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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 endo-cellulase and cellulose crystals. Schematic representation of (a) an endo-cellulase adsorbed onto the cellulose surface, (b) hydrogen bonds breaking between the monomers covered by the enzyme and (c) hydrolysis of the glycosidic bond.
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Figure 3: Interactions between endo-cellulase and cellulose crystals. Schematic representation of (a) an endo-cellulase adsorbed onto the cellulose surface, (b) hydrogen bonds breaking between the monomers covered by the enzyme and (c) hydrolysis of the glycosidic bond.

Mentions: Each endo-cellulase adsorbs to a randomly chosen available site. A site is a set of glucose units, as presented in Figure 3a, consisting of nine consecutive glucose units in three neighboring chains, for a total of 27 adjacent glucose units [35]. However, we assume that just a length of 4 glucose units in the middle chain is enough for it to form a productive complex. This choice was motivated by the empirical studies of Claeyssens et al. [41] and Biely et al. [42] who argued that the substrate binding site of EG I is an extended one, consisting of four sugar binding subsites with a catalytic group located in the middle. A site is available if all monomers in the middle glucan chain belong to the cellulose substrate and none of the twelve monomers is covered by another enzyme nor are they locked. Desorption of the cellulase might take place at any time. If the glycosidic bond in the catalytic region is already hydrolyzed, the cellulase desorbs into solution within an exponentially distributed time interval with rate parameter kofffast (see Figure 2). The catalytic region of an endo-cellulase is considered to be the glycosidic bond between the second and third glucose units in the middle chain covered by the enzyme, shown in Figure 3c. The hydrolysis of the glycosidic bond can only take place after all inter-chain hydrogen bonds between the covered glucose units are broken (Figure 3b). The time it takes to break the hydrogen bonds is proportional to the number of bonds that need to be broken, denoted by ‘nrHB’ in Figure 2. If there is at least one hydrogen bond that needs to be broken, the cellulase breaks it or desorbs into solution. Similarly, if all hydrogen bonds have already been broken, as shown in Figure 3b, the cellulase either hydrolyzes the glycosidic bond at the catalytic region or desorbs into solution. These decisions are implemented using Gillespie’s algorithm [40]. Hydrolysis of a glycosidic bond is always followed by desorption of the cellulase within an exponentially distributed time with rate parameter koff.


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 endo-cellulase and cellulose crystals. Schematic representation of (a) an endo-cellulase adsorbed onto the cellulose surface, (b) hydrogen bonds breaking between the monomers covered by the enzyme and (c) hydrolysis of the glycosidic bond.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Interactions between endo-cellulase and cellulose crystals. Schematic representation of (a) an endo-cellulase adsorbed onto the cellulose surface, (b) hydrogen bonds breaking between the monomers covered by the enzyme and (c) hydrolysis of the glycosidic bond.
Mentions: Each endo-cellulase adsorbs to a randomly chosen available site. A site is a set of glucose units, as presented in Figure 3a, consisting of nine consecutive glucose units in three neighboring chains, for a total of 27 adjacent glucose units [35]. However, we assume that just a length of 4 glucose units in the middle chain is enough for it to form a productive complex. This choice was motivated by the empirical studies of Claeyssens et al. [41] and Biely et al. [42] who argued that the substrate binding site of EG I is an extended one, consisting of four sugar binding subsites with a catalytic group located in the middle. A site is available if all monomers in the middle glucan chain belong to the cellulose substrate and none of the twelve monomers is covered by another enzyme nor are they locked. Desorption of the cellulase might take place at any time. If the glycosidic bond in the catalytic region is already hydrolyzed, the cellulase desorbs into solution within an exponentially distributed time interval with rate parameter kofffast (see Figure 2). The catalytic region of an endo-cellulase is considered to be the glycosidic bond between the second and third glucose units in the middle chain covered by the enzyme, shown in Figure 3c. The hydrolysis of the glycosidic bond can only take place after all inter-chain hydrogen bonds between the covered glucose units are broken (Figure 3b). The time it takes to break the hydrogen bonds is proportional to the number of bonds that need to be broken, denoted by ‘nrHB’ in Figure 2. If there is at least one hydrogen bond that needs to be broken, the cellulase breaks it or desorbs into solution. Similarly, if all hydrogen bonds have already been broken, as shown in Figure 3b, the cellulase either hydrolyzes the glycosidic bond at the catalytic region or desorbs into solution. These decisions are implemented using Gillespie’s algorithm [40]. Hydrolysis of a glycosidic bond is always followed by desorption of the cellulase within an exponentially distributed time with rate parameter koff.

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