Towards Sustainable Biofuels: A Coarse-Grained Approach to Modeling Cellulose

Abstract

Caldicellulosiruptor is a unique genus of bacteria that produces lignocellulose-degrading Carbohydrate Active enZymes (CAZymes). CAZymes are of particular interest because of their potential utility in processing cellulose for sustainable biofuel pathways. However, studying the CAZyme efficiently has been difficult both experimentally and computationally due to the enzyme’s large size, over 1700 amino acid residues in length. Previous computational studies have studied the CAZyme in a limited capacity, simulating only small sections of the protein with atomistic approaches. In this paper, I present Mpipi- Cellulose, the extension of the coarse-grained Mpipi force field to cellulose. Mpipi-Cellulose represents each monomer of cellulose as a single interaction site (or bead), allowing for more efficient computations yet still accurately capturing the cellulose-protein interactions of CAZyme binding to cellulose. Through a series of umbrella sampling simulations, potentials of mean force were constructed for interactions between cellulose and a variety of ligands, including peptide fragments and subdomains of CelA, the primary CAZyme produced by the Caldicellulosiruptor genus of bacteria. Mpipi-Cellulose demonstrated strong qualitative agreement with Martini3, a higher resolution coarse-grained model optimized for cellulose, across these simulations. Mpipi-Cellulose was then used to simulate the entire CelA interacting with a slab of crystalline cellulose. Using the newly developed model, I tracked the number of contacts between the enzyme and the cellulose, showing that the majority of the residues that interact with the cellulose come from the binding domains as predicted by experiments. Further simulations were performed with various CelA mutants, removing different binding domains and exploring the impact on interaction with the cellulose. These simulations demonstrated that the second and third binding domains in CelA are particularly important for proper binding to the cellulose surface. With this knowledge and further use of the Mpipi-Cellulose model, a wide number of mutants can be screened to optimize CAZyme performance for degradation of cellulose to produce biofuels.