The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds

Abstract

A multiscale simulation model is used to construct potential and free energy surfaces for the carbohydrate-binding module [CBM] from an industrially important cellulase, Trichoderma reesei cellobiohydrolase I, on the hydrophobic face of a coarse-grained cellulose Ibeta polymorph. We predict from computation that the CBM alone exhibits regions of stability on the hydrophobic face of cellulose every 5 and 10 A, corresponding to a glucose unit and a cellobiose unit, respectively. In addition, we predict a new role for the CBM: specifically, that in the presence of hydrolyzed cellulose chain ends, the CBM exerts a thermodynamic driving force to translate away from the free cellulose chain ends. This suggests that the CBM is not only required for binding to cellulose, as has been known for two decades, but also that it has evolved to both assist the enzyme in recognizing a cellulose chain end and exert a driving force on the enzyme during processive hydrolysis of cellulose.

Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium

“…7B suggests that the enzyme is enthalpically stable above glycosidic linkages separated by ϳ10 Å, where the enzyme can abstract accessible hydrogen atoms. The stabilization every 10 Å, which is approximately the length of a cellobiose unit, is similar to that observed for a family 1 CBM (19,54).…”

“…Last, a potential energy surface (PES) for the PchGH61D-cellulose interaction was also constructed to examine the location of stable energetic wells. This closely follows previous work conducted on the family 1 CBM (19,54). Details of the PES construction can be found in the supplemental material.…”

“…The PES was constructed with explicit solvation using methods similar to those used in previous work conducted on a family 1 CBM (19,54). The PES in Fig.…”

Single-molecule Imaging Analysis of Binding, Processive Movement, and Dissociation of Cellobiohydrolase Trichoderma reesei Cel6A and Its Domains on Crystalline Cellulose

“…Alternatively, the absence of the CBM-linker may significantly decrease the processivity. Regarding this second possibility, Bu et al (38) predicted that the CBM has important roles in not only binding but also introducing a single cellulose chain to the catalytic site and increasing the processivity of the reaction. Their molecular simulation showed that the CBM exerts a driving force and assists processive movement by biased sliding when the CBM binds near the cellulose chain end.…”

The impact of Trichoderma reesei Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study

“…Recently, the CBD cellulose complex has been modeled in order to investigate the binding mechanism by molecular dynamics (MD) simulations. It has been suggested that CBD may assist with the recognition of the cellulose chain end and facilitate the processivity of Cel7A [11][12][13]. Beckham et al predicted that electrostatic interactions dominate the energy changes in the Cel7A CBD processivity [12].…”