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DOE OSTI2025

Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.

Diffusion↗

DOE OSTI2022

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å −1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q -range to <0.5 Å −1 , but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H 2 O and in D 2 O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å −1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Evaluation of Copper Chelation Therapy in a Transgenic Rat Model of Cerebral Amyloid Angiopathy

Cerebral amyloid angiopathy (CAA) is characterized by the accumulation of the amyloid β (Aβ) protein in blood vessels and leads to hemorrhages, strokes, and dementia in elderly individuals. Recent reports have shown elevated copper levels colocalized with vascular amyloid in human CAA and Alzheimer’s disease patients, which have been suggested to contribute to cytotoxicity through the formation of reactive oxygen species. Here, we treated a transgenic rat model of CAA (rTg-DI) with the copper-specific chelator, tetrathiomolybdate (TTM), via intraperitoneal (IP) administration for 6 months to determine if it could lower copper content in vascular amyloid deposits and modify CAA pathology. In this work, results showed that TTM treatment led to elevated Aβ load in the hippocampus of the rTg-DI rats and increased microbleeds in the wild type (WT) animals. X-ray fluorescence microscopy was performed to image the distribution of copper and revealed a surprising increase in copper colocalized with Aβ aggregates in TTM-treated rTg-DI rats. Unexpectedly, we also found an increase in the copper content in unaffected vessels of both rTg-DI and WT animals. These results show that IP administration of TTM was ineffective in removing copper from vascular Aβ aggregates in vivo and increased the development of disease pathology in CAA.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The effect of low temperature on poly(3-methyl- N -vinylcaprolactam)- b -poly( N -vinylpyrrolidone) diblock copolymer nanovesicles assembled from all-aqueous media

Nanosized polymeric vesicles (polymersomes) self-assembled from double hydrophilic copolymers of poly(3-methyl-N-vinylcaprolactam) n -b-poly(N-vinylpyrrolidone) m (PMVC n -b-PVPON m ) using all aqueous media are a promising platform for biomedical applications, because of their superior stability over liposomes in vivo and high loading capacity. Herein, we explored the temperature-sensitive behavior of PMVC 58 -b-PVPON 65 vesicles using transmission electron microscopy (TEM), dynamic light scattering (DLS), atomic force microscopy (AFM), and small-angle neutron scattering (SANS) in response to lowering the solution temperature from 37 to 25, 20, 14 and 4 °C. The copolymer vesicles with an average size of 350 nm at 37 °C were assembled from the diblock copolymer dissolved in aqueous solution at 4 °C. We show that while the polymersome's size gradually decreases upon the temperature decrease from 37 to 4 °C, the average shell thickness increases from 17 nm to 25 nm, respectively. SANS study revealed that the PMVC 58 -b-PVPON 65 vesicle undergoes a gradual structure evolution from a dense-shell vesicle at 37–25 °C to a highly-hydrated shell vesicle at 20–14 °C to molecular chain aggregates at 4 °C. From SANS contrast matching study, this vesicle behavior is found to be driven by the gradual rehydration of PMVC block at 37–14 °C. The shell hydration at 20–14 °C also correlated with the 4.4-fold decrease in the relative fluorescence intensity from vesicle-encapsulated fluorescent dye, indicating ~80% of the dye release within 12 hours after the vesicle exposure to 14 °C. No significant (<5%) dye release was observed for the vesicle solutions at 37–20 °C, indicating excellent cargo retention inside the vesicles. Our study provides new fundamental insights on temperature-sensitive polymer vesicles and demonstrates that the copolymer assembly into polymersomes can be achieved by decreasing a copolymer aqueous solution temperature below 14 °C followed by solution exposure to ≥20 °C. This type of all-aqueous assembly, instead of nanoprecipitation from organic solvents or solvent exchange, can be highly desirable for encapsulating a wide range of biological molecules, including proteins, peptides, and nucleic acids, into stable polymer vesicles without a need for organic solvents for dissolution of the copolymers that are amphiphilic at physiologically relevant temperatures of 20–37 °C.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Effects of Microbial-Mineral Interactions on Organic Carbon Stabilization in a Ponderosa Pine Root Zone: A Micro-Scale Approach

Soil microbial communities affect the formation of micro-scale mineral-associated organic matter (MAOM) where complex processes, including adhesion, aggregate formation, microbial mineral weathering and soil organic matter stabilization occur in a narrow zone of large biogeochemical gradients. Here we designed a field study to examine carbon stabilization mechanisms by using in-growth mesh bags containing biotite that were placed in a ponderosa pine root zone for 6 months and compared to the surrounding bulk soil. We sought to determine the composition of the microbial community in the mesh bags compared to the surrounding soils, analyze the direct interactions between microbes and biotite, and finally identify the nature of the newly formed MAOM within the mesh-bags. Our results revealed that minerals in the mesh bags were colonized by a microbial community that produced organic matter in situ. The 16S rRNA gene sequencing and ITS2 region characterization showed phylogenetic similarity between the mesh bag and bulk soil archaea/bacteria and fungi microbiomes, with significant differences in alpha- and beta-diversity and species abundances. Organic matter pools in the mesh bags, analyzed by Fourier transform ion cyclotron resonance mass spectrometry, contained protein- (peptides) and lipid-like compounds while the bulk soil OM was comprised of lignin-like and carboxyl-rich alicyclic molecules. These results support that the newly formed biotite associated organic compounds have a microbial signature in the mesh bags. High-resolution electron microscopy documented strongly adhered organic compounds to biotite surfaces, formation of microaggregates, elemental uptake at the microbe (organic matter)-mineral interface, and distortion of biotite layers. Overall, this study shows the direct and indirect involvement of soil microbial communities from the root zone of ponderosa pine in the formation of MAOM, soil organic carbon stabilization, microaggregation, and mineral weathering at micro- and nano-scales.

58 GEOSCIENCES↗

DOE OSTI2023

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD , CTD , and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Unraveling the Heterogeneous but Ordered Microstructure of the Nonionic Deep Eutectic Solvent Formed by Lauric Acid and N -Methylacetamide

The nonionic deep eutectic solvent, formed by lauric acid (LA) and N-methylacetamide (NMA), has been shown to have a heterogeneous molecular structure in which the LA and NMA form nonpolar and polar domains, respectively. Previous vibrational spectroscopy experiments demonstrated that the ability of the LA domains to solvate compounds was limited to long carbon chains, whereas other nonpolar molecules, such as W(CO) 6 , were found to be solvated by both LA and NMA. These experiments were not fully compatible with the previously proposed micelle-like structure of the nonpolar domains of the LA-NMA DES. In this work, the modeling of the DES molecular structure is pursued using classical molecular dynamics simulations. The new classical model reproduces both the SAXS structural factors and the previously experimentally derived interaction map for these LA-NMA DESs. In addition, the simulation also shows that LA-NMA DESs form highly organized LA aggregates that are difficult to disorganize. Further evidence of the correct description provided by the newly derived model is obtained using a moderately polar probe: chloroform-d. Computations using the classical model have a good agreement with the solvation behavior of the probe derived from experiments, in which the location of the probe is found to be mostly within the polar domain of the DES. The computational model also demonstrates that the probe solvation is a consequence of the tightly packed LA structure, which causes nonpolar molecules to be located at the interphase of the DES nonpolar domains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Geographically Dependent Sustainability Indicators for Comparison of Conventional Vegetable Production to Controlled-Environment Agriculture

Many food system lifecycle analyses distill agricultural production and supply chain impacts into single-value sustainability metrics for various food categories. These studies provide an overview of the food supply system that highlight striking results such as the GHG impacts of meat production. The supply chain impacts of vegetable production occupy the middle ground; higher than average food loss and waste, lower than average overall energy use, etc. However, aggregated results obscure the sustainability implications of the location of food production, especially for vegetables. Moreover, the increasing instability of food production systems are not captured, as illustrated by a recent Washington Post article. According to a UC Merced study conducted for the state, California farmers left nearly 400,000 acres of agricultural land unplanted last year because of a lack of water. The result, the study found, was a direct economic cost to farmers of $1.1 billion and the loss of nearly 9,000 agricultural jobs. (The Washington Post, March 21, 2022.) Previous work quantified the food-energy-water nexus implications of transitioning vegetable production from large, centralized agricultural operations to smaller distributed production in controlled-environment farms (CEA). The importance of location-specific data is especially evident for water use. Water impacts of the food system are primarily local to the region where food is produced, water impacts vary significantly between locations, and water stress is a major concern in locations that currently host large agricultural operations. Location-specific data is needed to accurately assess the water impacts of transitioning to CEA. The location of farms in relation to consumers impacts transportation energy use, food loss and waste, and requirements for food processing (e.g., to reduce weight, preserve foods for long storage, and package foods to reduce damage and loss) Reducing transport is particularly relevant for agricultural products that could be grown in CEAs (fruits, vegetables, protein). Access to nutritious food is not evenly distributed in the population. Remote communities, communities in harsh environments, and economically-disadvantaged communities often have poor access to healthy foods. CEA is ideally suited to these environments. However, the energy and water use of CEA, while in many respects lower overall than conventional supply chains, are concentrated within communities and could have significant local impacts. This paper reports on development of sustainability metrics that seek to capture the tradeoffs between the current supply chain and a CEA supply chain for vegetables; focusing on the location-dependent implications of water use, the transition from largely fossil fuel based energy use to electricity, and the food access, resilience and wellbeing implications of urban versus rural food production.

controlled-environment agriculture↗

DOE OSTI2023

Cell Free and Immobilization Technologies (CFIT)

Today, several key factors negatively impact the production of fuels and chemicals from renewable sources. Common hindrances in the biological production of biochemicals are: (1) end-product or intermediate toxicity to the microbial biocatalyst, (2) the diversion of carbon to biomass formation, and (3) co-production of undesired byproducts. A particularly attractive alternative is to eliminate the biocatalyst entirely and instead operate the desired metabolic pathways in isolation, thus circumventing the roadblocks of biological toxicity, lower yields, and lack of specificity. However, cell-free enzyme systems still suffer from low productivities owing in part to the effects of free diffusion of intermediates, lack of long term enzyme stability, cofactor cost or inefficient recycling rates, and finally, the cost of enzyme production/purification. This project represents a new effort to propose innovative and cost competitive routes to producing biochemicals from a variety of feedstocks using cell free approaches. These routes will help reduce the current risk and cost associated with classical cell free production. Cell free technologies show promise for application to the production of toxic/inhibitory products or products difficult to separate from microbial growth media and can help reduce the production barriers in multiple areas of biological conversion of feedstocks to biochemicals. More specifically, we are developing new technologies and routes that could be used to produce high value biochemicals such as 2,3 BDO and terpenes (among many others) from biomass derived C5/C6 sugars or lignin but also from waste byproducts such as glycerol. This project will lead to significant innovation and also lead to new concepts and rational design of pathways and enzymes. Within this project, we will develop new metabolic enzyme cascades that will represent natural or artificial combinations of enzymes to produce the desired biochemicals from a variety of feedstocks. We are also developing basic design principals for constructing synthetic metabolons, using fusion proteins and synthetic protein scaffolds, to promote substrate channeling and stability while conserving peak activity. Additionally, our efforts include a techno economic analysis (TEA) of cell free approaches to provide the sensitivities of the process to enzyme loading, activity, pH, reactor volumes, cofactor recycling rates. Finally, we are focusing on further increasing stability, operating lifetime and efficiency of the pathway enzymes by immobilization on support surfaces. We are also focus on immobilizing pathway enzymes or combinations of enzymes on several different conducting polymers and evaluate the effect on stability and operating lifetime. As more combinations become available we will conduct a more systematic study of the means of immobilizing these enzymes. This preliminary work will enable the in-depth study of cofactor recycling at these interfaces using mediators for electron transfer. Taken together, these approaches will enable process intensification, continuous operation, lower capital and separations costs and end-product flexibility, and thus has the potential to contribute significantly to BETO's goals of cost competitive biofuels and bioproducts. To date we have demonstrated 1) the conversion of pyruvate to 2,3 BDO (4 enzymes with cofactor recycling, no additional cofactors needed) at >100g/L (>3g/L/h) using our enzyme tethering approach, 2) Generated mutants of a key redox enzyme with >180- fold improvement in NADH utilization over WT to >85% of NADPH utilization. 3) Produced mevalonate at >10g/L from glucose, limonene at >10g/L from mevalonate and more than >5g/L from glucose with crude enzyme preparations and complete cofactor recycling. 4) successfully generated fully active cross-linked aggregates (CLEAs) of NOX, a cofactor-regenerating water-forming oxidase that is key to our process with increased stability 5) Engineered and identified enzymes able to use the biomimetic cofactor NMN and synthesized new synthetic cofactors.

biocatalysis↗

DOE OSTI2025

Probing Nanoscale Chemical Environments of Zinc in Diatoms

Diatoms impact the biogeochemical cycling of zinc (Zn) due to elevated cellular Zn levels over other phytoplankton, and their strong biological uptake of Zn in the Southern Ocean sets the global distribution of Zn in ocean water columns. Past studies have revealed the abundance and spatial distribution of Zn in individual diatoms, while others have shown diverse Zn chemical species in whole-cell aggregates. However, intracellular and intercellular variations in Zn chemical forms remained unknown. For the first time, we applied a synchrotron X-ray nanoprobe to cultured diatoms (Phaeodactylum tricornutum and Chaetoceros muelleri) and resolved spatial heterogeneities of Zn chemistry. The result shows the partitioning of Zn between intracellular contents (soft parts) and frustules (mainly in the intracellular contents for P. tricornutum and similar Zn concentrations in the intracellular contents and frustules for C. muelleri). We found multiple Zn chemical species unevenly distributed within individual cells, where Zn–phosphoryl complexes were the most abundant followed by cysteine, histidine, biogenic silica, and carboxyl complexes. Cellular Zn species varied between individual organisms and were influenced by Zn availability. To our knowledge, this work presents the first X-ray measurements of trace metal speciation at sub-100 nm resolution in biological samples in their natural state. In conclusion, this research improves our ability to examine the biogeochemistry of Zn on the nanoscale and can help us understand the role of Zn in plankton growth and the Zn cycle in ocean waters.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗

DOE OSTI2025

The congenital APOA1 K107del mutation disrupts the lipid-free conformation of monomeric APOA1 and impairs oligomerization

Apolipoprotein A-I (APOA1) oligomerization is thought to be essential for high-density lipoprotein (HDL) formation and metabolism. Naturally occurring mutations can disrupt normal APOA1 folding and self-association, leading to dysfunctional HDL formation and cardiovascular disease. The congenital APOA1 variant p.K131del (APOA1 K107del ) has been associated with cardiovascular pathologies such as low HDL-cholesterol levels and aortic amyloidosis, and multiple studies indicate structural changes in APOA1 conformation underlie associated dysfunction. In the current study, we confirmed that APOA1 K107del exhibits no notable defect in lipid-binding. However, using polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC), we found that loss of lysine 107 resulted in a remarkable shift in the distribution of APOA1 oligomers with a much higher proportion of monomers present in APOA1 K107del compared to wild-type APOA1. Further investigation using quantitative cross-linking revealed a major disruption of interactions in helical regions reported to participate in domain swaps necessary for proper self-association. This structural disruption appears to impair N- and C-termini interactions and dynamics that lead to non-specific aggregation. In conclusion, these findings support the hypothesis that lysine 107 is critical for proper folding and self-association of lipid-free APOA1 which could impact HDL biogenesis.

APOA1 (p.K131del)↗