Systems-level modeling with molecular resolution elucidates the rate-limiting mechanisms of cellulose decomposition by cellobiohydrolases.
Interprotein and enzyme-substrate couplings in interfacial biocatalysis induce spatial correlations beyond the capabilities of classical mass-action principles in modeling reaction kinetics. To understand the impact of spatial constraints on enzyme kinetics, we developed a computational scheme to simulate the reaction network of enzymes with the structures of individual proteins and substrate molecules explicitly resolved in the three-dimensional space. This methodology was applied to elucidate the rate-limiting mechanisms of crystalline cellulose decomposition by cellobiohydrolases. We illustrate that the primary bottlenecks are slow complexation of glucan chains into the enzyme active site and excessive enzyme jamming along the crowded substrate. Jamming could be alleviated by increasing the decomplexation rate constant but at the expense of reduced processivity. We demonstrate that enhancing the apparent reaction rate required a subtle balance between accelerating the complexation driving force and simultaneously avoiding enzyme jamming. Via a spatiotemporal systems analysis, we developed a unified mechanistic framework that delineates the experimental conditions under which different sets of rate-limiting behaviors emerge. We found that optimization of the complexation-exchange kinetics is critical for overcoming the barriers imposed by interfacial confinement and accelerating the apparent rate of enzymatic cellulose decomposition.
From the Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720.
Barry Z
BZ
Shang
Rakwoo
R
Chang
Jhih-Wei
JW
Chu
D055162:Biocatalysis; D002482:Cellulose / Q000378:metabolism*; D043366:Cellulose 1,4-beta-Cellobiosidase / Q000378:metabolism*; D003198:Computer Simulation; D004789:Enzyme Activation; D007700:Kinetics; D008954:Models, Biological; D013269:Stochastic Processes; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors; D014242:Trichoderma / Q000201:enzymology*
D002482:Cellulose; D043366:Cellulose 1,4-beta-Cellobiosidase
Cellulase; Computational Biology; Enzyme Inactivation; Enzyme Kinetics; Interfacial Biocatalysis; Macromolecular Crowding; Molecular Modeling; Spatiotemporal Modeling; Systems Biology