Structural features of ß-(1→4)-D-galactomannans of plant origin as a probe for ß-(1→4)-mannanase polymeric substrate specificity.

Statistical modeling was applied for describing structural features of ß-(1→4)-D-galactomannans. According to the model suggested theoretical ratios of limiting degrees of locust bean, tara gum and guar gum galactomannan conversions by two ß-(1→4)-mannanases of different origin (Myceliophthora thermophila and Trichoderma reesei) were calculated. Then the enzymes were tested for enzymatic hydrolysis of three considered galactomannans. Experimentally observed results were compared with theoretically calculated ones. It was shown that T. reesei ß-mannanase attacks sequences of four and more unsubstituted mannopyranosyl residues in a row, while M. thermophila ß-mannanase is a more specific enzyme and attacks sequences of five and more mannopyranosyl residues in a row. Considered statistical model and approach allows to characterize both galactomannan structures and enzyme requirements for regions of unsubstituted mannose residues for substrate hydrolysis.

Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the foundation for "molecular history", in which the principal tool is high-technology analysis of DNA molecules of both our contemporaries and excavated ancient DNA samples, along with their biological kinetics.

Class 2 aldehyde dehydrogenase. Characterization of the hamster enzyme, sensitive to daidzin and conserved within the family of multiple forms.

Mitochondrial (class 2) hamster aldehyde dehydrogenase has been purified and characterized. Its primary structure has been determined and correlated with the tertiary structure recently established for this class from another species. The protein is found to represent a constant class within a complex family of multiple forms. Variable segments that occur in different species correlate with non-functional segments, in the same manner as in the case of the constant class of alcohol dehydrogenases (class III type) of another protein family, but distinct from the pattern of the corresponding variable enzymes. Hence, in both these protein families, overall variability and segment architectures behave similarly, with at least one 'constant' form in each case, class III in the case of alcohol dehydrogenases, and at least class 2 in the case of aldehyde dehydrogenases.

Daidzin inhibits mitochondrial aldehyde dehydrogenase and suppresses ethanol intake of Syrian golden hamsters.

Daidzin is the major active principle in extracts of radix puerariae, a traditional Chinese medication that suppresses the ethanol intake of Syrian golden hamsters. It is the first isoflavone recognized to have this effect. Daidzin is also a potent and selective inhibitor of human mitochondrial aldehyde dehydrogenase (ALDH-2). To establish a link between these two activities, we have tested a series of synthetic structural analogs of daidzin. The results demonstrate a direct correlation between ALDH-2 inhibition and ethanol intake suppression and raise the possibility that daidzin may, in fact, suppress ethanol intake of golden hamsters by inhibiting ALDH-2. Hamster liver contains not only mitochondrial ALDH-2 but also high concentrations of a cytosolic form, ALDH-1, which is a very efficient catalyst of acetaldehyde oxidation. Further, the cytosolic isozyme is completely resistant to daidzin inhibition. This unusual property of the hamster ALDH-1 isozyme accounts for the fact we previously observed that daidzin can suppress ethanol intake of this species without blocking acetaldehyde metabolism. Thus, the mechanism by which daidzin suppresses ethanol intake in golden hamsters clearly differs from that proposed for the classic ALDH inhibitor disulfiram. We postulate that a physiological pathway catalyzed by ALDH-2, so far undefined, controls ethanol intake of golden hamsters and mediates the antidipsotropic effect of daidzin.

Possible role of liver cytosolic and mitochondrial aldehyde dehydrogenases in acetaldehyde metabolism.

To provide a molecular basis for understanding the possible mechanism of action of antidipsotropic agents in laboratory animals, aldehyde dehydrogenase (ALDH) isozymes were purified and characterized from the livers of hamsters and rats and compared with those from humans. The mitochondrial ALDHs from these species exhibit virtually identical kinetic properties in the oxidation and hydrolysis reactions. However, the cytosolic ALDH of human origin differs significantly from those of the rodents. Thus, for human ALDH-1, the Km value for acetaldehyde is 180 +/- 10 micromolar, whereas those for hamster ALDH-1 and rat ALDH-1 are 12 +/- 3 and 15 +/- 3 micromolar, respectively. Km values determined at pH 9.5 are virtually identical to those measured at pH 7.5. In vitro human ALDH-1 is 10 times less sensitive to disulfiram inhibition than are the hamster and rat cytosolic ALDHs. Competition between acetaldehyde and aromatic aldehydes or naphthaldehydes for the binding and catalytic sites of ALDHs shows their topography to be complex with more than one binding site. This also follows from data on substrate inhibition and activation, effects of NAD+ on ALDH-catalyzed hydrolysis of p-nitrophenyl esters, substrate specificity toward aldehydes and p-nitrophenyl esters, and inhibition by disulfiram in relation to oxidation and hydrolysis catalyzed by the ALDHs. The data further suggest that acetaldehyde cannot be considered as a "standard" ALDH substrate for studies aimed at aromatic ALDH substrates, e.g. biogenic aldehydes. Apparently, in human liver, only mitochondrial ALDH oxidizes acetaldehyde at physiological concentrations, whereas in hamster or rat liver, both the mitochondrial and cytosolic isozymes will do so.

Kinetics and specificity of human liver aldehyde dehydrogenases toward aliphatic, aromatic, and fused polycyclic aldehydes.

Human mitochondrial aldehyde dehydrogenase (ALDH-2) has a Km for acetaldehyde that is 900-fold lower than that for the cytosolic isozyme, ALDH-1. An increase in aliphatic aldehyde chain length decreases the ALDH-2 Km by up to 10-fold but decreases that of ALDH-1 by 5 orders of magnitude. As a consequence, the Km of ALDH-1 for decanal is 8 times lower than that of ALDH-2, i.e. 2.9 +/- 0.4 and 22 +/- 3 nM, respectively. Determination of these low Km values required kinetic analysis of the simultaneous enzymatic conversion of two aldehyde substrates, an approach also applied to aromatic and fused polycyclic aldehydes. For most of these substrates, maximum velocities are 5-100 times lower than those for acetaldehyde. Addition of one of these tight-binding, slow-turnover substrates to a reaction mixture containing ALDH, NAD+, and a "reference" aldehyde substrate (e.g. acetaldehyde) blocks the principal (reference) enzymatic reaction temporarily and reversibly. Once the first substrate is converted to product, the enzyme can act on the reference substrate. In terms of apparent affinity and blocking capacity, naphthalene and phenanthrene aldehydes were the most potent effectors. Other aromatic and fused polycyclic and heterocyclic aldehydes, as well as derivatives of coumarin, quinoline, indole, and pyridine, are tight-binding, slow-turnover substrates for ALDH-2 and relatively weak inhibitors of ALDH-1. The hydrophobicity of substituents of benzaldehydes, and particularly of naphthaldehydes, correlates with their binding constants toward ALDH-2. Vitamin A1 aldehydes are specific natural substrates for ALDH-1; at pH 7.5, for all-trans- and 13-cis-retinal, Km = 1.1 and 0.37 micromolar, respectively, and kcat/Km is 50-100 times higher than that for acetaldehyde. At the same time, the retinals are inhibitors of ALDH-2, all-trans-retinal being a particularly potent inhibitor (competitive Ki = 43 nM, noncompetitive Ki = 316 nM). These properties suggest that all-trans-retinal is a possible regulatory compound for ALDH-2 in vivo. The data in general point to specialized roles for both major human liver ALDH isozymes in the oxidation of bulky/hydrophobic natural compounds, with Km values in the low nanomolar range.

Human liver aldehyde dehydrogenases: new method of purification of the major mitochondrial and cytosolic enzymes and re-evaluation of their kinetic properties.

A new purification procedure, based on dye-adsorption and affinity chromatography, has been developed for the isolation of the two major ALDH isozymes from human liver: ALDH-1 (cytosolic, pI 5.2) and ALDH-2 (mitochondrial, pI 4.9). The procedure affords milligram quantities of ALDH-1 and -2 at 850- and 275-fold purifications, respectively, from 50 g of liver in two days. Kinetic parameters for acetaldehyde oxidation were determined with these purified enzymes, because there is a wide discrepancy in the absolute magnitude of these parameters in the biochemical literature. The Michaelis constants for ALDH-1 and -2, determined from initial velocities (for ALDH-1) and single reaction progress curves (for ALDH-2), are 180 +/- 10 microM and 0.20 +/- 0.02 microM, respectively (pH 7.5 and 9.5, saturating NAD+ in both cases). This three orders of magnitude difference in Km values is much greater than that reported previously in all but one study.

A method for detection of cellulases in polyacrylamide gels using 5-bromoindoxyl-beta-D-cellobioside: high sensitivity and resolution.

The assay of endo-1,4-beta-glucanases (cellulases) from Trichoderma reesei, T. longibrachiatum, and Sporotrichum pulverulentum by 5-bromoindoxyl-beta-D-cellobioside is described. The substrate is enzymatically cleaved to afford 5-bromoindoxyl and latter undergoes immediate azo coupling with Fast Red or oxidation by nitroblue monotetrazolium chloride, various forms of endoglucanases which can thus be assayed in polyacrylamide gel.

Continuous photometric determination of endo-1,4-beta-D-glucanase (cellulase) activity using 4-methylumbelliferyl-beta-D-cellobioside as a substrate.

A very simple and sensitive procedure for the determination of the activity of highly purified endo-1,4-beta-glucanase from the microscopic fungus Trichoderma reesei using 4-methylumbelliferyl-beta-D-cellobioside has been developed. The HPLC study has shown that this substrate is cleaved by endo-1,4-beta-glucanase to form predominantly free 4-methylumbelliferone, Km and kcat being 1.25 mM and 7.9 s-1, respectively (30 degrees C, pH 5.0). The possibility of continuous photometric determination of the enzyme using the difference absorptivity coefficient of 1600 M-1 cm-1 at 350 nm has been demonstrated.

The titration of the active centers of cellobiohydrolase from Trichoderma reesei.

A novel approach has been developed for the titration of enzyme active centers and for the determination of the molecular activity of enzymes. It is based on the simultaneous use of a nonspecific chromogenic substrate and a specific ligand (a substrate or an inhibitor), the latter being tightly bound with the enzyme's active center. The approach is demonstrated using the titration (that is, the determination of the molar concentration of the enzyme active centers) of purified cellobiohydrolase I (CBH I) (EC 3.2.1.91) of the fungus Trichoderma reesei. p-Nitrophenyl-beta-D-lactoside was used as a reference substrate (Km = 0.5 mM), and cellobiose and CM-cellulose as specific ligands. The molecular weight of CBH I as it was determined by the titration with cellobiose was 42,000 +/- 3,000. The inhibition constant by cellobiose was (6 +/- 1) X 10(-6) M. The value of the catalytic constant for the hydrolysis of p-nitrophenyl-beta-D-lactoside calculated from the titration data was equal to 0.063 s-1. CM-cellulose turned out to be more efficient titration agent for cellobiohydrolase than cellobiose, and might be used for the titration of the enzyme in concentrations of the latter of 0.008-0.02 mg/ml. The titration data showed that the inhibition constant of CM-cellulose toward CBH I was equal to (1.0 +/- 0.2) X 10(-7) M.

The activation of cellulases from different sources by actin.

Actin has been shown to be a potent activator of the enzymatic hydrolysis of cellulose, its addition to the reaction mixture leading to an increase in the hydrolysis rate of up to 6-7 fold. The action of actin is directed primarily towards endoglucanases of cellulase complexes. The degree of activation varies in relation to the cellulases from different microbial sources. The activation of the enzymatic hydrolysis of an insoluble cellulose by actin does not affect the Michaelis constant but increases the maximum velocity of the reaction. Increasing the actin concentration leads to a linear increase in the activation effect which indicates a rather poor binding of actin with the cellulases under study.

The thermostability of glucoamylase immobilized in different ways has a certain limit.

Thermostability of glucoamylase from Aspergillus niger is increased both by immobilization and substrate binding. However, the total superimposed stabilization effect at a given condition is apparently restricted by a certain limit which hardly depends on the mode of immobilization of the enzyme, and is determined mostly by the enzyme-substrate complex formation.

Circular dichroism-inhibitor titrations of arsanilazotyrosine-248 carboxypeptidase A.

Coupling of carboxypeptidase with diazotized arsanilic acid specifically modifies a single tyrosyl residue. Yet, owing to the fact that the resultant azoTyr-248 can form an intramolecular chelate with zinc, two different circular dichroism probes result: azoTyr-248 itself and the azoTyr-248-Zn chelate. Both are environmentally sensitive and, characteristically, each can signal the same or different perturbations, as is apparent from circular dichroic spectra. This dual probe function greatly magnifies the scope of these chromophores in mapping the topography of the active center with respect to sites of interaction of inhibitors (or substrates). Titration of the azoenzyme with a series of synthetic, competitive inhibitors, e.g., L-benzylsuccinate, L-phenyllactate, and L-Phe, and with the pseudosubstrate, Gly-L-Tyr, in turn generates characteristic circular dichroic spectra. Their analysis yields a single binding constant for each of these agents, one molecule of each binding to the active center. Mixed inhibitions, as seen with beta-phenylpropionate and phenylacetate, resolved previously into competitive and noncompetitive components, are characterized by different spectral effects. Two molecules of these agents bind to the enzyme, consistent with both thermodynamic and enzymatic studies. The interactions leading to competitive and noncompetitive inhibition, respectively, can be recognized and assigned, based on the manner in which the extrema at 340 and 420 nm, reflecting azoTyr-248, and the negative 510-nm circular dichroism band, typical of its chelate with zinc, are affected and on the pH dependence of spectral and kinetic data. Certai4 noncompetitive inhibitors and modifiers induce yet other spectral features. Each probe is very sensitive to changes in its particular active center environment, though both can be relatively insensitive to inhibitors interacting at a distance from the active center.

The reactions of alpha-chymotrypsin and related proteins with ester substrates in non-aqueous solvents.

1. The reactivity of alpha-chymotrypsin toward p-nitrophenylacetate has been studied in dimethylformamide, dimethylsulfoxide, formamide and methylacetamide. p-Nitrophenol is liberated in dimethylsulfoxide only. 2. The reactions of alpha-chymotrypsin in dimethylsulfoxide are characterized by the same kinetic and equilibrium constants with either the p-nitrophenyl esters of straight chain carboxylic acids (from acetic to n-caprylic) or with the "specific substrate", N-carbobenzoxy-DL-phenylalanine p-nitrophenyl ester. This signifies that reactions of alpha-chymotrypsin in dimethylsulfoxide, unlike those in aqueous medium, have no specificity toward su-strate structure. 3. The stoichiometry of alpha-chymotrypsin reactions in dimethylsulfoxide was shown to be about five moles of substrate per mole of enzyme. After attaining this stoichiometry, the reaction is completed. 4. Optical rotatory dispersion spectra indicate that in non-aqueous media alpha-chymotrypsin undergoes a large conformational transition which results in a random coil. 5. Chymotrypsinogen, trypsin, trysinogen, lysozyme and serum albumin react with p-nitrophenylacetate in dimethylsulfoxide at rates which are approximately equal to those of alpha-chymotrypsin. Thus, the "activity" of alpha-chymotrypsin in dimethylsulfoxide toward p-nitrophenylacetate does not differ from the "activity" of other proteins, some of which are not even hydrolytic enzymes.

[Conformation aspects of peptide interaction with proteolytic enzymes. Alpha-chymotrypsin catalyzed hydrolysis of the cyclopeptides containing leucyltyrosyl fragments].

The studies were made on the interaction of alpha-chymotrypsin with a series of cyclopeptides cyclo(-L-leucyl-L-tyrosyl-glycyln-), n=4, 6 and 8 (I, II and III respectively), and cyclo(-L-leucyl-L-tryosyl-beta-aminovalero-yl2-) (IV). Compounds I and IV are resistant to enzyme action whereas cyclopeptides II and III proved to be the substrates, their kinetic constants being Km=15.4 and 13.2 mM and kcat=0.54 and 9.53 sec-1 respectively. The binding capacity of cyclopeptides I-IV is evaluated by their competitive inhibition of alpha-chymotrypsin catalyzed hydrolysis of N-acetyl-L-tyrosine methyl ester.