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A coarse-grained model for synergistic action of multiple enzymes on cellulose.

Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, Gnanakaran S - Biotechnol Biofuels (2012)

Bottom Line: We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level.Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails.This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA. gnana@lanl.gov.

ABSTRACT

Background: Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates.

Results: We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose.

Conclusions: Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.

No MeSH data available.


Related in: MedlinePlus

(a) Hydrolysis by endo-cellulases. Time course of hydrolysis by endo-cellulases.The inset shows the variation in the conversion time needed to degrade 5%, 50% and 80% of the substrate as a function of the adsorption rate constant kon. (b) Total sugar production and individual monomer and oligomer component distribution over time.
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Figure 7: (a) Hydrolysis by endo-cellulases. Time course of hydrolysis by endo-cellulases.The inset shows the variation in the conversion time needed to degrade 5%, 50% and 80% of the substrate as a function of the adsorption rate constant kon. (b) Total sugar production and individual monomer and oligomer component distribution over time.

Mentions: First we simulate and analyze the hydrolysis of a crystalline cellulose layer solely by endo-cellulases. Figure 7a shows the timeline of percent cellulose degradation. After an initial slow hydrolysis phase, the simulation results agree qualitatively with published experimental results [50]. Using parameter values listed in Table 4, our model reproduces well the observed experimental hydrolysis time scales. As expected, the time it takes to convert a given percent of the substrate decreases as kon increases (Figure 7a inset). Similarly, the relative production of soluble oligosaccharides shown in Figure 7b agrees well with the experiments [11]. Cellobiose is the major type of soluble sugar, both in experiments and in our model. In our model, the final molar ratio between glucose and cellobiose is close to 1:10, while the final molar ratio between cellotriose and cellobiose is close to 7:10. In experiments, the glucose concentration is observed to be higher than the cellotriose concentration, while our model shows the opposite. Our model assumes that cellulose oligomers of length less than 4 enter solution and none of the modeled cellulases can digest them after they enter solution phase. This simplified assumption leads to disagreement with experiments.


A coarse-grained model for synergistic action of multiple enzymes on cellulose.

Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, Gnanakaran S - Biotechnol Biofuels (2012)

(a) Hydrolysis by endo-cellulases. Time course of hydrolysis by endo-cellulases.The inset shows the variation in the conversion time needed to degrade 5%, 50% and 80% of the substrate as a function of the adsorption rate constant kon. (b) Total sugar production and individual monomer and oligomer component distribution over time.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475064&req=5

Figure 7: (a) Hydrolysis by endo-cellulases. Time course of hydrolysis by endo-cellulases.The inset shows the variation in the conversion time needed to degrade 5%, 50% and 80% of the substrate as a function of the adsorption rate constant kon. (b) Total sugar production and individual monomer and oligomer component distribution over time.
Mentions: First we simulate and analyze the hydrolysis of a crystalline cellulose layer solely by endo-cellulases. Figure 7a shows the timeline of percent cellulose degradation. After an initial slow hydrolysis phase, the simulation results agree qualitatively with published experimental results [50]. Using parameter values listed in Table 4, our model reproduces well the observed experimental hydrolysis time scales. As expected, the time it takes to convert a given percent of the substrate decreases as kon increases (Figure 7a inset). Similarly, the relative production of soluble oligosaccharides shown in Figure 7b agrees well with the experiments [11]. Cellobiose is the major type of soluble sugar, both in experiments and in our model. In our model, the final molar ratio between glucose and cellobiose is close to 1:10, while the final molar ratio between cellotriose and cellobiose is close to 7:10. In experiments, the glucose concentration is observed to be higher than the cellotriose concentration, while our model shows the opposite. Our model assumes that cellulose oligomers of length less than 4 enter solution and none of the modeled cellulases can digest them after they enter solution phase. This simplified assumption leads to disagreement with experiments.

Bottom Line: We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level.Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails.This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA. gnana@lanl.gov.

ABSTRACT

Background: Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates.

Results: We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose.

Conclusions: Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.

No MeSH data available.


Related in: MedlinePlus