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 Contours of constant solvent density for water above the (1,1,0) cellulose surface as seen from the (0,0,1) face, where: Blue contour mesh encloses regions where water density exceeds bulk solvent density by 25%, Yellow contour mesh encloses regions where solvent density exceeds average bulk solvent density by 50%, and Red contour mesh encloses regions where solvent density is 75% above bulk density. |
 Contours of water density around the E1 linker polypeptide as calculated from the unconstrained simulation with 6469 water molecules. The blue contour level encloses regions with a density 50% less than the bulk density, and it essentially enclosed the outer surface and van der Waals surface of the peptide. The yellow grid encloses regions with a density 50% greater than the bulk density, and the red grid encloses those regions with a density 75% greater than bulk density. |
 The polypeptide structure in the new, larger simulation in which the glycopeptide is kept as extended as possible. A white tube is superimposed on the backbone to make it easy to follow its path in space. |
Our Challenge
We seek to understand the atomic-level details of the process of hydrolyzing cellulose to glucose for bioethanol fermentation, and determine the limiting factors in both acidic and enzymatic hydrolysis.
Our Approach
NREL's IBM computer and superCHARMM are key assets to our maintaining cutting-edge research that supports the U.S Department of Energy Office of the Biomass Program. Researchers at Cornell University and the Colorado School of Mines use these resources to conduct subcontract research in NREL's Cellulase Enzyme Fundamentals program.
This joint project involves using molecular mechanics calculations to study the atomic-level details of the process of hydrolyzing cellulose to glucose for bioethanol fermentation. The overall goals are to determine the limiting factors in both acid and enzymatic hydrolysis. The specific projects for which we used the NREL Carter IBM SP3 system involved using molecular dynamics simulations to model the structuring of water above cellulose surfaces and the conformational significance of the linker polypeptide segment from the CBH I cellulase from T. reesei CBH I cellulase.
Our Results
In one study, we examine how a velocity gradient, representative of a fluid flowing as in a shrinking bed reactor, perturbs the specific surface functional groups in the microcrystalline cellulose structure of the water adjacent to the surface. The strong localization of the water in layers adjacent to the surface can impede the approach of enzymes or acid to the surface and the escape of product. So understanding how these structures might be perturbed by such variables as macroscopic flow will be of considerable utility in the field. The linker peptide project involves examining the conformational behavior of the linker segment found between the catalytic and binding domains of CBH I and how this polypeptide influences activity.
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