SusChEM: Carbohydrate Recognition in Type B Carbohydrate Binding Modules

University Of Kentucky Research Foundation, Lexington KY

Investigators

Abstract

Plant cell walls are constructed from a solid polymer of carbohydrate molecules called cellulose. Microbes produce enzymes capable of breaking down the cellulose into individual sugar molecules, which can then be used in chemical processes to make fuel. The enzymes often consist of at least two domains: one responsible for cleaving chemical bonds and one responsible for locating the cellulose surface (Carbohydrate Binding Modules or CBMs). CBMs also help the enzyme differentiate between perfect, crystalline regions and imperfect, non-crystalline regions, yet how the structure of the protein is capable of this distinction remains unknown. Understanding how this happens will enable development of new biotechnology for biofuels production as well as many other applications. This study will train graduate and undergraduate students in the development of realistic protein-carbohydrate models and in advanced thermodynamic calculations. This project will also be integrated into an outreach program intended to promote interest in high performance computing among underrepresented researchers and provide the necessary tools to generate successful results. NSF-EPSCoR and the Chemistry of Life Processes Program in the Chemistry Division are funding Dr. Christina Payne from the University of Kentucky to determine the mechanisms of carbohydrate recognition in CBMs and the means by which these proteins are capable of binding non-crystalline cellulose more tightly than soluble oligomers. Molecular dynamics simulations and enhanced sampling free energy methods will be used to evaluate the molecular-level origins of oligomeric carbohydrate recognition within and across three families of cellulose-specific, Type B CBMs. Non-crystalline cellulose-binding CBMs will be modeled bound to the insoluble substrate, and alchemical free energy pathways will be used to determine the free energy of binding to non-crystalline cellulose. Molecular dynamics simulations of a tandem CBM construct in solution and in proximity to representative non-crystalline cellulose substrate will be used to relate findings from the individual modules to the tandem construct behavior. Principle component analysis and elastic network modeling will uncover residue correlation and mechanical coupling contributing to cooperative binding and avidity. The outcome of this study will provide an unprecedented level of insight into the complex solid and soluble carbohydrate substrate recognition mechanisms of CBMs, the findings of which hold considerable promise for enhancing biomass conversion technology.