Combining gel and capillary electrophoresis, nano-LC and mass spectrometry for the elucidation of post-translational modifications of Trichoderma reesei cellobiohydrolase I

N-Glycosylation of cellobiohydrolase I from the fungus Trichoderma reesei (strain Rut-C30) is studied using a combination of electrophoretic, chromatographic and mass spectrometric techniques. As four potential N-glycosylation sites and several uncharged and phosphorylated high-mannose glycans are present, a large number of glycoforms and phospho-isoforms can be expected. Isoelectric focusing both in gel and in capillary format was successfully applied for the separation of the phospho-isoforms. They were extracted in their intact form from the gel and subsequently analysed by nanospray-Q-TOF-MS, thereby making use of a powerful two-dimensional technique. Nano-LC/MS/MS on a Q-Trap MS further allowed the determination of the glycosylation sites. As a novel approach, an oxonium ion was used in precursor ion scanning for selective detection of glycopeptides containing phosphorylated high-mannose glycans.     

Small-angle X-ray scattering and structural modeling of full-length: cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations.     

A model explaining declining rate in hydrolysis of lignocellulose substrates with cellobiohydrolase I (cel7A) and endoglucanase I (cel7B) of Trichoderma reesei

It is commonly observed that the rate of enzymatic hydrolysis of solid cellulose substrates declines markedly with time. In this work the mechanism behind the rate reduction was investigated using two dominant cellulases of Trichoderma reesei: exoglucanase Cel7A (formerly known as CBHI) and endoglucanase Cel7B (formerly EGI). Hydrolysis of steam-pretreated spruce (SPS) was performed with Cel7A and Cel7B alone, and in reconstituted mixtures. Throughout the 48-h hydrolysis, soluble products, hydrolysis rates, and enzyme adsorption to the substrate were measured. The hydrolysis rate for both enzymes decreases rapidly with hydrolysis time. Both enzymes adsorbed rapidly to the substrate during hydrolysis. Cel7A and Cel7B cooperate synergistically, and synergism was approximately constant during the SPS hydrolysis. Thermal instability of the enzymes and product inhibition was not the main cause of reduced hydrolysis rates. Adding fresh substrate to substrate previously hydrolyzed for 24 h with Cel7A slightly increased the hydrolysis of SPS; however, the rate increased even more by adding fresh Cel7A. This suggests that enzymes become inactivated while adsorbed to the substrate and that unproductive binding is the main cause of hydrolysis rate reduction. The strongest increase in hydrolysis rate was achieved by adding Cel7B. An improved model is proposed that extends the standard endo-exo synergy model and explains the rapid decrease in hydrolysis rate. It appears that the processive action of Cel7A becomes hindered by obstacles in the lignocellulose substrate. Obstacles created by disordered cellulose chains can be removed by the endo activity of Cel7B, which explains some of the observed synergism between Cel7A and Cel7B. The improved model is supported by adsorption studies during hydrolysis.     

A dendritic active site: catalysis of the Henry reaction

[reaction: see text] Dendrimers containing an encapsulated tertiary amine were prepared by coupling tris(2-aminoethyl)amine with dendritic branches derived from L-lysine. These dendrimers were used as catalysts in the Henry (nitroaldol) reaction between 4-nitrobenzaldehyde and nitroethane, and their catalytic performance was compared with that of triethylamine. Attachment of the dendritic shell alters the rate of reaction and influences the syn:anti ratio of products. It is proposed that the dendritic shell generates an encapsulated catalytically active site, mimicking the behavior of a protein superstructure.     

The effect of Trichoderma reesei cellulases and hemicellulases on the paper technical properties of never-dried bleached kraft pulp

Four purified cellulases, a xylanase and mannanase from Trichoderma reesei were used to treat never-dried bleached pine kraft pulp prior to refining, and the effects on pulp properties were evaluated. The enzymatic treatments hydrolysed up to 0.8% of pulp dry weight. The results demonstrated that the individual cellulases have profoundly different modes of action in modifying pulp carbohydrates. This is especially clear when comparing their effects at the same level of hydrolysis. Pretreatment with cellobiohydrolases I (CBH I) and II (CBH II) had virtually no effect on the development of pulp properties during refining, except for a slight decrease in strength properties. On the contrary, endoglucanase I (EG I) and endoglucanase II (EG II) improved the beatability of the pulp as measured by Schopper--Riegler value, sheet density and Gurley air resistance. Of the endoglucanases, EG II was most effective in improving the beating response. The combinations of CBH I with EG I and EG II had similar effects on the pulp properties as the endoglucanases alone, although the amount of hydrolysed cellulose was increased. Pretreatments with xylanase or mannanase did not appear to modify the pulp properties. The same enzyme treatments which improved the beatability, however, slightly impaired the pulp strength, especially tear index at the enzyme dosages used. When compared at a given level of cellulose hydrolysis, the negative effect of EG II on strength properties was more pronounced compared with EG I. Thus, the exploitation of cellulases for fibre treatments requires careful optimization of both enzyme composition and dosage. Since the endoglucanases had no positive effect on the development of tensile strength, it is suggested that the explanation for the increased beating response is increased fibre breakage and formation of fines, rather than improved flexibilization. This revised version was published online in August 2006 with corrections to the Cover Date.     

Cellulases from the fungi Phanerochaete chrysosporium and Trichoderma reesei as chiral selectors in capillary electrophoresis: applications with displacer plugs and sample preconcentration

The cellulases CBH 58 from the fungus Phanerochaete chrysosporium and CBH I from the fungus Trichoderma reesei were compared as chiral selectors in capillary electrophoresis (CE) applying the partial filling technique. Amines, e.g., norephedrine, two bambuterol analogs, as well as acids, e.g., di-p-toluoyl tartaric acid and dibenzoyl tartaric acid, which could not be enantioseparated in the liquid chromatographic use of the selectors, could be separated in the corresponding CE experiments. Due to the very high enantioselectivities, terbutaline, alprenolol and propranolol could be completely enantioresolved with selector plugs shorter than the sample plugs. The affinity of propranolol to CBH 58 was so high at pH 7.0 that neither of the enantiomers reached the detector; therefore, a plug of the displacing disaccharide cellobiose was injected after the sample to elute the propranolol enantiomers. The enantiomers could also be made to leave the capillary at opposite ends, thereby causing an infinite enantioresolution. A new preconcentration technique was introduced, which takes advantage of the very high affinity of propranolol to CBH 58 and the eluting ability of cellobiose. A 12.5 cm long plug of rac-propranolol could be preconcentrated and enantioseparated in a single procedure.     

Real-time observation of the swelling and hydrolysis of a single crystalline cellulose fiber catalyzed by cellulase 7B from Trichoderma reesei

The biodegradation of cellulose involves the enzymatic action of cellulases (endoglucanases), cellobiohydrolases (exoglucanases), and β-glucosidases that act synergistically. The rate and efficiency of enzymatic hydrolysis of crystalline cellulose in vitro decline markedly with time, limiting the large-scale, cost-effective production of cellulosic biofuels. Several factors have been suggested to contribute to this phenomenon, but there is considerable disagreement regarding the relative importance of each. These earlier investigations were hampered by the inability to observe the disruption of crystalline cellulose and its subsequent hydrolysis directly. Here, we show the application of high-resolution atomic force microscopy to observe the swelling of a single crystalline cellulose fiber and its-hydrolysis in real time directly as catalyzed by a single cellulase, the industrially important cellulase 7B from Trichoderma reesei. Volume changes, the root-mean-square roughness, and rates of hydrolysis of the surfaces of single fibers were determined directly from the images acquired over time. Hydrolysis dominated the early stage of the experiment, and swelling dominated the later stage. The high-resolution images revealed that the combined action of initial hydrolysis followed by swelling exposed individual microfibrils and bundles of microfibrils, resulting in the loosening of the fiber structure and the exposure of microfibrils at the fiber surface. Both the hydrolysis and swelling were catalyzed by the native cellulase; under the same conditions, its isolated carbohydrate-binding module did not cause changes to crystalline cellulose. We anticipate that the application of our AFM-based analysis on other cellulolytic enzymes, alone and in combination, will provide significant insight into the process of cellulose biodegradation and greatly facilitate its application for the efficient and economical production of cellulosic ethanol.     

On origin and evolution of carbonic anhydrase isozymes: A phylogenetic analysis from whole-enzyme to active site

Genetic evolution of carbonic anhydrase enzyme provides an interesting instance of functional similarity in spite of structural diversity of the members of a given family of enzymes. Phylogenetic analysis of α-, β- and γ-carbonic anhydrase was carried out to determine the evolutionary relationships among various members of the family with the enzyme marking its presence in a wide range of cellular and chromosomal locations. The presence of more than one class of enzymes in a particular organism was revealed by phylogenetic time tree. The evolutionary relationships among the members of animal, plant and microbial kingdom were developed. The study revises a long-established notion of kingdom-specificity of the different classes of carbonic anhydrases and provides a new version of the presence of multiple classes of carbonic anhydrases in a single organism and the presence of a given class of carbonic anhydrase across different kingdoms.     

Preparation of the Pd/C catalysts: A molecular-level study of active site formation

This review summarizes the results of molecular-level studies on the mechanism of Pd/C catalyst formation from the PdCl₂ precursor. Two processes occur in acidic media during the contact of H₂PdCl₄ with carbon: (a) adsorption of palladium chloride to form surface complexes and (b) redox interaction between PdCl₂ and carbon with the formation of palladium metal particles. The ratio between these adsorbed palladium species depends on the conditions of adsorption and especially on the size of carbon support grains and the oxidative atmosphere. The observations are explained by the fact that carbon support exhibits electrochemical and ligand properties. X-ray diffraction, X-ray scattering, XPS, and high-resolution electron microscopy revealed that the nanostructure of carbon materials, in particular the extent of their three-dimensional ordering, is crucial for the ligand properties. The presence of two forms, metallic and ionic, of sorbed palladium determines the bimodal size distribution of the metal. After the reduction of ionic species, metal particles are “blocked” with support. The nature of the ionic forms of palladium (mostly (PdCl₂)_n) clusters chemically and epitaxially bound to the carbon surface suggests the mechanisms of the bimodal distribution of the supported metal particles on the surface and the methods for the control of the ratio between “blocked,” low-dispersed, and highly-dispersed particles in the catalyst. One of these methods is the use of palladium polynuclear hydroxo complexes (PHCs) with low oxidation potentials as starting compounds for catalysts preparation. The data on the PHC structure in a solution and its change upon the adsorption of PHC on the surface of the carbon material obtained by the¹⁷O,²³Na,¹³³Cs, and³⁵Cl NMR techniques are discussed. PHCs are shown to be a clew of the [Pd(OH)₂]_n polymeric filament, whose fractions are bound with alkali metal ions. When PHC is adsorbed on the surface of the carbon support and then dried, palladium oxide is formed from which highly dispersed metal particles are formed during reduction. The nature of alkali metal ions in PHC affects the activity of the Pd/C catalyst. An important role of the ligand, electrochemical, and lyophilic properties of carbon material during the formation of the species of the active catalyst component is discussed.     

Structural and functional analogue of the active site of polysulfide reductase from Wolinella succinogenes

Synthesis of [PPh4]2[Mo(SPh)2(S2C2(CN)2)2] (2) from [PPh4]2[MoO(S2C2(CN)2)2] (1) has been achieved to mimic the postulated [Mo(S)6] core of polysulfide reductase with two thiolates and two bis(ene-dithiolate) ligands. Compound 2 reacts with polysulfide to yield H2S, modeling the function of polysulfide reductase. The facile conversion of 2 back to 1 in moist solvent suggests that the interconversion of the [MoIV = O] and [MoIV - X] (X = O-Ser, S-Cys, Se-Cys) moieties might occur in the DMSO reductase class of enzymes under appropriate hydrophobic/hydrophilic conditions.     

A DFT investigation on structural and redox properties of a synthetic Fe6S6 assembly closely related to the [FeFe]-hydrogenases active site

In the present contribution, a density functional theory (DFT) investigation is described regarding a recently synthesized Fe₆S₆ complex – see C. Tard, X. Liu, S.K. Ibrahim, M. Bruschi, L. De Gioia, S.C. Davies, X. Yang, L.-S. Wang, G. Sawers, C.J. Pickett, Nature 433 (2005) 610 – that is structurally and functionally related to the [FeFe]-hydrogenases active site (the so-called H-cluster, which includes a binuclear subsite directly involved in catalysis and an Fe₄S₄ cubane). The analysis of relative stabilities and atomic charges of different isomers evidenced that the structural and redox properties of the synthetic assembly are significantly different from those of the enzyme active site. A comparison between the hexanuclear cluster and simpler synthetic diiron models is also described; the results of such a comparison indicated that the cubane moiety can favour the stabilization of the cluster in a structure closely resembling the H-cluster geometry when the synthetic Fe₆S₆ complex is in its dianionic state. However, the opposite effect is observed when the synthetic cluster is in its monoanionic form.     

A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction

In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.     

A carbohydrate-based approach for the total synthesis of aculeatin D and 6-epi-aculeatin D

A concise approach for the total synthesis of aculeatin D and 6-epi-aculeatin D employing differentially protected anti, anti-1,3,5-triol alkyne prepared from alpha-D-glucoheptonic-gamma-lactone derivative is documented. Phenol protecting group manipulation for selective O-debenzylation during the hydrogenation of the diyne intermediate and one-pot phenolic oxidation with concomitant spiroketalization highlight the accomplished total synthesis.     

A nickel hydride complex in the active site of methyl-coenzyme m reductase: implications for the catalytic cycle

Methanogenic archaea utilize a specific pathway in their metabolism, converting C1 substrates (i.e., CO2) or acetate to methane and thereby providing energy for the cell. Methyl-coenzyme M reductase (MCR) catalyzes the key step in the process, namely methyl-coenzyme M (CH3-S-CoM) plus coenzyme B (HS-CoB) to methane and CoM-S-S-CoB. The active site of MCR contains the nickel porphinoid F430. We report here on the coordinated ligands of the two paramagnetic MCR red2 states, induced when HS-CoM (a reversible competitive inhibitor) and the second substrate HS-CoB or its analogue CH3-S-CoB are added to the enzyme in the active MCR red1 state (Ni(I)F430). Continuous wave and pulse EPR spectroscopy are used to show that the MCR red2a state exhibits a very large proton hyperfine interaction with principal values A((1)H) = [-43,-42,-5] MHz and thus represents formally a Ni(III)F430 hydride complex formed by oxidative addition to Ni(I). In view of the known ability of nickel hydrides to activate methane, and the growing body of evidence for the involvement of MCR in "reverse" methanogenesis (anaerobic oxidation of methane), we believe that the nickel hydride complex reported here could play a key role in helping to understand both the mechanism of "reverse" and "forward" methanogenesis.     

Pyrene.pyrene complexes at the active site of cytochrome P450 3A4: evidence for a multiple substrate binding site

Cytochrome P450 monooxygenases (CYPs) metabolize nearly all drugs and toxins. Recently, it has become clear that CYPs exhibit both homotropic and heterotropic allosteric kinetics for many substrates. However, the mechanism of cooperative kinetics has not been established for any specific human CYP/substrate combination. Suggested mechanisms include binding of multiple substrates within distinct, static, subsites of a single large active site or binding of multiple substrates within a single fluid active site. CYP3A4 hydroxylates pyrene with positive cooperativity. Therefore, experiments were designed to exploit the fluorescence properties of pyrene, which diagnostically distinguish between pyrene.pyrene complexes versus spatially separated pyrene substrates. Pyrene complexes (excimers) yield an emission spectrum clearly distinct from pyrene monomers. In lipid-free aqueous/glycerol solutions of CYP3A4, addition of pyrene affords a concentration-dependent low-spin to high-spin conversion of the CYP3A4 heme prosthetic group, indicating occupancy of the active site by pyrene. Under the same conditions, in the presence of CYP3A4 but not other heme proteins, the excimer/monomer ratio (E/M) of pyrene was decreased in emission spectra, compared to pyrene alone. However, excitation spectra indicate a CYP3A4-dependent increase in the wavelength shift for the excimer excitation spectrum versus the monomer excitation spectrum, as well as changes in the excimer excitation peak shape and vibronic structure. These changes are reversed by the CYP3A4 substrate testosterone. Together, the results demonstrate that pyrene.pyrene ground-state complexes occupy the CYP3A4 active site, and they provide the first spectroscopic evidence for substrate complexes within a single fluid active site. Functional implications include the possibility that turnover rate, regioselectivity, and stereoselectivity of the reaction are determined by the substrate.substrate complex rather than individual substrates.