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Wen Zhou Heinz‐Bernd Schüttler Zhiqian Hao Ying Xu 《Biotechnology and bioengineering》2009,104(2):261-274
We develop a general framework for a realistic rate equation modeling of cellulose hydrolysis using non‐complexed cellulase. Our proposed formalism, for the first time, takes into account explicitly the time evolution of the random substrate morphology resulting from the hydrolytic cellulose chain fragmentation and solubilization. This is achieved by integrating novel geometrical concepts to quantitatively capture the time‐dependent random morphology, together with the enzymatic chain fragmentation, into a coupled morphology‐plus‐kinetics rate equation approach. In addition, an innovative site number representation, based on tracking available numbers of β(1,4) glucosidic bonds, of different “site” types, exposed to attacks by different enzyme types, is presented. This site number representation results in an ordinary differential equation (ODE) system, with a substantially reduced ODE system size, compared to earlier chain fragmentation kinetics approaches. This formalism enables us to quantitatively simulate both the hydrolytically evolving random substrate morphology and the profound, and heretofore neglected, morphology effects on the hydrolysis kinetics. By incorporating the evolving morphology on an equal footing with the hydrolytic chain fragmentation, our formalism provides a framework for the realistic modeling of the entire solubilization process, beyond the short‐time limit and through near‐complete hydrolytic conversion. As part I of two companion papers, the present paper focuses on the development of the general modelling formalism. Results and testable experimental predictions from detailed numerical simulations are presented in part II. Biotechnol. Bioeng. 2009; 104: 261–274 © 2009 Wiley Periodicals, Inc. 相似文献
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Maïté Huron Damien Hudebine Nicolas Lopes Ferreira Dominique Lachenal 《Biotechnology and bioengineering》2016,113(5):1011-1023
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A new functionally based kinetic model for enzymatic hydrolysis of pure cellulose by the Trichoderma cellulase system is presented. The model represents the actions of cellobiohydrolases I, cellobiohydrolase II, and endoglucanase I; and incorporates two measurable and physically interpretable substrate parameters: the degree of polymerization (DP) and the fraction of beta-glucosidic bonds accessible to cellulase, F(a) (Zhang and Lynd, 2004). Initial enzyme-limited reaction rates simulated by the model are consistent with several important behaviors reported in the literature, including the effects of substrate characteristics on exoglucanase and endoglucanase activities; the degree of endo/exoglucanase synergy; the endoglucanase partition coefficient on hydrolysis rates; and enzyme loading on relative reaction rates for different substrates. This is the first cellulase kinetic model involving a single set of kinetic parameters that is successfully applied to a variety of cellulosic substrates, and the first that describes more than one behavior associated with enzymatic hydrolysis. The model has potential utility for data accommodation and design of industrial processes, structuring, testing, and extending understanding of cellulase enzyme systems when experimental date are available, and providing guidance for functional design of cellulase systems at a molecular scale. Opportunities to further refine cellulase kinetic models are discussed, including parameters that would benefit from further study. 相似文献
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The projected cost for the enzymatic hydrolysis of cellulosic biomass continues to be a barrier for the commercial production of liquid transportation fuels from renewable feedstocks. Predictive models for the kinetics of the enzymatic reactions will enable an improved understanding of current limitations, such as the slow-down of the overall conversion rate, and may point the way for more efficient utilization of the enzymes in order to achieve higher conversion yields. A mechanistically based kinetic model for the enzymatic hydrolysis of cellulose was recently reported in Griggs et al. (2011) (Part I). In this article (Part II), the enzyme system is expanded to include solution-phase kinetics, particularly cellobiose-to-glucose conversion by β-glucosidase (βG), and novel adsorption and product inhibition schemes have been incorporated, based on current structural knowledge of the component enzymes. Model results show cases of cooperative and non-cooperative hydrolysis for an enzyme system consisting of EG(I) and CBH(I). The model is used to explore various potential rate-limiting phenomena, such as substrate accessibility, product inhibition, sterically hindered enzyme adsorption, and the molecular weight of the cellulose substrate. 相似文献
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Electricity can be directly generated by bacteria in microbial fuel cells (MFCs) from a variety of biodegradable substrates, including cellulose. Particulate materials have not been extensively examined for power generation in MFCs, but in general power densities are lower than those produced with soluble substrates under similar conditions likely as a result of slow hydrolysis rates of the particles. Cellulases are used to achieve rapid conversion of cellulose to sugar for ethanol production, but these enzymes have not been previously tested for their effectiveness in MFCs. It was not known if cellulases would remain active in an MFC in the presence of exoelectrogenic bacteria or if enzymes might hinder power production by adversely affecting the bacteria. Electricity generation from cellulose was therefore examined in two-chamber MFCs in the presence and absence of cellulases. The maximum power density with enzymes and cellulose was 100 +/- 7 mW/m(2) (0.6 +/- 0.04 W/m(3)), compared to only 12 +/- 0.6 mW/m(2) (0.06 +/- 0.003 W/m(3)) in the absence of the enzymes. This power density was comparable to that achieved in the same system using glucose (102 +/- 7 mW/m(2), 0.56 +/- 0.038 W/m(3)) suggesting that the enzyme successfully hydrolyzed cellulose and did not otherwise inhibit electricity production by the bacteria. The addition of the enzyme doubled the Coulombic efficiency (CE) to CE = 51% and increased COD removal to 73%, likely as a result of rapid hydrolysis of cellulose in the reactor and biodegradation of the enzyme. These results demonstrate that cellulases do not adversely affect exoelectrogenic bacteria that produce power in an MFC, and that the use of these enzymes can increase power densities and reactor performance. 相似文献
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The slow down in enzymatic hydrolysis of cellulose with conversion has often been attributed to declining reactivity of the substrate as the more easily reacted material is thought to be consumed preferentially. To better understand the cause of this phenomenon, the enzymatic reaction of the nearly pure cellulose in Avicel was interrupted over the course of nearly complete hydrolysis. Then, the solids were treated with proteinase to degrade the cellulase enzymes remaining on the solid surface, followed by proteinase inhibitors to inactive the proteinase and successive washing with water, 1.0 M NaCl solution, and water. Next, fresh cellulase and buffer were added to the solids to restart hydrolysis. The rate of cellulose hydrolysis, expressed as a percent of substrate remaining at that time, was approximately constant over a wide range of conversions for restart experiments but declined continually with conversion for uninterrupted hydrolysis. Furthermore, the cellulose hydrolysis rate per adsorbed enzyme was approximately constant for the restart procedure but declined with conversion when enzymes were left to react. Thus, the drop off in reaction rate for uninterrupted cellulose digestion by enzymes could not be attributed to changes in substrate reactivity, suggesting that other effects such as enzymes getting \"stuck\" or otherwise slowing down may be responsible. 相似文献
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A fractal-like kinetics model was used to describe the synergistic hydrolysis of bacterial cellulose by Trichoderma reesei cellulases. The synergistic action of intact cellobiohydrolase Cel7A and endoglucanase Cel5A at low enzyme-to-substrate ratios showed an apparent substrate inhibition consistent with a case where two-dimensional (2-D) surface diffusion of the cellobiohydrolase is rate-limiting. The action of Cel7A core and Cel5A was instead consistent with a three-dimensional (3-D) diffusion-based mode of action. The synergistic action of intact Cel7A was far superior to that of the core at a high enzyme-to-substrate ratio, but this effect was gradually reduced at lower enzyme-to-substrate ratios. The apparent fractal kinetics exponent h obtained by nonlinear fit of hydrolysis data to the fractal-like kinetics analogue of a first-order reaction was a useful empirical parameter for assessing the rate retardation and its dependence on the reaction conditions. 相似文献
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Multi-stage and single-stage enzymatic hydrolysis of cellulose (Avicel PH-101) were conducted to investigate individual factors that affect the rate-reducing kinetics of enzymatic hydrolysis. Understanding factors affecting enzymatic hydrolysis of Avicel will help improve hydrolysis of various biomasses. Product inhibition, enzyme deactivation, and the changes of substrate are potential factors that can affect the hydrolysis efficiency of Avicel. Multi-stage enzymatic hydrolysis resulted in 36.9% and 25.4% higher carbohydrate conversion as compared to a single-stage enzymatic hydrolysis with an enzyme loading of 5 and 20 FPU/g in a 96 h reaction. However, a decline in carbohydrate conversion of 1.6% and 2.6% was observed through each stage with 5 and 20 FPU/g, respectively. This indicated that the substrate became more recalcitrant as hydrolysis progressed. The decreased reactivity was not due to crystallinity because no significant change in crystallinity was detected by X-ray diffraction. Product inhibition was significant at low enzyme loading, while it was marginal at high enzyme loading. Therefore, product inhibition can only partially explain this decreased conversion. Another important factor, enzyme deactivation, contributed to 20.3% and 25.4% decrease in the total carbohydrate conversion of 96 h hydrolysis with 5 and 20 FPU/g, respectively. This work shows that an important reason for the decreased Avicel digestibility is the effect of enzyme blockage, which refers to the enzymes that irreversibly adsorb on accessible sites of substrate. About 45.3% and 63.2% of the total decreased conversion at the end of the 8th stage with 5 and 20 FPU/g, respectively, was due to the presence of irreversibly adsorbed enzymes. This blockage of active sites by enzymes has been speculated by other researchers, but this article shows further evidence of this effect. 相似文献
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Takeshi Kawabata 《Proteins》2010,78(5):1195-1211
Detection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid‐based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocket‐finding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, Rinaccess (minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server ( http://biunit.naist.jp/ghecom ). Proteins 2010. © 2009 Wiley‐Liss, Inc. 相似文献
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A recombinant Trichoderma reesei cellulase was used for the ultrasound‐mediated hydrolysis of soluble carboxymethyl cellulose (CMC) and insoluble cellulose of various particle sizes. The hydrolysis was carried out at low intensity sonication (2.4–11.8 W cm?2 sonication power at the tip of the sonotrode) using 10, 20, and 40% duty cycles. [A duty cycle of 10%, for example, was obtained by sonicating for 1 s followed by a rest period (no sonication) of 9 s.] The reaction pH and temperature were always 4.8 and 50°C, respectively. In all cases, sonication enhanced the rate of hydrolysis relative to nonsonicated controls. The hydrolysis of CMC was characterized by Michaelis‐Menten kinetics. The Michaelis‐Menten parameter of the maximum reaction rate Vmax was enhanced by sonication relative to controls, but the value of the saturation constant Km was reduced. The optimal sonication conditions were found to be a 10% duty cycle and a power intensity of 11.8 W cm?2. Under these conditions, the maximum rate of hydrolysis of soluble CMC was nearly double relative to control. In the hydrolysis of cellulose, an increasing particle size reduced the rate of hydrolysis. At any fixed particle size, sonication at a 10% duty cycle and 11.8 W cm?2 power intensity improved the rate of hydrolysis relative to control. Under the above mentioned optimal sonication conditions, the enzyme lost about 20% of its initial activity in 20 min. Sonication was useful in accelerating the enzyme catalyzed saccharification of cellulose. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1448–1457, 2013 相似文献
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Information pertaining to enzymatic hydrolysis of cellulose by noncomplexed cellulase enzyme systems is reviewed with a particular emphasis on development of aggregated understanding incorporating substrate features in addition to concentration and multiple cellulase components. Topics considered include properties of cellulose, adsorption, cellulose hydrolysis, and quantitative models. A classification scheme is proposed for quantitative models for enzymatic hydrolysis of cellulose based on the number of solubilizing activities and substrate state variables included. We suggest that it is timely to revisit and reinvigorate functional modeling of cellulose hydrolysis, and that this would be highly beneficial if not necessary in order to bring to bear the large volume of information available on cellulase components on the primary applications that motivate interest in the subject. 相似文献
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A new approach for modeling cellulase-cellulose adsorption and the kinetics of the enzymatic hydrolysis of microcrystalline cellulose 总被引:1,自引:0,他引:1
Two fractions of substrate in microcrystalline cellulose which differ in their adsorption capacities for the cellulases and their susceptibility to enzymatic attack have been identified. On the basis of a two-substrate hypothesis, mathematical models to describe enzyme adsorption and the kinetics of hydrolysis have been derived. A new nonequilibrium approach was chosen to predict cellulase-cellulose adsorption. A maximum binding capacity of 76 mg protein per gram substrate and a half-maximum saturation constant of 26 filter paper units (FPU) per gram substrate have been calculated, and a linear relationship of hydrolysis rate vs. adsorbed protein has been found. The fraction of substrate more easily hydrolyzed, as calculated from hydrolysis data, represents 19% of the total effective substrate concentration. This fraction is only slightly different from that of other celluloses and has been estimated to be 27% and 30% for NaOH- and H(3)PO(4)-swollen cellulose, respectively. The effective substrate concentration is equal to the maximum amount of the substrate which can be converted during exhaustive hydrolysis. This in turn is determined by the overall degradability of the substrate by the cellulases (85-90% for microcrystalline cellulose) and by the cellobiose concentration during hydrolysis. The kinetic model is based on a summation of two integrated first-order reactions with respect to the effective substrate concentration. Furthermore, it includes the principal factors influencing the reaction rates: the ratio of filter paper and beta-glucosidase units per gram substrate and the initial substrate concentration. (c) 1993 John Wiley & Sons, Inc. 相似文献
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In electron microscopic observation, neither wax nor cuticle was observed on the outermost layers of callus tissues. Chemical estimation of wax in the callus surface was attempted by thin-layer chromatography of solvent extracts of callus tissues in comparison with those of barley and rice leaves. Hydrocarbons and free alcohols were detected in lyophilized callus tissues, but no wax esters or ketones were detected. Germination test indicated that germination of spores of Aspergillus oryzae was less favored on hydrophobic membranes than that of spores of Alternaria sp. and Botrytis cinerea.From these results, we inferred that the lack of cuticle and wax in the outermost layer of callus tissues facilitated spore germination and penetration, and A. oryzae, a saprophytic fungus, could also readily penetrate into callus tissues. 相似文献
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Effect of surfactants on cellulose hydrolysis 总被引:14,自引:0,他引:14
The effect of surfactants on the heterogeneous enzymatic hydrolysis of Sigmacell 100 cellulose and of steam-exploded wood was studied. Certain biosurfactants (sophorolipid, rhamnolipid, bacitracin) and Tween 80 increased the rate of hydrolysis of Sigmacell 100, as measured by the amount of reducing sugar produced, by as much as seven times. The hydrolysis of steam-exploded wood was increased by 67% in the presence of sophorolipid. At the same time, sophorolipid was found to decrease the amount of enzyme adsorbed onto the cellulose at equilibrium. Sophorolipid had the greatest effect on cellulose hydrolysis when it was present from the beginning of the experiment and when the enzyme/cellulose ratio was low. (c) 1993 John Wiley & Sons, Inc. 相似文献
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A quantitative model is proposed to describe the population dynamics of associative nitrogen-fixing microorganisms in the plant rhizosphere as dependent on the rate of carbon substrate exudation by plant roots. By changing the values of the basic model parameters, the effect of various factors on the behavior of two competing populations of rhizosphere microorganisms can be studied. 相似文献
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The in vitro conversion of chiral aliphatic monoalkylsubstituted oxiranes into 1,2-diols catalyzed by epoxide hydrolase of rat liver microsomes occurs with substrate enantioselectivity and regioselectivity. Substrate enantioselectivity is generally low, and has the same sense, for methyloxirane, vinyloxirane, epichloro-, and epibromohydrin. In the hydrolysis of t-butyloxirane inhibitory effects are involved leading to a complex pattern of enantioselectivity. All investigated monosubstituted aliphatic oxiranes are hydrolyzed with high regioselectivity by nucleophilic attack of water at the unsubstituted ring carbon atom. The enantiomeric excess of the unreacted oxirane substrates and the diol metabolites formed were determined by complexation and inclusion gas chromatography. 相似文献
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William D. Murray 《Journal of biotechnology》1985,3(3):131-140
The nutrient requirements of the cellulolytic anaerobe Bacteroides cellulosolvens were determined, and a new synthetic medium was formulated for its growth. B. cellulosolvens showed optimum cellobiose consumption and product formation in medium containing 40 mM ammonia nitrogen, 3 mM phosphate, 1 mM sulfide, 100 μM magnesium and 45 μM iron. This microbe had an essential-vitamin requirement for biotin; while zinc, manganese and copper slightly stimulated cellobiose degradation. In the new synthetic medium B. cellulosolvens was able to degrade 30% more cellulose. 相似文献