 25°C. The E decreased up to ≈4-fold at 5 and 0°C. Furthermore, a considerable decline in WUE was observed under cold stress in all C₃ plants, while St showed maximum WUE. Similarly, the g_s also declined gradually with the decrease in the temperature in all plants. Among C₃ plants, Pd and Po showed the maximum g_s of 0.07 mol m^?2 s^?1 at 25°C followed by Df and Cc. However, St showed the minimum g_s that further decreased up to ～4-fold at 0°C. In addition, the content of photosynthetic pigments [chlorophyll a, b, (a+b), and carotenoids] was varying in all studied plants at 0°C. Our findings clearly indicated the best photosynthetic potential of St compared to other studied plants. This species might be recommended for improving air quality in high-altitude closed environments.     

Comparison of microbial communities during the anaerobic digestion of <Emphasis Type="Italic">Gracilaria</Emphasis> under mesophilic and thermophilic conditions

Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH₄/g volatile solids (VS) and 246.1 ± 11 mL CH₄/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.     

OH Radicals in Radiation Sensitization

CELLS can be sensitized to ionizing radiation by chemical compounds and this offers opportunity for investigating the mechanisms intermediate between energy absorption and expression of biological effect. Concentration dependence seems to be an important factor for the effectiveness of a radiation sensitizer. The inactivation constant k for X-irradiated suspensions of Bacillus megaterium spores shows a peak at 3 × 10^?3 M diacetyl (CH₃COCOCH₃) concentration¹. Although the mechanism of this effect is unknown, certain free radical reactions have been suggested^2–4. The decrease of k with increasing sensitizer concentration, envisaged as a protective action, indicates a competitive reaction in which the species contributing to the lethality are removed.