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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Charge transfer excitations, pair density waves, and superconductivity in moiré materials

Transition-metal dichalcogenide (TMD) bilayers are a new class of tunable moiré systems attracting interest as quantum simulators of strongly interacting electrons in two dimensions. In particular, recent theory predicts that the correlated insulator observed in WSe 2 /WS 2 at half filling is a charge-transfer insulator similar to cuprates and, upon further hole doping, exhibits a transfer of charge from anionlike to cationlike orbitals at different locations in the moiré unit cell. In this work, we demonstrate that in this doped charge-transfer insulator, tightly bound charge-2$\textit{e}$ excitations can form to lower the total electrostatic repulsion. This composite excitation, which we dub a trimer, consists of a pair of holes bound to a charge-transfer exciton. When the bandwidth of doped holes is small, trimers crystallize into insulating pair density waves at a sequence of commensurate doping levels. Further, when the bandwidth becomes comparable to the pair binding energy, itinerant holes and charge-2$\textit{e}$ trimers interact resonantly, leading to unconventional superconductivity similar to superfluidity in an ultracold Fermi gas near Feshbach resonance. Our theory is broadly applicable to strongly interacting charge-transfer insulators, such as WSe 2 /WS 2 or TMD homobilayers under an applied electric field.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Coexisting paramagnetic spins and long-range magnetic order in Ba4⁢(Ru0.92⁢Ir0.08)3⁢O10

We investigate the effect of dilute Ir substitution on the magnetism of the trimer-based ruthenate Ba4⁢Ru3⁢O10 using neutron diffraction, magnetic susceptibility measurements, first-principles calculations, and atomistic simulations. Neutron diffraction shows that Ir doping preserves the zigzag antiferromagnetic structure and the ordered-moment magnitude of the parent compound, in which the moments reside exclusively on the two outer Ru(2) sites of each Ru3⁢O12 trimer, while the central Ru(1) site remains nonmagnetic. The Néel temperature is reduced from ∼105 to 84.0(1) K upon 8% Ir substitution, while magnetic susceptibility reveals a pronounced low-temperature Curie-like upturn, indicating the coexistence of paramagnetic spins with long-range antiferromagnetic order. Density-functional calculations show that Ir preferentially occupies the central Ru(1) site, which disrupts the exchange pathways of the affected Ru3⁢O12 trimer state. Atomistic simulations incorporating this paramagnetic dilution reproduce the suppressed ordering temperature and the coexistence of ordered and paramagnetic components.

Islam, Farhan [Ames Laboratory]↗
NASA NTRS1982

Oxidation and formation of deposit precursors in hydrocarbon fuels

A practical fuel, home heating oil no. 2 (Fuel C), and the pure hydrocarbon, n-dodecane, were subjected to mild oxidation at 130 C and the resulting oxygenated reaction products, deposit precursors, were analyzed using field ionization mass spectrometry. Results for fuel C indicated that, as oxidation was initially extended, certain oxygenated reaction products of increasing molecular weights in the form of monomers, dimers and some trimers were produced. Further oxidation time increase resulted in further increase in monomers but a marked decrease in dimers and trimers. This suggests that these larger molecular weight products have proceeded to form deposit and separated from the fuel mixture. Results for a dodecane indicated that yields for dimers and trimers were very low. Dimers were produced as a result of interaction between oxygenated products with each other rather than with another fuel molecule. This occurred even though fuel molecule concentration was 50 times, or more greater than that for these oxygenated reaction products.

Buttrill, S. E., Jr.↗
NASA NTRS1992

Concerted hydrogen atom exchange between three HF molecules

We have investigated the termolecular reaction involving concerted hydrogen exchange between three HF molecules, with particular emphasis on the effects of correlation at the various stationary points along the reaction. Using an extended basis, we have located the geometries of the stable hydrogen-bonded trimer, which is of C(sub 3h) symmetry, and the transition state for hydrogen exchange, which is of D(sub 3h) symmetry. The energies of the exchange reation were then evaluated at the correlated level, using a large atomic natural orbital basis and correlating all valence electrons. Several correlation treatments were used, namely, configration interaction with single and double excitations, coupled-pair functional, and coupled-cluster methods. We are thus able to measure the effect of accounting for size-extensivity. Zero-point corrections to the correlated level energetics were determined using analytic second derivative techniques at the SCF level. Our best calculations, which include the effects of connected triple excitations in the coupled-cluster procedure, indicate that the trimer is bound by 9 +/- 1 kcal/mol relative to three separate monomers, in excellent agreement with previous estimates. The barrier to concerted hydrogen exchange is 15 kcal/mol above the trimer, or only 4.7 kcal/mol above three separated monomers. Thus the barrier to hydrogen exchange between HF molecules via this termolecular process is very low.

Komornicki, Andrew↗
NASA NTRS1999

Proton-bound cluster ions in ion mobility spectrometry

Gaseous oxygen and nitrogen bases, both singly and as binary mixtures, have been introduced into ion mobility spectrometers to study the appearance of protonated molecules, and proton-bound dimers and trimers. At ambient temperature it was possible to simultaneously observe, following the introduction of molecule A, comparable intensities of peaks ascribable to the reactant ion (H2O)nH+, the protonated molecule AH+ and AH+ H2O, and the symmetrical proton bound dimer A2H+. Mass spectral identification confirmed the identifications and also showed that the majority of the protonated molecules were hydrated and that the proton-bound dimers were hydrated to a much lesser extent. No significant peaks ascribable to proton-bound trimers were obtained no matter how high the sample concentration. Binary mixtures containing molecules A and B, in some cases gave not only the peaks unique to the individual compounds but also peaks due to asymmetrical proton bound dimers AHB+. Such ions were always present in the spectra of mixtures of oxygen bases but were not observed for several mixtures of oxygen and nitrogen bases. The dimers, which were not observable, notable for their low hydrogen bond strengths, must have decomposed in their passage from the ion source to the detector, i.e. in a time less than approximately 5 ms. When the temperature was lowered to -20 degrees C, trimers, both homogeneous and mixed, were observed with mixtures of alcohols. The importance of hydrogen bond energy, and hence operating temperature, in determining the degree of solvation of the ions that will be observed in an ion mobility spectrometer is stressed. The possibility is discussed that a displacement reaction involving ambient water plays a role in the dissociation.

Non-NASA Center↗
DOE OSTI2020

Scaffolded HIV-1 vaccine immunogens

The present invention provides novel scaffolded HIV-1 vaccine immunogens. Some of the scaffolded immunogens contain a soluble gp140 trimer linked to the N-terminus of the nanoparticle subunit and a T-helper epitope that is fused via a short peptide spacer to the C-terminus of the nanoparticle subunit. Some other immunogens of the invention contain a soluble gp140 trimer protein that is linked to a stable nanoparticle via a short peptide spacer that is a T-helper epitope. Some of the scaffolded immunogens contain a gp140 trimer immunogen presented on a nanoparticle platform formed with I3-01 protein, E2p, or variants of protein 1VLW. Also provided in the invention are nucleic acids that encode the various vaccine immunogens described herein, and expression vectors and host cells harboring the nucleic acids. The invention further provides methods of using the scaffolded HIV-1 vaccine immunogens for preventing or treating HIV infections.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Supported Organochromium Ethylene Oligomerization Enabled by Surface Lithiation

Here, in this work, supported organochromium ethylene polymerization catalysts have been tuned to mediate ethylene oligomerization via surface lithiation, which provides a generalizable protocol to control stereoelectronics and redox states of surface organometallic active sites. The homoleptic chromium(IV) alkyl complex Cr(CH 2 SiMe 3 ) 4 was grafted on high-surface-area anatase titania (TiO 2 ) nanoparticles as well as on silica to produce Cr/TiO 2 and Cr/SiO 2 , respectively. Treatment of these materials with excess n-butyllithium led to the reduced chromium complexes Cr/Li x TiO 2 and Cr/Li/SiO 2 , each of which still retains one hydrocarbyl ligand on chromium. A set of heterogeneous complexes were studied by electron paramagnetic resonance and X-ray absorption spectroscopy, which indicate a reduction in the oxidation state of the major chromium species to Cr II upon lithiation. Cr/Li x TiO 2 converts ethylene to hexenes with a high selectivity (>80%), which was persistent over 10 days at 80 °C, achieving >950 turnovers. The exclusive formation of C 4 and C 6 olefins, preferring the trimerization product, without a statistical (Flory–Schulz) distribution is characteristic of the oxidative cyclization oligomerization mechanism rather than the traditional Cossee–Arlman mechanism, whereas Cr/Li/SiO 2 produced a mixture of trimerization and polymerization products, suggesting site heterogeneity in the silica-based material. On the other hand, the unreduced chromium(IV) materials as well as low lithium-containing Cr/Li x TiO 2 (x < 0.16) exclusively produced ultrahigh molecular weight polyethylene, determined by differential scanning calorimetry and gel permeation chromatography analysis, likely formed via a linear-insertion mechanism, with a crossover from the polymerization to oligomerization regime observed at ~16% Li intercalation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Catalytic Membrane Reactors Based on Carbon Molecular Sieve Hollow Fiber Membranes for Sustainable and Modular H 2 Production

We aimed to develop a catalytic membrane reactor (CMR) that couples water–gas shift (WGS) reaction with in-situ H 2 separation to produce blue H 2 and a CO 2 -rich stream from coal- and biomass-derived syngas. Our core approach employs high-permeance carbon molecular sieve (CMS) hollow-fiber membranes (HFMs) with strong gas separation ability, which we further integrate into catalytic membrane reactors to intensify H 2 production and CO 2 capture in a single unit. Three organizations with complementary skills collaborated to achieve the goal, including the University at Buffalo (UB), Los Alamos National Laboratory (LANL), and Trimeric Corporation (Trimeric).

08 HYDROGEN↗
DOE OSTI2022

Photocatalytic Hydrogen Evolution by a De Novo Designed Metalloprotein that Undergoes Ni–Mediated Oligomerization Shift

De novo metalloprotein design involves the construction of proteins guided by specific repeat patterns of polar and apolar residues, which, upon self-assembly, provide a suitable environment to bind metals and produce artificial metalloenzymes. While a wide range of functionalities have been realized in de novo designed metalloproteins, the functional repertoire of such constructs towards alternative energy-relevant catalysis is currently limited. Here we show the application of de novo approach to design a functional H 2 evolving protein. The design involved the assembly of an amphiphilic peptide featuring cysteines at tandem a/d sites of each helix. Intriguingly, upon Ni II addition, the oligomers shift from a major trimeric assembly to a mix of dimers and trimers. The metalloprotein produced H 2 photocatalytically with a bell-shape pH dependence, having a maximum activity at pH 5.5. Transient absorption spectroscopy is used to determine the timescales of electron transfer as a function of pH. Selective outer sphere mutations are made to probe how the local environment tunes activity. Finally, a preferential enhancement of activity is observed via steric modulation above the Ni II site, towards the N-termini, compared to below the Ni II site towards the C-termini.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

MgO(111) Nanocatalyst for Biomass Conversion: A Study of Carbon Coating Effects on Catalyst Faceting and Performance

Solid base metal oxide catalysts such as MgO offer utility in a wide variety of syntheses from pharmaceuticals to fuels. The (111) facet of MgO shows enhanced, unique properties relative to the other facets. Carbon coatings have emerged as a promising modification to impart metal oxide catalyst stability. Here, we report the synthesis, characterization, and catalytic properties of commercial MgO, MgO(111), and carbon coated derivatives thereof for 2-pentanone condensation. The dimer and trimer products of this reaction can be used as precursors for biofuels upon oxygen removal and thus have relevance in environmental sustainability. Additionally, MgO(111) maintained impressive selectivity towards the dimer product after carbon coating, whereas the other catalysts experienced a decrease in conversion and selectivity as a consequence of the carbon coating. Our findings highlight the catalytic efficacy of MgO(111), provide insight into carbon coating for catalyst stability, and pave the way for continued mechanistic investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies

Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Production and Catalytic Upgrading of 2,3-Butanediol Fermentation Broth into Sustainable Aviation Fuel Blendstock and Fuel Properties Measurement

With the increasing demand for sustainable supplies of aviation fuel and need to address climate change, new conversion technologies are needed to efficiently process biomass, produce high quality jet fuel blendstock, and meet carbon emission targets. This study demonstrates the synthesis, conditioning, and catalytic upgrading of 2,3-butanediol (BDO) fermentation broth into a jet fuel blendstock candidate. A high-titer 2,3-BDO fermentation broth (i.e., ~90 g/L) was produced at a 100-L scale and pretreated via nanofiltration to decrease the impurities level in the broth from 4.6 to 0.6 wt%. A novel process for catalytic upgrading of aqueous 2,3-BDO into a jet fuel blendstock candidate was developed, and each step was efficiently demonstrated. The catalytic steps include 1) 2,3-BDO dehydration into methyl ethyl ketone (MEK) over AlPO4, 2) MEK conversion into olefins over Zn1Zr10Ox, 3) oligomerization of olefins over a zeolite beta, and 4) hydrogenation over platinum/carbon. Both the model feed and real 2,3-BDO fermentation broth were tested for upgrading 2,3-BDO to MEK. With the real feed, a continuous loss of conversion (i.e., >50% loss over ~140 h time-on-stream [TOS]) was partly attributed to reversible deactivation from coking species. However, the conversion remained stable with the model feed, which demonstrates the efficiency of the first step for converting aqueous 2,3-BDO (10 wt% in water). For upgrading MEK to olefins, high selectivity to olefins (i.e., 82.5%) was obtained at high conversion levels (i.e., 93-98%) with stable conditions being achieved for > 70-hours TOS. Oligomerization of light olefins, which was demonstrated for > 270 h TOS, mainly led to the formation of dimers (C8-10) and trimers (C13-14). The oligomerized product was hydrogenated and distilled to recover the jet fraction (35 mass% or 40.9% carbon based yield), which consists mostly of desired isoalkanes (31.7 wt%), n-alkanes (24.5 wt%), and cycloalkanes (29.6 wt%). While some improvement is still needed to meet ASTM D7566 specifications for viscosity and final boiling point temperature, freezing point, density, aromatics content, and sulfur content of the jet blendstock candidate were within acceptable ranges, thus highlighting the potential of this process for production of jet fuel blendstock.

ADVANCED PROPULSION SYSTEMS,BIOMASS FUELS↗
DOE OSTI2022

Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes

Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Volatility Basis Set Distributions and Viscosity of Organic Aerosol Mixtures: Insights from Chemical Characterization Using Temperature-Programmed Desorption–Direct Analysis in Real-Time High-Resolution Mass Spectrometry

Quantitative assessment of gas-particle partitioning of individual components within complex atmospheric organic aerosols (OA) mixtures is critical for predicting and comprehending the formation and evolution of OA particles in the atmosphere. This investigation leverages previously documented data obtained through a temperature programmed desorption - direct analysis in real time – high resolution mass spectrometry (TPD-DART-HRMS) platform. This methodology facilitates the bottom-up construction of volatility basis set (VBS) distributions for constituents found in three biogenic secondary organic aerosol (SOA) mixtures produced through the ozonolysis of a-pinene, limonene, and ocimene. The apparent enthalpies (ΔH*, kJ mol -1 ) and saturated vapor mass concentrations (C T *, µg∙m -3 ) of individual SOA components, determined as a function of temperature (T, K), facilitated an assessment of changes in VBS distributions and gas-particle partitioning with respect to T and atmospheric total organic mass loadings (tOM, µg∙m -3 ). Further, the VBS distributions reveal distinct differences in volatilities among monomers, dimers, and trimers, enabling their categorization into separate volatility bins. At the ambient temperature of T = 298 K, only monomers efficiently partition between gas and particle phases across a broad range of atmospherically relevant total organic mass loadings (tOM) values of 1–100 µg∙m -3 . Partitioning of dimers and trimers becomes notable only at T > 360 K and T > 420 K, respectively. The viscosity of SOA mixtures is assessed using a bottom-up calculation approach, incorporating the input of elemental formulas, ΔH*, C T *, and particle-phase mass fractions of the SOA components. Through this approach, we are able to accurately estimate the variations in SOA viscosity that result from the evaporation of its components. These variations are, in turn, influenced by atmospherically relevant changes in tOM and T. Comparison of the calculated SOA viscosity and diffusivity values with literature reported experimental results shows close agreement, thereby validating the employed calculation approach. These findings underscore the significant potential for TPD-DART-HRMS measurements in enabling the untargeted analysis of organic molecules within OA mixtures. This approach facilitates quantitative assessment of their gas-particle partitioning and allows for the estimation of their viscosity and condensed-phase diffusion, thereby contributing valuable insights to atmospheric models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Frequency-Domain Spectroscopic Study of the Photosystem I Supercomplexes, Isolated IsiA Monomers, and the Intact IsiA Ring

The PSI 3 -IsiA 18 supercomplex is one of the largest and most complicated assemblies in photosynthesis. The IsiA ring, composed of 18 IsiA monomers (IsiA 18 ) surrounding the PSI trimer (PSI 3 ), forms under iron-deficient condition in cyanobacteria and acts as a peripheral antenna. Based on the supercomplex structure recently determined via cryo-EM imaging, we model various optical spectra of the IsiA monomers and IsiA 18 ring. Comparison of the absorption and emission spectra of the isolated IsiA monomers and the full ring reveals that about 2.7 chlorophylls (Chls) are lost in the isolated IsiA monomers. The best fits for isolated monomers spectra are obtained assuming the absence of Chl 508, Chl 517 and 70% loss of Chl 511. The best model describing all three hexamers and the entire ring suggests that the lowest energy pigments are Chls 511, 514 and 517. Based on the modeling results presented in this work we conclude that there are most likely three entry points for EET from the IsiA6 hexamer to the PSI core monomer, with two of these entry points likely being located next to each other (i.e. nine entry points from IsiA 18 to the PSI 3 trimer). Lastly, we show that excitation energy transfer inside individual monomers is fast (< 2 ps at T = 5 K) and at least 20 times faster than inter-monomer energy transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Entropic Control of HD Exchange Rates over Dilute Pd-in-Au Alloy Nanoparticle Catalysts

Dilute Pd-in-Au alloy catalysts are promising materials for selective hydrogenation catalysis. Extensive surface science studies have contributed mechanistic insight on the energetic aspect of hydrogen dissociation, migration and recombination on dilute alloy systems. Yet, translating these fundamental concepts to the kinetics and free energy of hydrogen dissociation on nanoparticle catalysts operating at ambient pressures and temperatures remains challenging. Here, the effect of the Pd concentration and Pd ensemble size on the catalytic activity, apparent activation energy and rate limiting process is addressed by combining experiment and theory. Experiments in a flow reactor show that a compositional change from 4 to 8 atm% Pd of the Pd-in-Au alloy catalyst leads to strong increase in activity, even exceeding the activity per Pd atom of monometallic Pd under the same conditions, albeit with an increase in apparent activation energy. First-principles calculations show that the rate and apparent activation enthalpy for HD exchange increase when increasing the Pd ensemble size from single Pd atoms to Pd trimers in a Au surface, suggesting that the ensemble size distribution shifts from mainly single Pd atoms on the 4 atm% Pd alloy to larger Pd ensembles of at least three atoms for the 8 atm% Pd/Au catalyst. The DFT studies also indicated that the rate-controlling process is different: H 2 (D 2 ) dissociation determines the rate for single atoms whereas recombination of adsorbed H and D determines the rate on Pd trimers. Both experiment and theory suggest that the increased reaction rate with increasing Pd content and ensemble size stems from an entropic driving force. Lastly, our results support hydrogen migration between Pd sites via Au and indicate that the dilute alloy design prevents the formation of subsurface hydrogen, which is crucial in achieving high selectivity in hydrogenation catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo , the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo . Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceu m model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗