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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 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Switching it up: New mechanisms revealed in wurtzite-type ferroelectrics

Wurtzite-type ferroelectrics have drawn increasing attention due to the promise of better performance and integration than traditional oxide ferroelectrics with semiconductors such as Si, SiC, and III-V compounds. However, wurtzite-type ferroelectrics generally require enormous electric fields, approaching breakdown, to reverse their polarization. The underlying switching mechanism(s), especially for multinary compounds and alloys, remains elusive. Here, we examine the switching behaviors in Al 1-x Sc x N alloys and wurtzite-type multinary candidate compounds we recently computationally identified. We find that switching in these tetrahedrally coordinated materials proceeds via a variety of nonpolar intermediate structures and that switching barriers are dominated by the more-electronegative cations. For Al 1-x Sc x N alloys, we find that the switching pathway changes from a collective mechanism to a lower-barrier mechanism enabled by inversion of individual tetrahedra with increased Sc composition. Our findings provide insights for future engineering and realization of wurtzite-type materials and open a door to understanding domain motion.

36 MATERIALS SCIENCE↗
DOE OSTI2025

High-voltage water-scarce hydrogel electrolytes enable mechanically safe stretchable Li-ion batteries

Soft Li-ion batteries, based on conventional organic electrolytes, face performance degradation challenges due to moisture penetration and safety concerns due to possible leakage of toxic fluorine compounds and flammable solvents under mechanical damage. We design a water-scarce hydrogel electrolyte with fluorine-free lithium salt to achieve wide electrochemical stability window (up to 3.11 volts) in ambient air without hermetic packaging while balancing high stretchability (1348%), ion conductivity (41 millisiemens per centimeter), and self-healing capabilities for mechanically and chemically safe stretchable Li-ion batteries. Molecular synergy between hydrophilicity and lithiophilicity of zwitterionic polymer backbone is revealed by molecular dynamics simulations. The battery exhibits capacity retention under harsh mechanical stresses—enduring stretching, twisting, folding, and multiple through-punctures by a needle—while self-healing from repeated through cuts by a razor blade. Stable ambient operation for 1 month over 500 charge-discharge cycles (average coulomb efficiency, 95%) is achieved. A prototype self-healing electronic system with embedded soft batteries demonstrates practical application as a durable embodied energy source.

Science & Technology - Other Topics↗
DOE OSTI2021

Parallel molecular mechanisms for enzyme temperature adaptation

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. Furthermore, we identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

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

Mechanism and dynamics of fatty acid photodecarboxylase

Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Solid-state batteries: The critical role of mechanics

Solid-state batteries with lithium metal anodes have the potential for higher energy density, longer lifetime, wider operating temperature, and increased safety. Although the bulk of the research has focused on improving transport kinetics and electrochemical stability of the materials and interfaces, there are also critical challenges that require investigation of the mechanics of materials. In batteries with solid-solid interfaces, mechanical contacts, and the development of stresses during operation of the solid-state batteries, become as critical as the electrochemical stability to keep steady charge transfer at these interfaces. In conclusion, this review will focus on stress and strain that result from normal and extended battery cycling and the associated mechanisms for stress relief, some of which lead to failure of these batteries.

25 ENERGY STORAGE↗
DOE OSTI2024

Super-relaxed myosins contribute to respiratory muscle hibernation in mechanically ventilated patients

Patients receiving mechanical ventilation in the intensive care unit (ICU) frequently develop contractile weakness of the diaphragm. Consequently, they may experience difficulty weaning from mechanical ventilation, which increases mortality and poses a high economic burden. Because of a lack of knowledge regarding the molecular changes in the diaphragm, no treatment is currently available to improve diaphragm contractility. We compared diaphragm biopsies from ventilated ICU patients (N= 54) to those of non-ICU patients undergoing thoracic surgery (N= 27). By integrating data from myofiber force measurements, x-ray diffraction experiments, and biochemical assays with clinical data, we found that in myofibers isolated from the diaphragm of ventilated ICU patients, myosin is trapped in an energy-sparing, super-relaxed state, which impairs the binding of myosin to actin during diaphragm contraction. Studies on quadriceps biopsies of ICU patients and on the diaphragm of previously healthy mechanically ventilated rats suggested that the super-relaxed myosins are specific to the diaphragm and not a result of critical illness. Exposing slow- and fast-twitch myofibers isolated from the diaphragm biopsies to small-molecule compounds activating troponin restored contractile force in vitro. These findings support the continued development of drugs that target sarcomere proteins to increase the calcium sensitivity of myofibers for the treatment of ICU-acquired diaphragm weakness.

Cell Biology↗
DOE OSTI2025

Fluid Mechanics Challenges in Direct-Ink-Writing Additive Manufacturing

Direct-ink writing (DIW) has rapidly become a versatile 3D fabrication method due to its ability to deposit a wide range of complex fluids into customizable 3D geometries. This review highlights key fundamental fluid mechanics and soft matter challenges across the different stages of the DIW printing process. The rheology of fluids and suspensions governs the flow behavior through narrow nozzles, posing questions about extrudability, confined flow dynamics, and clogging mechanisms. Downstream, the formation and deposition of extruded filaments involve extensional flows and potential instabilities, while postdeposition dynamics introduces complexities related to yield stress and structural stability. These stages are inherently interdependent, as optimizing material composition without considering filament stability risks compromising the final structure. As DIW applications expand through advanced ink formulations, developing fundamental fluid mechanics frameworks is essential to replace trial-and-error approaches with predictive design methodologies to enable more precise control and improved reliability of the printing process.

3D printing↗
DOE OSTI2020

Mechanism of Electrochemical Oxidation of Nitroxide Radicals in Ethaline Deep Eutectic Solvent

Deep eutectic solvents (DESs) are emerging as promising electrolytes for electrochemical energy storage applications. Electroactive nitroxide-radical-containing organics can be dissolved in DESs to facilitate redox reactions; however, mechanistic know-how of their charge transfer kinetics at the electrode surface is rather limited. Here, we investigate the mechanism underlying the electrochemical oxidation of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and 4-hydroxy-2,2,6,6-tetramethyl-piperidine-1-oxyl (4-hydroxy-TEMPO). Using polarization measurements on a platinum rotating disk electrode and micro-electrode, we show that the anodic charge transfer coefficient (a) for one-electron transfer oxidations of TEMPO and4-hydroxy-TEMPO approaches 0.9 in DES as well as in aqueous electrolytes, i.e., a significant deviation fromα≈0.5 expected for symmetric redox behavior. To explain this observation, a two-step oxidation mechanism is proposed wherein the nitroxide-containing species undergo fast charge transfer at an electrode surface followed by slow rate-limiting desorption of the adsorbed oxidized species. Numerical simulations are reported to characterize how the proposed two-step mechanism manifests intransient cyclic voltammetry behavior of the 4-hydroxy-TEMPO oxidation reaction, and good agreement with experiments is noted.

25 ENERGY STORAGE↗
DOE OSTI2023

Exploring the Storage Mechanism of Alkali Ions in Non-Graphitic Hard Carbon Anodes

This study aims to develop high-capacity hard carbon anode materials for alkali-ion batteries by controlling the microstructures of non-graphitic hard carbon through an annealing protocol and investigating the effects on the alkali-ion storage mechanisms using physical, chemical, and electrochemical analytical techniques. The hard carbon materials were synthesized at temperatures ranging from 900 °C to 1600 °C. Those synthesized at 1100 °C with high surface area and abundant defects exhibited the highest reversible capacity in Li- and K-ion systems, with the storage dominated by surface-adsorption mechanisms. In contrast, the hard carbon compounds prepared at 1400 °C with numerous curve-featured pores delivered the highest reversible capacity in the Na-ion system, indicating that these pores are the preferred Na-ion storage sites, particularly in low-voltage plateau regions. This study provides a comprehensive understanding of the relationship between microstructures and alkali-ion storage mechanisms in non-graphitic hard carbon and highlights the importance of tailoring the microstructures of hard carbon to achieve high specific capacity for the desired alkali-ion species.

25 ENERGY STORAGE↗
DOE OSTI2025

On Rate-Limiting Mechanisms in NMC Cathodes: The Interplay of Low and High Current Constraints

In this study, we investigate the rate performance limits in LiNi 0.6 Mn 0.2 Co 0.2 O 2 cathodes for lithium-ion batteries, focusing on how cathode thickness, porosity, and threshold voltage impact discharge capacity. By conducting galvanostatic discharge experiments across a wide range of current densities using cathodes of varying thicknesses and porosities, we identify two distinct rate-limiting mechanisms: ionic liquid-diffusion and Ohmic/charge-transfer limitations. Our findings show that thick, dense cathodes are primarily limited by lithium diffusion in the electrolyte, while thinner and more porous cathodes are dominated by Ohmic/charge-transfer limitations, particularly at higher lower cutoff voltages. Crucially, these results allow us to identify the rate-limiting mechanisms in different cathode configurations, offering clear insights into how cathode design can be optimized for improved performance. Understanding these mechanisms is essential for designing next-generation batteries with enhanced rate performance, which is critical for applications such as electric vehicles and renewable energy storage systems.

Brischetto, Martin (ORCID:0000000339865813)↗
DOE OSTI2021

Mechanical Response of Castlegate Sandstone under Hydrostatic Cyclic Loading

The stress history of rocks in the subsurface affects their mechanical and petrophysical properties. Rocks can often experience repeated cycles of loading and unloading due to fluid pressure fluctuations, which will lead to different mechanical behavior from static conditions. This is of importance for several geophysical and industrial applications, for example, wastewater injection and reservoir storage wells, which generate repeated stress perturbations. Laboratory experiments were conducted with Castlegate sandstone to observe the effects of different cyclic pressure loading conditions on a common reservoir analogue. Each sample was hydrostatically loaded in a triaxial cell to a low effective confining pressure, and either pore pressure or confining pressure was cycled at different rates over the course of a few weeks. Fluid permeability was measured during initial loading and periodically between stress cycles. Samples that undergo cyclic loading experience significantly more inelastic (nonrecoverable) strain compared to samples tested without cyclic hydrostatic loading. Permeability decreases rapidly for all tests during the first few days of testing, but the decrease and variability of permeability after this depend upon the loading conditions of each test. Cycling conditions do affect the mechanical behavior; the elastic moduli decrease with the increasing loading rate and stress cycling. The degree of volumetric strain induced by stress cycles is the major control on permeability change in the sandstones, with less compaction leading to more variation from measurement to measurement. The data indicate that cyclic loading degrades permeability and porosity more than static conditions over a similar period, but the petrophysical properties are dictated more by the hydrostatic loading rate rather than the total length of time stress cycling is imposed.

58 GEOSCIENCES↗
DOE OSTI2022

Combined Effect of the Wegener–Bergeron–Findeisen Mechanism and Large Eddies on Microphysics of Mixed-Phase Stratiform Clouds

Abstract The process of glaciation in mixed-phase stratiform clouds was investigated by a novel Lagrangian–Eulerian model (LEM) in which thousands of adjoining Lagrangian parcels moved within a turbulent-like velocity field with statistical parameters typical of the Arctic boundary layer. We used detailed bin microphysics to describe the condensation/evaporation processes in each parcel, in which droplets, aerosols, and ice particles were described using size distributions of 500 mass bins. The model also calculated aerosol mass inside droplets and ice particles. Gravitational sedimentation of droplets and ice particles was also accounted for. Assuming that droplet freezing is the primary source of ice particles, the Arctic clouds observed in Indirect and Semi-Direct Aerosol Campaign (ISDAC) were successfully simulated. The model showed that at a low ice particle concentration typical of ISDAC, large vortices (eddies) led to a quasi-stationary regime, in which mixed-phase St existed for a long time. The large eddies controlled the water partitioning in the mixed-phase clouds. Droplets formed and grew in updrafts, typically reaching the cloud top, and evaporated in downdrafts. Ice particles grew in updrafts and downdrafts. The Wegener–Bergeron–Findeisen (WBF) mechanism was efficient in downdrafts and some parts of updrafts, depending on ice concentration and vertical velocity. At low ice concentrations, the effect of ice on the phase partitioning was negligible. In this regime, liquid droplets were found near the cloud top, whereas ice particles precipitated through the cloud base. When ice concentration exceeded about 10 L −1 , the WBF mechanism led to glaciation of almost the entire cloud, with the exception of narrow cloud regions associated with strong updrafts. At ice particle concentrations of a few tens per liter, the oscillatory regime took place due to the ice–liquid interaction. The microphysical structure of mixed-phase St forms as a combined effect of cloud dynamics (large eddies) and the WBF mechanism.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Subtropical Jet Regulates Arabian Winter Precipitation: A Viable Mechanism

The present study explores the mechanism governing wintertime (November–April) precipitation over the Arabian Peninsula (AP) using a 17-yr-long (2002–18) high-resolution WRF simulation. The composite analysis of strong precipitation events suggests that the equatorward extension of the upper-level jet together with the embedded upper-level trough creates a positive (cyclonic) midlevel vorticity and subsequently generates an anomalous lower-level convergence through Ekman pumping. This leads to the development of an anomalous surface low, which is further enhanced in the presence of the existing Red Sea trough over the AP. This surface low weakens the persistent anticyclone over the AP, shifting it further eastward to the Arabian Sea. The eastward shift in the lower-level anticyclone contributes to the transport of warm, moist air from the Arabian Sea and the Red Sea toward the AP. This warm, moist air converges with the cold and dry air advected by the midlatitude jet and creates a moisture convergence zone, leading to the initiation of convection. We test the proposed mechanism through numerical experiments with modified upper-level wind and demonstrate that a strong, southward intrusion of the jet can indeed lead to precipitation over the AP. The above mechanism also explains the interannual variability of precipitation over the AP. During wet years, we notice approximately 3 m s -1 stronger jet core magnitude and about a 2° equatorward shift of the jet compared to dry years. While the equatorward extension of the jet explains about 21% of the interannual variability, the jet magnitude explains around 7% of the variability during wet years.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Mechanical and Thermal Forcing for Upslope Flows and Cumulus Convection over the Sierras de Córdoba

Abstract The upslope flow processes affecting the vertical extent of orographic cumulus convection are examined using observations from the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign. Specifically, clear air returns from the U.S. Department of Energy (DOE) second-generation C-band scanning Atmospheric Radiation Measurement (ARM) precipitation radar (CSAPR2) are used to characterize the structure and variability of the ridge-normal (i.e., up/downslope) flow components, which transport mass to the crest of Argentina’s Sierras de Córdoba and contribute to convective initiation. Data are compiled for the entire CACTI period (October–April), including days with clear skies, shallow cumuli, cumulus congestus, and deep convection. To examine shared variability among >70 000 radar scans, we use (i) a principal component analysis (PCA) to isolate modes of variability in the upslope flow and (ii) composite analysis based on convective outcomes, determined from GOES-16 satellite observations. These data are contextualized with observed surface sensible heat fluxes, thermodynamic profiles, and synoptic-scale analysis. Results indicate distinct thermally and mechanically forced upslope flow modes, modulated by diurnal heating and synoptic-scale variations, respectively. In some instances, there is a superposition of thermal and mechanical forcing, yielding either deeper or shallower upslope flow. The composite analyses based on satellite data show that successively deeper convective outcomes are associated with successively deeper upslope flow layers that more readily transport mass to the ridge crest in conjunction with lower lifting condensation levels, facilitating convective initiation. These results help to isolate the forcing mechanisms for orographic convection and thus provide a foundation for parameterizing orographic convective processes in coarse resolution models.

Meteorology & Atmospheric Sciences↗
DOE OSTI2020

Predictive biomarkers and mechanisms underlying resistance to PD1/PD-L1 blockade cancer immunotherapy

Immune checkpoint blockade targeting PD-1/PD-L1 has promising therapeutic efficacy in a variety of tumors, but resistance during treatment is a major issue. In this review, we describe the utility of PD-L1 expression levels, mutation burden, immune cell infiltration, and immune cell function for predicting the efficacy of PD-1/PD-L1 blockade therapy. Furthermore, we explore the mechanisms underlying immunotherapy resistance caused by PD-L1 expression on tumor cells, T cell dysfunction, and T cell exhaustion. Based on these mechanisms, we propose combination therapeutic strategies. We emphasize the importance of patient-specific treatment plans to reduce the economic burden and prolong the life of patients. The predictive indicators, resistance mechanisms, and combination therapies described in this review provide a basis for improved precision medicine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Mechanisms influencing and prediction of tool influence function spots during hemispherical sub-aperture tool polishing on fused silica

Sub-aperture tool polishing of precision optics requires a detailed understanding of the local material removal [tool influence function (TIF)] at the contact spot between the workpiece and tool to achieve high removal determinism and hence precision of the optic relative to the desired/design surface figure. In this study, the mechanisms influencing and the quantitative prediction of the removal rate and shape of TIF spots during polishing of fused silica glass with cerium oxide slurry using a rotating hemispherical pad-foam tool for a wide variety of process conditions (including tool properties, kinematics, and applied displacements) are investigated. The TIF volumetric removal rate can be estimated utilizing the average relative velocity and contact area using a simple analytical model. In addition, stability of the volumetric removal rate for fixed process conditions is shown to be greatly dependent on the pad preparation and amount of tool use (affecting both pad topography and slurry buildup), whose general behavior shows an increase in removal rate followed by stabilization with polishing time. The determination of the TIF removal shape is more complex. An extended version of the Preston removal model is developed to explain a comprehensive set of measured TIF removal shapes to within ∼ <#comment/> 22 % <#comment/> . This model incorporates a number of phenomena impacting the TIF removal shape including: (a) temporal and spatial dependent relative velocity between the workpiece and tool; (b) an elastic mechanics based, as well as hydrodynamic, pressure distribution; (c) a spatially dependent friction coefficient possibly caused by both reduced slurry replenishment in low velocity regions and pad slurry islands (100 µm scale) and porosity (millimeter scale); and (d) a shear-based removal mechanism on the periphery of the contact spot.

Suratwala, T. (ORCID:0000000190861039)↗
DOE OSTI2026

Subsurface mechanical damage of fused silica glass during grinding by various sub-aperture tools with and without ultrasonics

The subsurface mechanical damage (SSD) depth after grinding fused silica glass with a comprehensive set of sub-aperture fixed abrasive grinding tools [cup, wheel, belt, pad, and rotary face mill (with and without ultrasonics)] and process parameters has been statistically measured using the taper wedge technique and evaluated. Consistent with a previously reported grinding model [J. Non-Cryst. Solids 352, 5601–5617 (2006) Crossref , Materials Science and Technology of Optical Fabrication (Wiley & Sons, 2018)], based on the sliding indentation fracture by sliding particles or asperities where the normal load per particle determines the depth of the fracture (and ultimately the overall SSD depth), the dominant factor controlling SSD depth was found to be the abrasive size regardless of the tool type and process conditions. Compared to full aperture grinding methods, the overall SSD depth was higher using the sub-aperture tools, likely due to the higher effective pressure and higher load per particle distribution. Here, in addition to abrasive size, a significant reduction in SSD depth was achieved by: (1) reducing the load distribution on the abrasive particles via increase in contact area and/or decrease in mechanical loading; (2) using a more compliant host tool medium; and (3) in what we believe is a more novel way, using ultrasonics. Combining low abrasive size, larger contact area, and a compliant host, the 6 µm diamond in a resin matrix (Trizact) on a foam pad led to very low SSD depth (~ 4.6 µm), relatively fast grinding rate (186 mm 3 /h), and little or no figure degradation. This grinding tool/process is an attractive choice for final grind, resulting in significantly reduced polish out (i.e., “grey out”) times. With the rotary face mill tool, the use of ultrasonics consistently led to a SSD depth reduction (ranging from 17%–34%). A new fracture mechanics-based model, to the best of our knowledge, where the relevant normal load is parallel to the feed direction, has been developed to explain how ultrasonics leads to lower SSD depth. The key factors, supported by finite element stress analysis and load measurements, are (1) the initiation of fractures at higher z heights during the tool’s ultrasonic vertical oscillations, thus propagating less deep into workpiece; (2) reduction in load (and therefore reduction in fracture propagation distance) due to smaller tool-workpiece feed direction contact area (again caused by higher heights relative to depth of cut); (3) upward movement of the tool during oscillation leads to fracturing toward the surface instead into the depth; and finally (4) at tool’s lowest point of oscillation cycle, there may not be enough time for the fracture to propagate to its full length.

Optics and optical instruments↗
DOE OSTI2021

Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.

59 BASIC BIOLOGICAL SCIENCES↗