Engineering topics

Vermaas, Joshua

Publications and source records attributed to Vermaas, Joshua.

8 records

DOE OSTI2020

Advances in Multiscale Modeling of Lignocellulosic Biomass

Applications and associated processing technologies of lignocellulosic biomass are becoming more important as we endeavor to meet societal demand for fuels, chemicals, and materials from renewable resources. Meanwhile, the rapidly expanding availability and capabilities of high-performance computing present an unprecedented opportunity to accelerate development of technologies surrounding lignocellulose utilization. In order to realize this potential, suitable modeling frameworks must be constructed that effectively capture the multiscale complexity and tremendous variety exhibited by lignocellulosic materials. In our assessment of previous endeavors towards this goal, several important shortcomings have been identified: (1) the lack of multiscale integration strategies that capture emergent properties and behaviors spanning different length scales, and (2) the inability of many modeling approaches to effectively capture the variability and diversity of lignocellulose that arise from both natural and process-induced sources. In this perspective, we survey previous modeling approaches for lignocellulose and simulations processes involving its chemical and mechanical transformation, and suggest opportunities for future development to enhance the utility of computational tools to address barriers to widespread adoption of a renewable bioeconomy.

09 BIOMASS FUELS↗

DOE OSTI2019

Molecular Interactions at the Cellulose-Lignin Interface Explored via Molecular Simulation

Lignin and cellulose are found ubiquitously in plant cell walls, making them two of the most abundant biopolymers on Earth. In spite of their ubiquity, comparatively little is known quantitatively about their interactions within native biomass, and by extension how their interaction may play a role in biomaterials. The possible binding faces for lignin on crystalline cellulose I-ss and the heterogeneous chemistries found in native lignin typically preclude the isolation of specific interactions for quantitative comparison in the laboratory. In this study, we use molecular simulation to examine individual combinations of binding face and lignin chemistry to quantify lignin-cellulose interactions, including contributions from both specific hydrogen bonds and nonspecific van der Waals interactions. For all lignin chemistries simulated, the hydrophobic 200 face is the preferred for cellulose interactions. For hydrophilic crystalline faces, lignin is found to bind most effectively to the 110 face. The affinity between lignin and cellulose increases as additional lignin methoxy groups are added. These groups increase the lignin-cellulose contact area, increasing the binding affinity. These trends are extended to larger lignin polymers, where the relationships between lignin polymer size and binding affinity are quantified through biased simulation. In this case, the binding surface area between the lignin polymer and the cellulose surface dictates the interaction strength.

09 BIOMASS FUELS↗

DOE OSTI2019

The Dissociation Mechanism of Processive Cellulases

Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.

09 BIOMASS FUELS↗

DOE OSTI2019

Computational Insights into Fuels and Chemicals Extraction from Microbial Biorefineries

Over the past two decades, substantial investments have been made in engineering microorganisms to produce specific fuels and chemicals as part of the global bioeconomy. Many target molecules accumulate intracellularly, and a challenge is how to effectively extract the product from the cells without needing to destroy them due to the barrier imposed by the cell membrane. For some hydrophobic compounds, an organic overlay is an effective strategy for nondestructive product extraction, although the relationship between functional groups on the product and the rate of extraction are not well understood. Through both biased and unbiased molecular dynamics simulations for a range of fatty acyl compounds and terpenoids, we directly compute permeability coefficients for different steps of the extraction process. Via comparative analysis between the calculated permeability coefficients and observed interactions between the compounds and the membrane, we determine how the rate limiting steps vary depending on product chemistry. For instance, fatty aldehydes are found to transfer very rapidly across the membrane bilayer relative to alcohols, although their comparable rate of extraction into the organic phase makes them equally effective at extraction from the cell. In assessing the terpenoids, it is found that in general a modestly hydrophilic product improves desorption rates into an organic phase sufficiently to make up for their lower bilayer crossing rate. With this new insight, we can more effectively engineer microorganisms towards the production of these modestly hydrophilic fuel precursors or chemicals.

09 BIOMASS FUELS↗

DOE OSTI2019

Dissociation Mechanism of Processive Cellulases Explored Through Molecular Simulation

Cellulose is the most abundant biopolymer on the planet, with significant potential as a feedstock for bioderived products. In nature, fungi and bacteria secrete cellulases to hydrolyze cellulose into smaller carbohydrates for incorporation into their own metabolic processes. For effective biomass utilization at industrial scale, these cellulases are coupled together to produce a clean sugar stream. One such cellulase is Cel7A from Trichoderma reesei, which is used extensively in biotechnological applications. However, dissociation of Cel7A from a bound cellulose strand is rate-limiting, reducing catalytic efficiency and yields within industrial applications. To explore this unknown dissociation mechanism and devise potential enzyme engineering strategies to mitigate slow dissociation, we conduct Hamiltonian replica exchange molecular dynamics simulations. Two postulated dissociation mechanisms were tested ('dethreading' of the bound cellulose strand from the binding tunnel and 'clamshell'-like opening of the binding tunnel and recrystallization of the bound cellulose). For each mechanism, free energy profiles were determined together with estimated diffusion coefficients. The kinetics for both mechanisms were then estimated and compared against experimentally measured dissociation rates, which suggest that the dethreading mechanism ought to be preferred. These findings are further supported by dissociation rates measured on engineered mutants incapable of undergoing the clamshell mechanism.

09 BIOMASS FUELS↗

DOE OSTI2019

Binding Affinity Dependence of Lignin-Cellulose Complexes on Cellulose Faces and Lignin Composition

The interaction between lignin and cellulose is essential to the structural integrity of plant cell walls, and these strong interactions are key to biomass recalcitrance. Previous studies have indicated that the hydrophobic face of cellulose is the primary face of interaction between cellulose and lignin. However, due to the structural inhomogeneity of lignin and the small lengthscales that would need to be probed, the relative binding affinities for lignin to different cellulose faces has not been previously determined. Through the creation of idealized infinite cellulose faces for the (200), (110), (1-10) and, (010) planes, we determine through computation the relative binding affinities for selected lignin compounds to these different faces of cellulose. The preference for individual lignin monomers to bind to hydrophobic faces of cellulose is found to be remarkably weak. We develop a mathematical model to determine the structural features of lignin have the strongest relationship with the computed binding affinities for large lignin polymers.

09 BIOMASS FUELS↗

DOE OSTI2019

Membrane Binding of Soluble Enzymes, Explored Through Simulation of Bacterial P450s

Members of the P450 enzyme family catalyze the oxidation of many different, but primarily lipophillic, substrates. In eukaryotic P450s, a membrane-anchored N-terminal helix tethers the enzyme to the membrane. However, in bacterial P450s, no N-terminal helix is present in the sequence, and the proteins are found to be soluble and amenable to solution experiments. Through unbiased classical molecular dynamics simulations, we demonstrate that these soluble enzymes bind to lipid membranes in the same orientation as tethered P450s. We postulate that the observed membrane binding improves the turnover of the enzyme by co-locating the enzyme at regions of high substrate concentration. Through mathematical modeling, we determine that the small cellular volume in prokaryotes is the primary reason that no N-terminal helix is found in these enzymes, as fewer enzymes are mistargeted into the small cytoplasmic space.

09 BIOMASS FUELS↗

DOE OSTI2018

Lignin Forcefield Source Datafiles

Three archives are provided here comprising the development of a CHARMM36-compatible lignin forcefield suitable for use in biomolecular simulations. One archive parameters.zip contains the output topology and parameter files in CHARMM format suitable for use in constructing simulation systems. The remaining two hold the logic of the parameterization featuring scripts that do the optimization including the source for the GPU-accelerated objective function evaluation and target data creation scripts.zip as well as minimal outputs needed to recreate the work datafiles.zip. Due to licensing restrictions Gaussian log files that created the target data are not provided here. Instead only binary-formatted parsed target data as well as the input decks used to create the target data are provided in datafiles.zip. Readme files for individual directories created within the directory structure are contained within scripts.zip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗