A novel bifunctional peptidic aspartic protease inhibitor inhibits chitinase A from Serratia marcescens: Kinetic analysis of inhibition and binding affinity

Background

Chitinase inhibitors have chemotherapeutic potential as fungicides, pesticides and antiasthmatics. The majority of chitinase inhibitors reported are natural products like argifin, argifin linear fragments, argadin, allosamidin and disulfide-cyclized peptides. Here, we report a novel peptidic inhibitor API (Aspartic Protease Inhibitor), isolated from Bacillus licheniformis that inhibits chitinase A (ChiA) from Serratia marcescens.

Methods

The binding affinity of API with ChiA and type of inhibition was determined by the inhibition kinetics assays. Fluorescence and CD spectroscopic analysis and chemical modification of API with different affinity reagents elucidated the mechanism of binding of API with ChiA.

Results and conclusions

The peptide has an amino acid sequence N-Ile¹-Cys²-Glu³-Ala⁴-Glu⁵-His⁶-Lys⁷-Trp⁸-Gly⁹-Asp¹⁰-Tyr¹¹-Leu¹²-Asp¹³-C. The ChiA–API kinetic interactions reveal noncompetitive, irreversible and tight binding nature of API with I₅₀ = 600 nM and K_i = 510 nM in the presence of chromogenic substrate p-nitrophenyl-N,N′-diacetyl-β-chitobioside[p-NP-(GlcNAc)₂]. The inhibition progress curves show a two-step slow tight binding inhibition mechanism with the rate constant k₅ = 8.7 ± 1 × 10^− 3 s^− 1 and k₆ = 7.3 ± 0.6 × 10^− 5 s^− 1. CD-spectra and tryptophanyl fluorescence analysis of ChiA incubated with increasing API concentrations confirms conformational changes in enzyme structure which may be due to irreversible denaturation of enzyme upon binding of API. Chemical modifications by WRK abolished the anti-chitinase activity of API and revealed the involvement of carboxyl groups in the enzyme inactivation. Abolished isoindole fluorescence of OPTA-labeled ChiA demonstrates the irreversible denaturation of ChiA upon incubation with API for prolonged time and distortion of active site of the enzyme.

General significance

The data provide useful information that could lead to the generation of drug-like, natural product-based chitinase inhibitors.     

Inhibition of plasma membrane Ca-ATPase by CrATP. LaATP but not CrATP stabilizes the Ca-occluded state

The bidentate complex of ATP with Cr³⁺, CrATP, is a nucleotide analog that is known to inhibit the sarcoplasmic reticulum Ca²⁺-ATPase and the Na⁺,K⁺-ATPase, so that these enzymes accumulate in a conformation with the transported ion (Ca²⁺ and Na⁺, respectively) occluded from the medium. Here, it is shown that CrATP is also an effective and irreversible inhibitor of the plasma membrane Ca²⁺-ATPase. The complex inhibited with similar efficiency the Ca²⁺-dependent ATPase and the phosphatase activities as well as the enzyme phosphorylation by ATP. The inhibition proceeded slowly (T_1/2 = 30 min at 37 °C) with a K_i = 28 ± 9 μM. The inclusion of ATP, ADP or AMPPNP in the inhibition medium effectively protected the enzyme against the inhibition, whereas ITP, which is not a PMCA substrate, did not. The rate of inhibition was strongly dependent on the presence of Mg²⁺ but unaltered when Ca²⁺ was replaced by EGTA. In spite of the similarities with the inhibition of other P-ATPases, no apparent Ca²⁺ occlusion was detected concurrent with the inhibition by CrATP. In contrast, inhibition by the complex of La³⁺ with ATP, LaATP, induced the accumulation of phosphoenzyme with a simultaneous occlusion of Ca²⁺ at a ratio close to 1.5 mol/mol of phosphoenzyme. The results suggest that the transport of Ca²⁺ promoted by the plasma membrane Ca²⁺-ATPase goes through an enzymatic phospho-intermediate that maintains Ca²⁺ ions occluded from the media. This intermediate is stabilized by LaATP but not by CrATP.     

Development of a scintillation proximity assay binding method for the human 5-hydroxytryptamine 6 receptor using intact cells

We describe the first validated scintillation proximity assay (SPA) binding method for quantitation of ³H-labeled d-lysergic acid diethylamide (LSD) binding to recombinant human 5-hydroxytryptamine 6 (5-HT₆) receptors expressed in Chinese hamster ovary (CHO)-Dukx and HeLa cells. The assay was developed using intact cells as a receptor source because membrane fractions derived from these cells failed to discern specific binding from a high level of nonspecific binding. The pharmacological binding profile of seven 5-HT₆ agonists and antagonists using intact CHO-Dukx/5-HT₆ cells in the SPA format was similar to data obtained from a filtration binding assay using HeLa/5-HT₆ membranes. K_i values and rank order of potencies obtained in the SPA format were consistent with published filtration data as follows: SB-271046 (K_i = 1.9 nM) > methiothepin (K_i = 6.2 nM) > mianserin (K_i = 74.3 nM) > 5-methoxytryptamine (5-MeOT, K_i = 111 nM) > 5-HT (K_i = 150 nM) > ritanserin (K_i = 207 nM) > 5-carboxamidotryptamine (5-CT, K_i = 704 nM). Additional evaluation with four antipsychotics demonstrated strong agreement with previous literature reports. A high specific binding signal and low assay variability, as determined by Z′ = 0.81 ± 0.017, make the SPA format amenable to automation and higher throughput; hence, this assay can be a viable alternative to the more labor-intensive filtration and centrifugation methods.     

Reactivity study of arene(azido)ruthenium N∩O-base complexes with activated alkynes

Substitution reaction of chloro η⁶-arene ruthenium N∩O-base complexes [(η⁶-arene)Ru(N∩O)Cl] [N∩O = pyrazine-2-carboxylic acid (pca-H), 8-hydroxyquinoline (hq-H); arene = p-ⁱPrC₆H₄Me, N∩O = hq (1); arene = C₆Me₆, N∩O = hq (2)] with NaN₃ yield the neutral arene ruthenium azido complexes of the general formula [(η⁶-arene)Ru(N∩O)N₃] [N∩O = pca, arene = p-ⁱPrC₆H₄Me (3), arene = C₆Me₆ (4); N∩O = hq, arene = p-ⁱPrC₆H₄Me (5), arene = C₆Me₆ (6)]. These complexes undergo [3 + 2] dipolar cycloaddition reaction with activated alkynes dimethyl and diethyl acetylenedicarboxylates to yield the arene triazole complexes [(η⁶-arene)Ru(N∩O){N₃C₂(CO₂R)₂}] [N∩O = pca, R = Me, arene = p-ⁱPrC₆H₄Me (7), C₆Me₆ (8); R = Et, arene = p-ⁱPrC₆H₄Me (9), C₆Me₆ (10); N∩O = hq, R = Me, arene = p-ⁱPrC₆H₄Me (11) C₆Me₆ (12); R = Et, arene = p-ⁱPrC₆H₄Me (13), C₆Me₆ (14)]. On the bases of proton NMR study, in the above triazole complexes N(2) isomers are assigned with dimethylacetylenedicarboxylate whereas N(1) isomers with diethylacetylenedicarboxylate. All complexes have been characterized by IR and NMR spectroscopy as well as by elemental analysis. The molecular structures of the azido complexes [(η⁶-p-ⁱPrC₆H₄Me)Ru(pca)N₃] (3), [(η⁶-p-ⁱPrC₆H₄Me)Ru(hq)N₃] (5) and [(η⁶-C₆Me₆)Ru(hq)N₃] (6) have been established by single crystal X-ray diffraction studies.     

Bio-kinetic analysis on treatment of textile dye wastewater using anaerobic batch reactor

An anaerobic digestion technique was applied to textile dye wastewater aiming at the colour and COD removal. Pet bottles of 5 L capacity were used as reactor which contains methanogenic sludge of half a liter capacity which was used for the treatment of combined synthetic textile dye and starch wastewater at different mixing ratios of 20:80, 30:70, 40:60, 50:50 and 60:40 with initial COD concentrations as 3520, 3440, 3360, 3264 and 3144 mg L⁻¹, respectively. The reactor was maintained at room temperature (30 ± 3 °C) with initial pH of 7. The maximum COD and colour removal were 81.0% and 87.3% at an optimum mixing ratio of 30:70 of textile dye and starch wastewaters. Both Monod’s and Haldane’s models were adopted in this study. The kinetic constants of cell growth under Haldane’s model were satisfactory when compared to Monod’s model. The kinetic constants obtained by Haldane’s model were found to be in the range of μ_max = 0.037-0.146 h⁻¹, K_s = 651.04-1372.88 mg L⁻¹ and K_i = 5681.81-18727.59 mg L⁻¹.     

Interaction of human 3-phosphoglycerate kinase with L-ADP, the mirror image of D-ADP

l-Nucleoside-analogues, mirror images of the natural d-nucleosides, are a new class of antiviral and anticancer agents. In the cell they have to be phosphorylated to pharmacologically active triphosphate forms, the last step seems to involve human 3-phosphoglycerate kinase (hPGK). Here we present a steady state kinetic and biophysical study of the interaction of the model compound l-MgADP with hPGK. l-MgADP is a good substrate with k_cat and K_m values of 685 s⁻¹ and 0.27 mM, respectively. Double inhibition studies suggest that l-MgADP binds to the specific adenosine-binding site and protects the conformation of hPGK molecule against heat denaturation, as detected by microcalorimetry. Structural details of the interaction in the enzyme active site are different for the d- and l-enantiomers (e.g. the effect of Mg²⁺), but these differences do not prevent the occurrence of the catalytic cycle, which is accompanied by the hinge-bending domain closure, as indicated by SAXS measurements.     

Molecular hybridization of 4-azahexacyclo[5.4.1.0(2,6).0(3,10).0(5,9).0(8,11)]dodecane-3-ol with sigma (σ) receptor ligands modulates off-target activity and subtype selectivity

A series of N-substituted 4-azahexacyclo[5.4.1.0^2,6.0^3,10.0^5,9.0^8,11]dodecan-3-ols incorporating the respective arylalkyl subunits from several known sigma (σ) receptor ligands were synthesized and evaluated for their affinity against σ receptors and dopamine receptors. The hybrid trishomocubane-derived ligands (4-6) showed good selectivity for σ₁ and σ₂ receptors over multiple dopamine receptors. The molecular hybrid obtained from haloperidol and 4-azahexacyclo[5.4.1.0^2,6.0^3,10.0^5,9.0^8,11]dodecan-3-ol (4, σ₁K_i = 27 nM, σ₂K_i = 55 nM) showed reduced affinity for D₁-D₅ dopamine receptors when compared to haloperidol itself. The compound with the greatest σ₁ affinity in the series, benzamide 4 (σ₁K_i = 7.6 nM, σ₂K_i = 225 nM) showed a complete reversal of the subtype selectivity displayed by the highly σ₂ selective parent benzamide, RHM-2 (3, σ₁K_i = 10412 nM, σ₂K_i = 13.3 nM).     

Biochemical characterization of a low molecular weight aspartic protease inhibitor from thermo-tolerant Bacillus licheniformis: Kinetic interactions with Pepsin

The present article reports a low molecular weight aspartic protease inhibitor, API, from a newly isolated thermo-tolerant Bacillus licheniformis. The inhibitor was purified to homogeneity as shown by rp-HPLC and SDS-PAGE. API is found to be stable over a broad pH range of 2–11 and at temperature 90 °C for 2 1/2 h. It has a Mr (relative molecular mass) of 1363 Da as shown by MALDI-TOF spectra and 1358 Da as analyzed by SDS-PAGE .The amino acid analysis of the peptide shows the presence of 12 amino acid residues having Mr of 1425 Da. The secondary structure of API as analyzed by the CD spectra showed 7% α-helix, 49% β-sheet and 44% aperiodic structure. The Kinetic studies of Pepsin–API interactions reveal that API is a slow-tight binding competitive inhibitor with the IC₅₀ and K_i values 4.0 nM and (3.83 nM–5.31 nM) respectively. The overall inhibition constant K_i? value is 0.107 ± 0.015 nM. The progress curves are time-dependent and consistent with slow-tight binding inhibition: E + I ? (k₄, k₅) EI ? (k₆, k₇) EI?. Rate constant k₆ = 2.73 ± 0.32 s^− 1 reveals a fast isomerization of enzyme–inhibitor complex and very slow dissociation as proved by k₇ = 0.068 ± 0.009 s^− 1. The Rate constants from the intrinsic tryptophanyl fluorescence data is in agreement with those obtained from the kinetic analysis; therefore, the induced conformational changes were correlated to the isomerization of EI to EI?.     

NMR for direct determination of Km and Vmax of enzyme reactions based on the Lambert W function-analysis of progress curves

¹H NMR spectroscopy was used to follow the cleavage of sucrose by invertase. The parameters of the enzyme's kinetics, K_m and V_max, were directly determined from progress curves at only one concentration of the substrate. For comparison with the classical Michaelis-Menten analysis, the reaction progress was also monitored at various initial concentrations of 3.5 to 41.8 mM. Using the Lambert W function the parameters K_m and V_max were fitted to obtain the experimental progress curve and resulted in K_m = 28 mM and V_max = 13 μM/s. The result is almost identical to an initial rate analysis that, however, costs much more time and experimental effort. The effect of product inhibition was also investigated. Furthermore, we analyzed a much more complex reaction, the conversion of farnesyl diphosphate into (+)-germacrene D by the enzyme germacrene D synthase, yielding K_m = 379 μM and k_cat = 0.04 s^− 1. The reaction involves an amphiphilic substrate forming micelles and a water insoluble product; using proper controls, the conversion can well be analyzed by the progress curve approach using the Lambert W function.     

Skeletal muscle glycogen phosphorylase is irreversibly inhibited by mercury: Molecular,cellular and kinetic aspects

Muscle glycogen phosphorylase (GP) plays an important role in muscle functions. Mercury has toxic effects in skeletal muscle leading to muscle weakness or cramps. However, the mechanisms underlying these toxic effects are poorly understood. We report that GP is irreversibly inhibited by inorganic (Hg²⁺) and organic (CH₃Hg⁺) mercury (IC₅₀ = 380 nM and k_inact = 600 M⁻¹ s⁻¹ for Hg²⁺ and IC₅₀ = 43 μM and k_inact = 13 M⁻¹ s⁻¹ for CH₃Hg⁺) through reaction of these compounds with cysteine residues of the enzyme. Our data suggest that the irreversible inhibition of GP could represent one of the mechanisms that contribute to mercury-dependent muscle toxicity.     

Structure and magnetic properties of a tetranuclear Cu4O4 open-cubane in [Cu(L)]4·4H2O with L = (E)-N′-(2-oxy-3-methoxybenzylidene)benzohydrazide

The in-situ formed hydrazone Schiff base ligand (E)-N′-(2-oxy-3-methoxybenzylidene)benzohydrazide (L²⁻) reacts with copper(II) acetate to a tetranuclear open cubane [Cu(L)]₄ complex which crystallizes as two symmetry-independent (Z′ = 2) S₄-symmetrical molecules in different twofold special positions with a homodromic water tetramer. The two independent (A and B) open- or pseudo-cubanes with Cu₄O₄ cores of 4 + 2 class (Ruiz classification) each have three different magnetic exchange pathways leading to an overall antiferromagnetic coupling with J_1B = J_2B = −17.2 cm⁻¹, J_1A = −36.7 cm⁻¹, J_2A = −159 cm⁻¹, J_3A = J_3B = 33.5 cm⁻¹, g = 2.40 and ρ = 0.0687. The magnetic properties have been analysed using the H = −Σ_i,jJ_ij(S_iS_j) spin Hamiltonian.     

Chemical implantation of Group 4 cations on silica via cyclopentadienyl- and N,N-dialkylcarbamato derivatives

Chemical implantation of Group 4 cations [Ti(III), Ti(IV), Zr(IV), Hf(IV)] has been carried out under mild conditions by the reaction of polycyclopentadienyl- (MCp_n; M = Ti, n = 3, 4; M = Zr, Hf, n = 4), mixed cyclopentadienyl/N,N-dialkylcarbamato (ML_x(O₂CNEt₂)_y; M = Ti, L = Cp, C₅Me₅ (Cp*), x = 2, y = 1; M = Hf, L = Cp, x = 1, y = 3), and N,N-dialkylcarbamato (M(O₂CNR₂)_n, M = Ti, n = 3, R = ⁱPr; M = Ti, Hf, n = 4, R = Et; M = Zr, n = 4, R = ⁱPr) derivatives, with the silanol groups of amorphous silica. Cyclopentadiene/pentamethylcyclopentadiene and/or carbon dioxide and the secondary amine are released in the process. The amount of implanted cations depends on the metal and on the ligands, the pentamethylcyclopentadienyl complex being less reactive than the unsubstituted congener. The starting complexes and the final products have been characterized by EPR or by ¹³C CP-MAS NMR spectroscopy.     

Synthesis and characterization of silver(I) derivatives containing acylpyrazolonate and phosphino ligands: X-ray crystal structures of monomeric [Ag(Q)(PPh3)2] and of dimeric [{Ag(Q)(PiBu3)}2] (Q = 1-phenyl-3-methyl-4-tert-butylacetylpyrazolon-5-ato)

New silver(I) acylpyrazolonate derivatives [Ag(Q)], [Ag(Q)(PR₃)]₂ and [Ag(Q)(PR₃)₂] (HQ = 1-R¹-3-methyl-4-R²(CO)pyrazol-5-one, HQ^Bn = R¹ = C₆H₅, R² = CH₂C₆H₅; HQ^CHPh2 = R¹ = C₆H₅, R² = CH(C₆H₅)₂; HQ^nPe = R¹ = C₆H₅, R² = CH₂C(CH₃)₃; HQ^tBu = R¹ = C₆H₅, R² = C(CH₃)₃; HQ^fMe = R¹ = C₆H₄-p-CF₃, R² = CF₃; HQ^fEt = R¹ = C₆H₅, R² = CF₂CF₃; R = Ph or iBu) have been synthesized and characterized in the solid state and solution. The crystal structure of 1-(4-trifluoromethylphenyl)-3-methyl-5-pyrazolone, the precursor of proligand HQ^fMe and of derivatives [Ag(Q^nPe)(PPh₃)₂] and [Ag(Q^nPe)(PiBu₃)]₂ have been investigated. [Ag(Q^nPe)(PPh₃)₂] is a mononuclear compound with a silver atom in a tetrahedrally distorted AgO₂P₂ environment, whereas [Ag(Q^nPe)(PiBu₃)]₂ is a dinuclear compound with two O₂N-exotridentate bridging acylpyrazolonate ligands connecting both silver atoms, their coordination environment being completed by a phosphine ligand.     

Kinetic mechanism and catalysis of Trypanosoma cruzi dihydroorotate dehydrogenase enzyme evaluated by isothermal titration calorimetry

Trypanosoma cruzi dihydroorotate dehydrogenase (TcDHODH) catalyzes the oxidation of l-dihydroorotate to orotate with concomitant reduction of fumarate to succinate in the de novo pyrimidine biosynthetic pathway. Based on the important need to characterize catalytic mechanism of TcDHODH, we have tailored a protocol to measure TcDHODH kinetic parameters based on isothermal titration calorimetry. Enzymatic assays lead to Michaelis-Menten curves that enable the Michaelis constant (K_M) and maximum velocity (V_max) for both of the TcDHODH substrates: dihydroorotate (K_M = 8.6 ± 2.6 μM and V_max = 4.1 ± 0.7 μM s^-1) and fumarate (K_M = 120 ± 9 μM and V_max = 6.71 ± 0.15 μM s^-1). TcDHODH activity was investigated using dimethyl sulfoxide (10%, v/v) and Triton X-100 (0.5%, v/v), which seem to facilitate the substrate binding process with a small decrease in K_M. Arrhenius plot analysis allowed the determination of thermodynamic parameters of activation for substrates and gave some insights into the enzyme mechanism. Activation entropy was the main contributor to the Gibbs free energy in the formation of the transition state. A factor that might contribute to the unfavorable entropy is the hindered access of substrates to the TcDHODH active site where a loop at its entrance regulates the open-close channel for substrate access.     

2-Arylimidazo[2,1-b]benzothiazoles: a new family of amyloid binding agents with potential for PET and SPECT imaging of Alzheimer's brain

We designed and synthesized a small series of 2-aryl-imidazo[2,1-b]benzothiazole, representing a combination of motifs from the two most potent amyloid imaging agents, PIB and IMPY. The binding affinity of the new compounds ranged from 6 to 133 nM. Among the best compounds, 3b (K_i = 6 nM) can be labeled with ¹¹CH₃ for PET imaging whereas 3j (K_i = 10.9 nM) can be labeled with ¹²³I for SPECT imaging.     

Rational design, synthesis and evaluation of first generation inhibitors of the Giardia lamblia fructose-1,6-biphosphate aldolase

Inhibitors of the Giardia lamblia fructose 1,6-bisphosphate aldolase (GlFBPA), which transforms fructose 1,6-bisphosphate (FBP) to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, were designed based on 3-hydroxy-2-pyridone and 1,2-dihydroxypyridine scaffolds that position two negatively charged tetrahedral groups for interaction with substrate phosphate binding residues, a hydrogen bond donor to the catalytic Asp83, and a Zn²⁺ binding group. The inhibition activities for the GlFBPA catalyzed reaction of FBP of the prepared alkyl phosphonate/phosphate substituted 3-hydroxy-2-pyridinones and a dihydroxypyridine were determined. The 3-hydroxy-2-pyridone inhibitor 8 was found to bind to GlFBPA with an affinity (K_i = 14 μM) that is comparable to that of FBP (K_m = 2 μM) or its inert analog TBP (K_i = 1 μM). The X-ray structure of the GlFBPA-inhibitor 8 complex (2.3 Å) shows that 8 binds to the active site in the manner predicted by in silico docking with the exception of coordination with Zn²⁺. The observed distances and orientation of the pyridone ring O=C-C-OH relative to Zn²⁺ are not consistent with a strong interaction. To determine if Zn²⁺coordination occurs in the GlFBPA-inhibitor 8 complex in solution, EXAFS spectra were measured. A four coordinate geometry comprised of the three enzyme histidine ligands and an oxygen atom from the pyridone ring O=C-C-OH was indicated. Analysis of the Zn²⁺ coordination geometries in recently reported structures of class II FBPAs suggests that strong Zn²⁺ coordination is reserved for the enediolate-like transition state, accounting for minimal contribution of Zn²⁺ coordination to binding of 8 to GlFBPA.     

Stoichiometry of electrocatalytic cycle of cytochrome P450 2B4

Stoichiometry of the electrocatalytical cycle of cytochrome P450 2B4 was studied in kinetic mode according to bielectrode scheme. Graphite screen-printed electrodes with immobilized cytochrome P450 2B4 were used as the operating electrode (at the potential E^0′ = −450 mV) and electrodes, modified with cytochrome c (E^0′ = −50 mV) or Prussian Blue (E^0′ = 0), as measuring electrodes (for H₂O₂) and Clark-type electrode (for O₂). Benzphetamine N-demethylation rate was 17 ± 3 nmol/nmol of enzyme/min, peroxide production was 4.8 ± 0.7 nmol/nmol of enzyme/min (substrate-free system), 3.3 ± 0.6 nmol/nmol of enzyme/min (0.5 mM benzphetamine), the oxygen consumption rate by Р450 2В4 was 19.4 ± 0.6 nmol/nmol of enzyme/min (in the presence of benzphetamine), 4.8 ± 0.4 nmol/nmol of enzyme/min (without substrate). Based on stoichiometry of P450 electrocatalysis adequacy of electrochemical reduction and P450-monooxygenase system was revealed.     

Effect of substituent dtp to optical properties of heterobimetallic M/Ag/S nest-shaped clusters (M = Mo, W)

Clusters [MoS₄Ag₃(PPh₃)₃{S₂P(OPrⁱ)₂}] (1), [WS₄Ag₃(PPh₃)₃{S₂P(OPrⁱ)₂}] (2) and [WOS₃Ag₃(PPh₃)₃{S₂P(OPrⁱ)₂}] (3) were synthesized by the reaction of (NH₄)₂MoS₄/(NH₄)₂WS₄, (NH₄)₂WOS₃ with Ag[S₂P(OPrⁱ)₂]. Their structures have been characterized by X-ray diffraction. The clusters consist of a distorted tetrahedral MS₄ (or MOS₃) (M = Mo, W) with three Ag atoms and three sulfur atom bridges (Fig. 1), and resemble roughly that of cubane-like clusters. The nonlinear optical (NLO) properties were studied with an 8 ns pulsed laser at 532 nm. Its optical response to the incident light exhibits good optical absorptive and refractive effects, with α₂ = 1.56 × 10⁻¹⁰ m W⁻¹, n₂ = 3.87 × 10⁻¹⁷ m² W⁻¹ for cluster 1; α₂ = 1.33 × 10⁻¹⁰ m W⁻¹, n₂ = 6.52 × 10⁻¹⁷ m² W⁻¹for cluster 2; and α₂ = 2.54 × 10⁻¹⁰ m W⁻¹, n₂ = 4.07 × 10⁻¹⁷ m² W⁻¹ for cluster 3 for a 1.56 × 10⁻⁴ mol dm⁻³ CH₂Cl₂ solution.     

Dynamic synergistic effect on Trichoderma reesei cellulases by novel β-glucosidases from Taiwanese fungi

Dynamic synergistic effects in cellulosic bioconversion have been revealed between Trichoderma reesei cellulases and β-glucosidases (BGLs) from six Taiwanese fungi. A high level of synergy (8.9-fold) was observed with the addition of Chaetomellaraphigera BGL to T. reesei cellulases. In addition, the C. raphigera BGL possessed the highest activity (V_max/K_m = 46.6 U/mg mM) and lowest glucose inhibition (Ki = 4.6 mM) with the substrate 4-nitrophenyl β-d-glucopyranoside. For the natural cellobiose substrate, however, the previously isolated Aspergillus niger BGL Novo-188 had the highest V_max/K_m (0.72 U/mg mM) and lowest Ki (59.5 mM). The demonstrated dynamic synergistic effects between some BGLs and the T. reesei cellulase system suggest that BGLs not only prevent the inhibition by cellobiose, but also enhance activities of endo- and exo-cellulases in cellulosic bioconversion. Comparisons of kinetic parameters and synergism analyses between BGLs and T. reesei cellulases can be used for further optimization of the cellulosic bioconversion process.     

Influence of DNA end structure on the mechanism of initiation of DNA unwinding by the Escherichia coli RecBCD and RecBC helicases

Escherichiacoli RecBCD is a bipolar DNA helicase possessing two motor subunits (RecB, a 3′-to-5′ translocase, and RecD, a 5′-to-3′ translocase) that is involved in the major pathway of recombinational repair. Previous studies indicated that the minimal kinetic mechanism needed to describe the ATP-dependent unwinding of blunt-ended DNA by RecBCD in vitro is a sequential n-step mechanism with two to three additional kinetic steps prior to initiating DNA unwinding. Since RecBCD can “melt out” ∼ 6 bp upon binding to the end of a blunt-ended DNA duplex in a Mg²⁺-dependent but ATP-independent reaction, we investigated the effects of noncomplementary single-stranded (ss) DNA tails [3′-(dT)₆ and 5′-(dT)₆ or 5′-(dT)₁₀] on the mechanism of RecBCD and RecBC unwinding of duplex DNA using rapid kinetic methods. As with blunt-ended DNA, RecBCD unwinding of DNA possessing 3′-(dT)₆ and 5′-(dT)₆ noncomplementary ssDNA tails is well described by a sequential n-step mechanism with the same unwinding rate (mk_U = 774 ± 16 bp s^− 1) and kinetic step size (m = 3.3 ± 1.3 bp), yet two to three additional kinetic steps are still required prior to initiation of DNA unwinding (k_C = 45 ± 2 s^− 1). However, when the noncomplementary 5′ ssDNA tail is extended to 10 nt [5′-(dT)₁₀ and 3′-(dT)₆], the DNA end structure for which RecBCD displays optimal binding affinity, the additional kinetic steps are no longer needed, although a slightly slower unwinding rate (mk_U = 538 ± 24 bp s^− 1) is observed with a similar kinetic step size (m = 3.9 ± 0.5 bp). The RecBC DNA helicase (without the RecD subunit) does not initiate unwinding efficiently from a blunt DNA end. However, RecBC does initiate well from a DNA end possessing noncomplementary twin 5′-(dT)₆ and 3′-(dT)₆ tails, and unwinding can be described by a simple uniform n-step sequential scheme, without the need for the additional k_C initiation steps, with a similar kinetic step size (m = 4.4 ± 1.7 bp) and unwinding rate (mk_obs = 396 ± 15 bp s^− 1). These results suggest that the additional kinetic steps with rate constant k_C required for RecBCD to initiate unwinding of blunt-ended and twin (dT)₆-tailed DNA reflect processes needed to engage the RecD motor with the 5′ ssDNA.