Limits...
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

Simulation timeline. Here an ‘EVENT’ may refer to any chemical reaction that involves a cellulase (adsorption, desorption) or is catalyzed by a cellulase (e.g., inter-chain hydrogen bond breaking, hydrolysis of glycosidic bond).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3475064&req=5

Figure 6: Simulation timeline. Here an ‘EVENT’ may refer to any chemical reaction that involves a cellulase (adsorption, desorption) or is catalyzed by a cellulase (e.g., inter-chain hydrogen bond breaking, hydrolysis of glycosidic bond).

Mentions: The outline of the overall simulation is sketched in Figure 6. Time is measured in seconds and is advanced in a continuous and asynchronous manner. The simulation starts with the adsorption of an individual cellulase (endo or exo) and it proceeds following the flowcharts presented in Figure 2 (for endo-cellulase) or Figure 4 (for exo-cellulase). Each individually adsorbed cellulase is followed separately over the course of the simulation. While in solution, they all compete with each other for adsorption, and once adsorbed, the selection of the chemical reactions they are involved in follows a well-defined, rule-based schematic (see below) that finally leads to the hydrolysis of the entire cellulose substrate. However, Gillespie’s algorithm [40,46,47] plays a crucial part in the simulation, as many chemical reactions, once selected by the rule-based scheme, are modeled as Poisson processes and therefore are implemented using this algorithm. Gillespie’s algorithm is a Monte Carlo technique that allows one to sample the ensemble of trajectories for a set of biochemical reactions. It models chemical reactions as a stochastic process and remains valid for low copy numbers of reactants. Here we implement the direct version of this method [46].


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)

Simulation timeline. Here an ‘EVENT’ may refer to any chemical reaction that involves a cellulase (adsorption, desorption) or is catalyzed by a cellulase (e.g., inter-chain hydrogen bond breaking, hydrolysis of glycosidic bond).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Simulation timeline. Here an ‘EVENT’ may refer to any chemical reaction that involves a cellulase (adsorption, desorption) or is catalyzed by a cellulase (e.g., inter-chain hydrogen bond breaking, hydrolysis of glycosidic bond).
Mentions: The outline of the overall simulation is sketched in Figure 6. Time is measured in seconds and is advanced in a continuous and asynchronous manner. The simulation starts with the adsorption of an individual cellulase (endo or exo) and it proceeds following the flowcharts presented in Figure 2 (for endo-cellulase) or Figure 4 (for exo-cellulase). Each individually adsorbed cellulase is followed separately over the course of the simulation. While in solution, they all compete with each other for adsorption, and once adsorbed, the selection of the chemical reactions they are involved in follows a well-defined, rule-based schematic (see below) that finally leads to the hydrolysis of the entire cellulose substrate. However, Gillespie’s algorithm [40,46,47] plays a crucial part in the simulation, as many chemical reactions, once selected by the rule-based scheme, are modeled as Poisson processes and therefore are implemented using this algorithm. Gillespie’s algorithm is a Monte Carlo technique that allows one to sample the ensemble of trajectories for a set of biochemical reactions. It models chemical reactions as a stochastic process and remains valid for low copy numbers of reactants. Here we implement the direct version of this method [46].

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