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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Reduction of Exciton Diffusion Length with Genetically Tuned Non-Photochemical Quenching in Plant Thylakoid Membranes

Non-photochemical quenching (NPQ) protects plants from excess light by dissipating excitation energy as heat. Limited exciton migration is a key feature of NPQ, reducing the energy flux to reaction centers; however, quantitative evidence for this mechanism in native thylakoid membranes has been lacking. Here, we investigate the correlation between NPQ activity and exciton diffusion length (LD) using Nicotiana benthamiana mutants with distinct NPQ capacities. NPQ under both light- and dark-acclimated conditions was quantified for each genotype via fluorescence lifetime snapshots, and exciton mobility was probed using transient absorption spectroscopy with exciton-exciton annihilation analysis. By comparing the relationship between chlorophyll fluorescence lifetime and LD across mutants, we observed that NPQ activation quantitatively limits the spatial range of exciton migration, thereby reducing the access to reaction centers. Our findings provide direct experimental evidence that NPQ modulates the dynamics of energy transport, advancing our understanding of photoprotective regulation in photosynthetic systems.

Diffusion↗
DOE OSTI2022

Electrostatic Interactions Control the Nanostructure of Conjugated Polyelectrolyte–Polymeric Ionic Liquid Blends

Polyelectrolyte complexation offers unique opportunities to compatibilize polymers with very different backbone chemistries and to control the morphology of the resulting blend via electrostatic manipulation. In this study, we demonstrate the ability to formulate homogeneous complexes of a conjugated polyelectrolyte with a polymeric ionic liquid, utilizing the electrostatic attraction among their oppositely charged side chains. Variation of electrostatic parameters, such as counterion concentration or polymer charge fraction, tunes the morphology of these polymer complexes from homogeneously disordered blend to weakly structured microemulsion where the local ordering arises from backbone-immiscibility-induced microphase segregation. Our experimental observations are in qualitative agreement with both field-theoretic simulation and random-phase approximation calculations. Simulated morphology snapshots suggest and experimental evidence also indicates that the microphase-segregated complex likely takes on a cocontinuous microemulsion structure. Our findings show that ionic interactions are an effective pathway to compatibilize polymers at macroscopic length scales while achieving controlled nanostructures in these ionic blends. Such systems have great potential for engineering the nanostructure of polymers to tailor applications such as nanofiltration, catalysis, and energy storage, where local ordering can enhance the physical properties of an otherwise macroscopically homogeneous structure.

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

Metabolomics Analysis of Bacterial Pathogen Burkholderia thailandensis and Mammalian Host Cells in Co-culture

The Tier 1 HHS/USDA Select Agent Burkholderia pseudomallei is a bacterial pathogen that is highly virulent when introduced into the respiratory tract and intrinsically resistant to many antibiotics. Transcriptomic- and proteomic-based methodologies have been used to investigate mechanisms of virulence employed by B. pseudomallei and Burkholderia thailandensis, a convenient surrogate; however, analysis of the pathogen and host metabolomes during infection is lacking. Changes in the metabolites produced can be a result of altered gene expression and/or post-transcriptional processes. Thus, metabolomics complements transcriptomics and proteomics by providing a chemical readout of a biological phenotype, which serves as a snapshot of an organism’s physiological state. However, the poor signal from bacterial metabolites in the context of infection poses a challenge in their detection and robust annotation. In this work, we coupled mammalian cell culture-based metabolomics with feature-based molecular networking of mono- and co-cultures to annotate the pathogen’s secondary metabolome during infection of mammalian cells. These methods enabled us to identify several key secondary metabolites produced by B. thailandensis during infection of airway epithelial and macrophage cell lines. Additionally, the use of in silico approaches provided insights into shifts in host biochemical pathways relevant to defense against infection. Using chemical class enrichment analysis, for example, we identified changes in a number of host-derived compounds including immune lipids such as prostaglandins, which were detected exclusively upon pathogen challenge. Taken together, our findings indicate that co-culture of B. thailandensis with mammalian cells alters the metabolome of both pathogen and host and provides a new dimension of information for in-depth analysis of the host–pathogen interactions underlying Burkholderia infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

An In Situ , Automated High-Explosives Aging Method Utilizing Two-Dimensional Gas Chromatography–Mass Spectrometry

Understanding chemical changes that occur in high explosives as they age is of great importance to the safe employment and storage of these compounds. Traditional methods of aging high explosives even under accelerated aging conditions are time intensive with durations on the order of months to years. The nature of traditional aging analyses reduces each sample to a snapshot data point often separated widely in time, requiring many assumptions as to how the degradation products develop. Further complicating matters, several analytical techniques are typically employed for each sample analysis in order to ascertain an entire picture of the decomposition pathways. To address these shortcomings with existing methods, a new method of accelerated aging of high explosives utilizing comprehensive two-dimensional gas chromatography coupled to high-resolution mass spectrometry (GC × GC-HRMS) was developed using 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) as a model compound for method development. This in situ automated method reduces the time scale of aging to a matter of hours using the inlet of the GC × GC as the aging vessel. GC × GC in combination with HRMS allowed for the collection of both evolved gases and other decomposition products produced during the entire aging process in real time with HRMS providing far greater certainty in identification of explosives aging products. Additionally, this method allowed for a higher throughput of samples with greatly simplified sample preparation. Chemometric analysis of the GC × GC-HRMS data set via the alteration analysis (ALA) enabled discovery of statistically significant chemical changes providing insight into the variation of decomposition pathways with varying aging temperatures.

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

High Resolution Infrared Spectroscopy of Highly Reactive Chemical Intermediates: Berkeley Inspiration and a C.B. Moore Retrospective

One of the long-standing paradoxes in chemistry is that the molecular species of greatest interest are often highly reactive chemical intermediates and thus present only at vanishingly small concentrations under typical steady state conditions. Here, this has proven both a key frustration and powerful motivation for physical chemists in probing such species, particularly for high resolution laser spectroscopic methods in the infrared. Over the past 4-5 decades, this fundamental sensitivity challenge has stimulated the development of many novel techniques for efficient generation, cooling, and infrared probing of such transient chemical intermediates, achieving increasingly sophisticated levels of spectroscopic detail, chemical insight, and a testbed for comparison with first principles ab initio quantum calculations. Two of the pioneering contributors to this scientific arena have been George Pimentel and C. Bradley Moore, both responsible for nourishing DJN’s own enduring fascination with spectroscopic IR study of elusive chemical intermediates. This chapter is not intended to provide a comprehensive review of this large and enormously successful field, but it rather more simply attempts to capture a few selective “Moore-centric” snapshots of the Nesbitt group scientific evolution, specifically in i) advances by Pimentel for the original development of rapid scan flash kinetic spectroscopy based on spectrometers with rapidly rotating IR gratings, ii) the modernization/extension of these methods in the Moore group toward the first high resolution IR laser spectroscopy of singlet/triplet methylene 1,3 CH 2 diradical, and finally to iii) the development of slit supersonic discharge expansion methods at JILA for sub-Doppler infrared laser study of multiple radicals, jet cooled molecular ions, and highly reactive chemical intermediates.

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

Critical Role of Framework Flexibility and Disorder in Driving High Ionic Conductivity in LiNbOCl 4

Understanding Li-ion transport is key for the rational design of superionic solid electrolytes with exceptional ionic conductivities. LiNbOCl 4 is reported to be one of the most highly conducting materials in the recently realized new class of soft oxyhalide solid electrolytes, exhibiting an ionic conductivity of ~11 mS·cm -1 . Here, we apply X-ray/neutron diffraction and pair distribution function analysis - coupled with density functional theory/ab-initio molecular dynamics - to determine a structural model that provides a rationale for the high conductivity that we observe experimentally in this nanocrystalline solid. We show that it arises from unusually high framework flexibility at room temperature. This owes to isolated 1-D [NbOCl 4 ] - anionic chains which exhibit energetically favorable orientational disorder that is - in turn - correlated to multiple, disordered and equi-energetic Li + sites in the lattice. As the Li-ions sample the 3-D energy landscape with a fast predicted diffusion coefficient of 5.1 x 10 -7 cm 2 /s at room temperature (σ i calc = 17.4 mS·cm -1 ), the inorganic polymer chains can reorient or vice versa. The activation energy barrier for Li migration through the frustrated energy landscape is especially reduced by the elastic nature of the NbO 2 Cl 4 octahedra evident from very widely dispersed Cl-Nb-Cl bond angles in AIMD snapshots at 300 K. The phonon spectra are predominantly influenced by Cl vibrations in the low energy range, and there is strong overlap between the framework (Cl, Nb) and Li partial pDOS in the region between 1.2 - 4.0 THz. The framework flexibility is also reflected in a relatively low bulk modulus of 22 GPa. In conclusion, our findings pave the way for investigation of future “flex-ion” inorganic solids and open up a new direction for the design of high conductivity, soft solid electrolytes for all-solid-state batteries.

AIMD↗
DOE OSTI2025

Tests of the DFT Ladder for the Fulminic Acid Challenge

Properties of the historically pivotal fulminic acid (HCNO) molecule have been computed with a panoply of 473 density functionals of all varieties, providing a snapshot of the performance of contemporary density functional theory (DFT) for a challenging chemical system. Exhaustive tabulations and statistical analyses have been carried out for geometric parameters, vibrational frequencies, barriers to linearity, and the HCN–O dissociation energy. As the DFT ladder is climbed, confusion rather than consensus ensues regarding the details of the distinctive, extremely flat H–C–N bending potential of fulminic acid and whether the equilibrium structure is linear or bent. While high-ranking DFT functionals produce the smallest errors for the HCN + O( 3 P) → HCNO reaction energy, lower rungs emerge as the best performers for many of the bond distances and harmonic vibrational frequencies. This research shows that the current DFT zoo of approximations does not constitute a transparent ladder of increasingly accurate methods that consistently converges on definitive predictions for various properties of HCNO. Additional analyses are performed on the side effects of popular dispersion corrections on the covalently bonded properties and thermochemistry of HCNO.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Enhancing Streamflow Forecast and Extracting Insights Using Long-Short Term Memory Networks With Data Integration at Continental Scales

Recent observations with varied schedules and types (moving average, snapshot, or regularly spaced) can help to improve streamflow forecasts, but it is challenging to integrate them effectively. Based on a long short-term memory (LSTM) streamflow model, we tested multiple versions of a flexible procedure we call data integration (DI) to leverage recent discharge measurements to improve forecasts. DI accepts lagged inputs either directly or through a convolutional neural network unit. DI ubiquitously elevated streamflow forecast performance to unseen levels, reaching a record continental-scale median Nash-Sutcliffe Efficiency coefficient value of 0.86. Integrating moving-average discharge, discharge from the last few days, or even average discharge from the previous calendar month could all improve daily forecasts. Directly using lagged observations as inputs was comparable in performance to using the convolutional neural network unit. Importantly, we obtained valuable insights regarding hydrologic processes impacting LSTM and DI performance. Before applying DI, the base LSTM model worked well in mountainous or snow-dominated regions, but less well in regions with low discharge volumes (due to either low precipitation or high precipitation-energy synchronicity) and large interannual storage variability. DI was most beneficial in regions with high flow autocorrelation: it greatly reduced baseflow bias in groundwater-dominated western basins and also improved peak prediction for basins with dynamical surface water storage, such as the Prairie Potholes or Great Lakes regions. However, even DI cannot elevate performance in high-aridity basins with 1-day flash peaks. Despite this limitation, there is much promise for a deep-learning-based forecast paradigm due to its performance, automation, efficiency, and flexibility.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Analysis of Fault Zone Resonance Modes Recorded by a Dense Seismic Array Across the San Jacinto Fault Zone at Blackburn Saddle

We present observations and modeling of spatial eigen-functions of resonating waves within fault zone waveguide, using data recorded on a dense seismic array across the San Jacinto Fault Zone (SJFZ) in southern California. The array consists of 5-Hz geophones that cross the SJFZ with ~10-30 m spacing at the Blackburn Saddle near the Hemet Stepover. Wavefield snapshots after the S wave arrival are consistent for more than 50 near-fault events, suggesting that this pattern is controlled by the fault zone structure rather than source properties. Data from example event with high signal to noise ratio shows three main frequency peaks at ~1.3 Hz, ~2.0 Hz, and ~2.8 Hz in the amplitude spectra of resonance waves averaged over stations near the fault. The data are modeled with analytical expressions for eigen-functions of resonance waves in a low-velocity layer (fault zone) between two quarter-spaces. Using a grid search-based method, we investigate the possible width of the waveguide, location within the array, and shear wave velocities of the media that fit well the resonance signal at ~1.3 Hz. The results indicate a ~300 m wide damaged fault zone layer with ~65% S wave velocity reduction compared to the host rock. The SW edge of the low-velocity zone is near the mapped fault surface trace, indicating that the damage zone is asymmetrically located at the regionally faster NE crustal block. The imaging resolution of the fault zone structure can be improved by modeling fault zone resonance modes and trapped waves together.

58 GEOSCIENCES↗
DOE OSTI2021

A Lagrangian perspective on tropical anvil cloud lifecycle in present and future climate

The evolution of tropical anvil clouds from their origin in deep convective cores to their slow decay determines the climatic effects of clouds in tropical convective regions. Despite the relevance of anvil clouds for climate and responses of clouds to global warming, processes dominating their evolution are not well understood. Currently available observational data reveal instantaneous snapshots of anvil cloud properties, but cannot provide a process-based perspective on anvil evolution. We therefore conduct simulations with the high resolution version of the Exascale Earth System Model in which we track mesoscale convective systems over the Tropical Western Pacific and compute trajectories that follow air parcels detrained from peaks of convective activity. With this approach we gain new insight into the anvil cloud evolution both in present day and future climate. Comparison with geostationary satellite data shows that the model is able to simulate maritime mesoscale convective systems reasonably well. Trajectory results indicate that anvil cloud lifetime is about 15 hours with no significant change in a warmer climate. The anvil ice mixing ratio is larger in a warmer climate due to a larger source of ice by detrainment and larger depositional growth leading to a more negative net cloud radiative effect along detrained trajectories. However, the increases in sources are counteracted by increases in sinks of ice, particularly snow formation and sedimentation. Furthermore, we find that the mean anvil cloud feedback along trajectories is positive and consistent with results from more traditional cloud feedback calculation methods.

climate, weather, mesocale cellular convection↗
DOE OSTI2023

Message in a Bottle—An Update to the Golden Record: 1. Objectives and Key Content of the Message

In the first part of this series, we delve into the foundational aspects of “Message in a Bottle (MIAB)” (henceforth referred to as MIAB). This study builds upon the legacy of the Voyager Golden Records, launched aboard Voyager 1 and 2 in 1977, which aimed to communicate with intelligent species beyond our world. These records not only offer a snapshot of Earth and human civilization but also represent our desire to establish contact with advanced alien civilizations. Given the absence of mutually understood signs, symbols, and semiotic conventions, MIAB, like its predecessor, uses scientific methods to design an innovative means of communication that encapsulates the story of humanity. Our goal is to share our collective knowledge, emotions, innovations, and aspirations in a way that provides a universal, yet contextually relevant, understanding of human society, the evolution of life on Earth, and our hopes and concerns for the future. Through this time and space traveling capsule, we also strive to inspire and unify current and future generations to celebrate and safeguard our shared human experience.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Efficient Super-Resolution of Near-Surface Climate Modeling Using the Fourier Neural Operator

Downscaling methods are critical in efficiently generating high-resolution atmospheric data. However, state-of-the-art statistical or dynamical downscaling techniques either suffer from the high computational cost of running a physical model or require high-resolution data to develop a downscaling tool. Here, we demonstrate a recently proposed zero-shot super-resolution method, the Fourier neural operator (FNO), to efficiently perform downscaling without the need for high-resolution data. Because the FNO learns dynamics in Fourier space, FNO is a resolution-invariant emulator; it can be trained at a coarse resolution and produces emulation at any high resolution. We applied FNO to downscale a 4-km resolution Weather Research and Forecasting (WRF) Model simulation of near-surface heat-related variables over the Great Lakes region. The FNO is driven by the atmospheric forcings, and topographic features used in the WRF model at the same resolution. We incorporated a physics-constrained loss in FNO by using the Clausius-Clapeyron relation to better constrain the relations among the emulated states. Trained on merely 600 WRF snapshots at 4-km resolution, the FNO shows comparable performance with a widely used convolutional network, U-Net, achieving averaged modified Kling-Gupta Efficiency of 0.88 and 0.94 on the test dataset for temperature and pressure, respectively. We then employed the FNO to produce 1-km emulations to reproduce the fine climate features. Further, by taking the WRF simulation as ground truth, we show consistent performances at the two resolutions, suggesting the reliability of FNO in producing high-resolution dynamics. Our study demonstrates the potential of using FNO for zero-shot super-resolution in generating first-order estimation on atmospheric modeling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Remote Sensing of Multitemporal Functional Lake‐To‐Channel Connectivity and Implications for Water Movement Through the Mackenzie River Delta, Canada

The Mackenzie River Delta in Canada is a mediator of hydrological transport between the expansive Mackenzie River watershed and the Beaufort Sea. Within the delta, lakes frequently act as water and sediment traps, limiting or delaying the movement of material to the coastal ocean. The degree to which this filtering takes place depends on the ease with which sediment-laden water is transported from distributary channels into deltaic lakes, referred to as functional lake-to-channel connectivity, which varies both spatially and temporally. Tracking of connectivity has previously been limited to either small regions of the delta or has focused on a snapshot of connectivity at a single instance in time. Here we describe an algorithm that uses Landsat imagery to track summertime functional lake-to-channel connectivity of 10,362 lakes between 1984 and 2022 on an image-by-image basis. We calculate a total average connected lake area of 1400.7 km 2 during the 2 weeks after peak discharge, 763.6 km 2 higher than previous estimates, suggesting a larger influence of connected lakes on water movement through the delta than previously estimated. We also identify water level thresholds that lead to the initiation of high sediment river water movement into 5,989 lakes (908 lakes with uncertainty ≤±0.5 m), and identify an additional 2899 lakes whose connectivity does not vary at all. As the Arctic hydrological cycle responds to climate change, this work lays a foundation for tracking the movement of water, and the matter it carries, from the Mackenzie River watershed to the Beaufort Sea.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Transition Zones at the Changing Coastal Terrestrial‐Aquatic Interface

Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience spatial and temporal variability in biogeochemical processes, driven by marsh‐to‐upland gradients and hydrological fluctuations. These fluctuations make it difficult to understand and predict biogeochemical processes in these highly dynamic systems. We studied coastal soil biogeochemistry and its variability (a) at regional scales and (b) across transects from upland forest to marsh, in two contrasting regions—Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity‐related analytes were a key source of variability in soil biogeochemistry, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI—however, contrary to expectations, transition soils were not consistently intermediate between upland and marsh endmembers; the non‐monotonic trends of C, P, Fe along our transects suggest that these do not behave as expected and may be difficult to model and predict—thus these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients (e.g., Ca, K, CEC, and TS) may act as precursors to ecosystem shifts. Our comprehensive soil characterization represents a snapshot of a single timepoint of surface soils and provides essential data for mechanistic modeling of ecosystem dynamics across coastal transects.

Patel, Kaizad F. [Pacific Northwest National Labor↗
DOE OSTI2024

Observation of a single protein by ultrafast X-ray diffraction

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large genetic circuit in different states: RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.

59 BASIC BIOLOGICAL SCIENCES↗