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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

Interactions between exo-cellulase and cellulose crystal. Schematic representation of (a) an exo-R cellulase adsorbed to the cellulose surface followed immediately by the breaking of hydrogen bonds between the monomers covered by the cellulase and (b) the processivity of the glucan chain by an exo-R cellulase; it comprises the hydrolysis of the glycosidic bond and cellulase directed movement along the chain.
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Figure 5: Interactions between exo-cellulase and cellulose crystal. Schematic representation of (a) an exo-R cellulase adsorbed to the cellulose surface followed immediately by the breaking of hydrogen bonds between the monomers covered by the cellulase and (b) the processivity of the glucan chain by an exo-R cellulase; it comprises the hydrolysis of the glycosidic bond and cellulase directed movement along the chain.

Mentions: The adsorption site of an exo-R cellulase consists of nine consecutive glucose units in three neighboring chains, for a total of 27 adjacent glucose units (shown in Figure 5a), subject to the condition that the middle glucan chain has a reducing end. This choice has been motivated by the three-dimensional structure of the catalytic domain of CBH I from T. reesei[34,43]. This catalytic site resides within a relatively long (~50 Å) cellulose binding tunnel holding ten glucose molecules, out of which three—near the outlet—form the product binding sites. As cellobiose is the main product released by CBH I [16,44], the exo-cellulase in our model has only two product binding sites, which, for the substrate, translates into a total of nine sugar binding sites. The adsorption site for an exo-cellulase is considered to be available if all monomers in the middle glucan chain belong to the cellulose substrate and none of the 27 monomers is covered by another enzyme nor are they locked.


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)

Interactions between exo-cellulase and cellulose crystal. Schematic representation of (a) an exo-R cellulase adsorbed to the cellulose surface followed immediately by the breaking of hydrogen bonds between the monomers covered by the cellulase and (b) the processivity of the glucan chain by an exo-R cellulase; it comprises the hydrolysis of the glycosidic bond and cellulase directed movement along the chain.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Interactions between exo-cellulase and cellulose crystal. Schematic representation of (a) an exo-R cellulase adsorbed to the cellulose surface followed immediately by the breaking of hydrogen bonds between the monomers covered by the cellulase and (b) the processivity of the glucan chain by an exo-R cellulase; it comprises the hydrolysis of the glycosidic bond and cellulase directed movement along the chain.
Mentions: The adsorption site of an exo-R cellulase consists of nine consecutive glucose units in three neighboring chains, for a total of 27 adjacent glucose units (shown in Figure 5a), subject to the condition that the middle glucan chain has a reducing end. This choice has been motivated by the three-dimensional structure of the catalytic domain of CBH I from T. reesei[34,43]. This catalytic site resides within a relatively long (~50 Å) cellulose binding tunnel holding ten glucose molecules, out of which three—near the outlet—form the product binding sites. As cellobiose is the main product released by CBH I [16,44], the exo-cellulase in our model has only two product binding sites, which, for the substrate, translates into a total of nine sugar binding sites. The adsorption site for an exo-cellulase is considered to be available if all monomers in the middle glucan chain belong to the cellulose substrate and none of the 27 monomers is covered by another enzyme nor are they locked.

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