Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “cooperative binding”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

SARS-CoV2 billion-compound docking

Abstract This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carried out using the AutoDock-GPU platform on the Summit supercomputer and Google Cloud. The docking procedure employed the Solis Wets search method to generate 20 independent ligand binding poses per compound. Each compound geometry was scored using the AutoDock free energy estimate, and rescored using RFScore v3 and DUD-E machine-learned rescoring models. Input protein structures are included, suitable for use by AutoDock-GPU and other docking programs. As the result of an exceptionally large docking campaign, this dataset represents a valuable resource for discovering trends across small molecule and protein binding sites, training AI models, and comparing to inhibitor compounds targeting SARS-CoV-2. The work also gives an example of how to organize and process data from ultra-large docking screens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Thick filament activation is different in fast- and slow-twitch skeletal muscle

The contractile properties of fast-twitch and slow-twitch skeletal muscles are primarily determined by the myosin isoform content and modulated by a variety of sarcomere proteins. X-ray diffraction studies of regulatory mechanisms in muscle contraction have focused predominately on fast- or mixed-fibre muscle with slow muscle being much less studied. Here, we used time-resolved X-ray diffraction to investigate the dynamic behaviour of the myofilament proteins in relatively pure slow-twitch-fibre rat soleus (SOL) and pure fast-twitch-fibre rat extensor digitorum longus (EDL) muscle during twitch and tetanic contractions at optimal length. During twitch contractions the diffraction signatures indicating a transition in the myosin heads from ordered OFF states, where heads are held close to the thick filament backbone, to disordered ON states, where heads are free to bind to thin filaments, were found in EDL and not in SOL muscle. During tetanic contraction, changes in the disposition of myosin heads as active tension develops is a quasi-stepwise process in EDL muscle whereas in SOL muscle this relationship appears to be linear. The observed reduced extensibility of the thick filaments in SOL muscle as compared to EDL muscles indicates a molecular basis for this behaviour. These data indicate that for the EDL, thick filament activation is a cooperative strain-induced mechano-sensing mechanism, whereas for the SOL, thick filament activation has a more graded response. Further, these different approaches to thick filament regulation in fast- and slow-twitch muscles may be adaptations for short-duration, strong contractions versus sustained, finely controlled contractions, respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 3f Raw Data

XPS of Si/GaN photocathode after 10 hour chronoamperometry (CA) testing. Surface chemical composition and valence band structure of GaN were obtained by X-ray photoemission spectroscopy (XPS) on a Kratos Axis Ultra DLD system at a takeoff angle of 0° relative to the surface normal. An Al Kα source (hν = 1486.6 eV) was used to excite the core level electrons. Pass energy of 20 eV was used for the narrow scan of core levels and valence band spectra, and step size of 0.05 eV and 0.025 eV, respectively. The Spectral fitting was conducted using CasaXPS analysis software. The binding energy scales of all core levels were corrected to the N 1s of Ga – N bond at 397.8 eV. XPS O1s core level spectra from 10 hours CA tested Si/GaN sample, and deconvolution shows O - Ga bond, O - N - Ga bond and OH - H2O bond.

photocathode↗
DOE OSTI2021

Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 3e Raw Data

XPS of Si/GaN photocathode after 4 hour chronoamperometry (CA) testing. Surface chemical composition and valence band structure of GaN were obtained by X-ray photoemission spectroscopy (XPS) on a Kratos Axis Ultra DLD system at a takeoff angle of 0° relative to the surface normal. An Al Kα source (hν = 1486.6 eV) was used to excite the core level electrons. Pass energy of 20 eV was used for the narrow scan of core levels and valence band spectra, and step size of 0.05 eV and 0.025 eV, respectively. The Spectral fitting was conducted using CasaXPS analysis software. The binding energy scales of all core levels were corrected to the N 1s of Ga – N bond at 397.8 eV. XPS O1s core level spectra from 4 hour CA tested Si/GaN sample, and deconvolution shows O - Ga bond, O - N - Ga bond and OH - H2O bond.

photocathode↗
DOE OSTI2023

Interaction of Anisole on Alumina-Supported Ni and Mo Oxide Hydrodeoxygenation Catalysts

The conversion of biomass to transportation fuels and value-added chemicals is a promising method to reduce reliance on fossil fuels. Mo-based catalysts have been shown to be highly active in the hydrodeoxygenation of biomass-derived phenolic compounds. The catalyst active phase, surface species, and the effect of adding additional metals is not comprehensively understood. Here we compare the temperature-dependent adsorption behavior of the model compound anisole 2 on an alumina-supported mixed nickel molybdenum oxide catalyst with two reference catalysts of molybdenum oxide and nickel oxide. Raman spectroscopy showed that the catalysts contain significant amounts of molybdates and molybdoaluminates, in addition to NiMoO 4 in the nickel molybdenum catalyst and MoO 3 in the molybdenum-only catalyst. Using transmission infrared spectroscopy under a controlled environment, we find that anisole chemisorbed largely through the oxygen in the methoxy group to form surface-bound phenoxy and methoxy species on all the catalysts. Ambient pressure X-ray photoelectrons spectroscopy measurements of the catalysts in anisole vapor showed reduced Mo atoms are the binding sites. The surface interaction and removal temperature of these species varied with the metal composition. The MoO x component dominated the adsorption behavior in both MoO x and NiMoO x catalysts. The formation of new aromatics, including methylated rings, depended on Ni composition. Upon adding hydrogen to induce the hydrodeoxygenation of anisole, undesirable polynuclear aromatic species were quickly formed on the Mo-based catalysts. In conclusion, these results suggest that the molybdenum oxide controls the adsorption and reactivity of the surface species, with a cooperative effect by Ni.

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

Oxophilicity Drives Oxygen Transfer at a Palladium–Silver Interface for Increased CO Oxidation Activity

A single-layer AgO x phase grown on Ag(111) efficiently transfers oxygen to Pd domains at room temperature, rendering the Pd-decorated surface highly reactive toward CO oxidation. Here, oxygen transfer from AgO x to Pd and the surface reactivity toward CO were investigated as a function of the Pd coverage using X-ray photoelectron spectroscopy, surface infrared spectroscopy of adsorbed CO, temperature-programmed reaction spectroscopy, and density functional theory (DFT) calculations. Our results show that all of the oxygen from the AgO x layer (~0.375 monolayer) migrates to the surface of Pd during formation of a nearly complete Pd bilayer at 300 K and that the oxygen coverages generated on Pd increase as the Pd cluster size decreases, reaching values that exceed the oxygen concentration in the AgO x layer by as much as a factor of 2. Experimental measurements and DFT calculations show that preferential binding of oxygen on the edges of the Pd clusters enhances the oxygen coverage on Pd clusters of decreasing size and produces a heterogeneous spatial distribution of oxygen. CO adsorbs in high coverages at 100 K by binding on both the terraces and O-rich edges of the Pd clusters. During subsequent heating, oxidation of the adsorbed CO consumes nearly all of the oxygen that transferred from AgO x to the Pd domains; in contrast, the pure AgO x layer exhibits limited reactivity toward CO adsorbed at 100 K. These results demonstrate that differences in oxophilicity drive facile oxygen transfer from Ag to the edges of Pd nanoclusters and thereby give rise to an efficient pathway for CO oxidation on bimetallic PdAg surfaces. The cooperation between the Pd and Ag domains results in near-interfacial chemistry that may be broadly important in catalysis by bimetallic alloys.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Catalytic Activation of Pyran Ethers in Self-Solvating Saccharides with Alkaline Earth Metals (Final Report)

Catalytic activation of cellulose ethers occurs via hydroxyl-stabilized cleavage of inter-monomer glycosidic bonds. Cooperativity between two hydroxyl groups lowers the ether cleavage transition state necessary to break apart long carbohydrate chains to initiate small molecule formation as fuel precursors. Metals existing with lignocellulosic materials including alkaline earth metals (Ca 2+ , Mg 2+ ) or alkali (Na + , K + ) also can catalyze ether scission cooperatively. By bonding with carbohydrate hydroxyl groups, a metal cation disrupt the hydrogen bonding network and free carbohydrate functional groups to react; a second metal cation stabilizes the carbohydrate ether transition state and enhances the rate of polymer scission. In this work, we expanded our initial understanding of metal-catalyzed glycoside ether scission. Within polysaccharides such as cellulose, two ether groups exist: one between monomers (glycosidic linkages) and one within a pyran ring. The hydroxyl-group hydrogen bonding network and bound metal ions form low energy binding states that interact with both ether oxygens simultaneously. Based on this interaction, our primary hypothesis was that the competition between stabilizing the two ether scission transition states determines the extent of the major pathways. Metals that disrupt the hydrogen bonding network of the C6 of sugars and stabilize the glycosidic ether promote transglycosylation to levoglucosan; in contrast, metals that stabilize the pyran ether oxygen promote sugar ring fragmentation to furans such as furfural. Varying characteristics of metal cation catalysts and configurations of bound polysaccharide chains dictate the relative rates of ether scission.

09 BIOMASS FUELS↗
DOE OSTI2025

Cooperative Effects Associated with High Electrolyte Concentrations in Driving the Conversion of CO2 to C2H4 on Copper

Compared to a conventional electrolyte concentration of 1 M HCOOK, the use of a highly concentrated 7.1 M HCOOK electrolyte increases the Faradaic efficiency (FE) ratio of C2H4/CO from 2.2 +- 0.3 to 18.3 +- 4.8 at -1.08 V vs. reversible hydrogen electrode (RHE) on a Cu gas-diffusion electrode. Based on electrochemical analysis and ab initio molecular dynamics (AIMD) simulation, the identity and concentration of the cation and anion play more important roles in controlling the CO2R reaction pathway than the bulk CO2 solubility and the bulk pH of electrolytes. In situ attenuated reflectance surface enhanced infrared absorption spectroscopy (ATR-SEIRAS) suggests that, unlike 1 M HCOOK, the *CO-bridge-binding mode on Cu is dominant in 7.1 M HCOOK electrolyte, which potentially results in less CO release and higher yield of C2H4. This study demonstrates that although we can tailor the electrolyte composition to shift product selectivity, the factors that control the product selectivity are numerous and cannot be distilled down into one correlated property-reactivity relationship.

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

Photoelectrochemically Self Improving Si/GaN Photocathode: Figure 3d Raw Data

XPS of Si/GaN photocathode after 1 hour chronoamperometry (CA) testing. Surface chemical composition and valence band structure of GaN were obtained by X-ray photoemission spectroscopy (XPS) on a Kratos Axis Ultra DLD system at a takeoff angle of 0° relative to the surface normal. An Al Kα source (hν = 1486.6 eV) was used to excite the core level electrons. Pass energy of 20 eV was used for the narrow scan of core levels and valence band spectra, and step size of 0.05 eV and 0.025 eV, respectively. The Spectral fitting was conducted using CasaXPS analysis software. The binding energy scales of all core levels were corrected to the N 1s of Ga – N bond at 397.8 eV. X-ray photoemission spectroscopy (XPS) O1s core level spectra from 1 hour chronoamperometry (CA) tested Si/GaN sample, and deconvolution shows O - Ga bond, O - N - Ga bond, and OH - H2O bond.

photocathode↗
DOE OSTI2026

Supramolecular Metal‐Organic Framework Electrocatalysts With Hydration‐Adaptive Gallery Expansion and Linker‐Mediated Distal Ni‐Co Cooperation Enable Framework‐Retentive Oxygen Evolution

Atomic‑level tailoring of electronic communication between spatially separated metal sites offers a route to accelerate multielectron electrocatalysis. We report Ni-TPTC, Co-TPTC, and heterobimetallic Ni-Co-TPTC supramolecular metal-organic frameworks (SMOFs) for the oxygen evolution reaction (OER) built from a terphenyl‑tetracarboxylate (TPTC) linker. Single-crystal X-ray diffraction of heterobimetallic Ni–Co–TPTC reveals trans-bis-aqua octahedral chains assembled into a π-stacked, hydrogen-bonded lattice and confirms retention of the parent architecture, while powder X-ray diffraction supports an isostructural Co analog. In 1.0 M KOH, Ni-Co-TPTC reaches 20 mA cm −2 at 350 mV and maintains operation at ∼60 mA cm −2 for 45 h with modest decay of the initial current. Time‑dependent ex situ diffraction shows dominant framework reflections with low‑angle shifts consistent with gallery dilation (d‑spacing ∼7.7 → ∼9.2 Å) during early operation, while Co K‑edge X‑ray absorption and microscopy reveal Co‑rich oxide/oxyhydroxide‑like domains at longer times that correlate with decay. X‑ray photoelectron spectroscopy, quantified by the Remote Binding‑Energy Differential, tracks composition‑dependent Ni-Co polarization, and DFT free‑energy analysis suggests that a model Ni-Co environment lowers the Co‑centered potential‑limiting step by ∼0.24 eV relative to the Co‑only framework. Furthermore, these results suggest that framework‑retentive expansion and distal Ni-Co coupling can drive OER activity before gradual deligation and oxide formation mark longer‑time degradation.

Supramolecular metal-organic frameworks (SMOFs)↗
NASA NTRS2016

Life Support and Environmental Monitoring International System Maturation Team Considerations

Human exploration of the solar system is an ambitious goal. Future human missions to Mars or other planets will require the cooperation of many nations to be feasible. Exploration goals and concepts have been gathered by the International Space Exploration Coordination Group (ISECG) at a very high level, representing the overall goals and strategies of each participating space agency. The Global Exploration Roadmap published by ISECG states that international partnerships are part of what drives the mission scenarios. It states "Collaborations will be established at all levels (missions, capabilities, technologies), with various levels of interdependency among the partners." To make missions with interdependency successful, technologists and system experts need to share information early, before agencies have made concrete plans and binding agreements. This paper provides an overview of possible ways of integrating NASA, ESA, and JAXA work into a conceptual roadmap of life support and environmental monitoring capabilities for future exploration missions. Agencies may have immediate plans as well as long term goals or new ideas that are not part of official policy. But relationships between plans and capabilities may influence the strategies for the best ways to achieve partner goals. Without commitments and an organized program like the International Space Station, requirements for future missions are unclear. Experience from ISS has shown that standards and an early understanding of requirements are an important part of international partnerships. Attempting to integrate systems that were not designed together can create many problems. Several areas have been identified that could be important to discuss and understand early: units of measure, cabin CO2 levels, and the definition and description of fluids like high purity oxygen, potable water and residual biocide, and crew urine and urine pretreat. Each of the partners is exploring different kinds of technologies. Different specific parameters may important to define or explore possible ranges depending on the system concepts. Early coordination between technology developers can create new possibilities for collaboration, and provide input to determine what combined options may provide the best overall system architecture.

Anderson, Molly↗
NASA NTRS2016

Life Support and Environmental Monitoring International System Maturation Team Considerations.

Human exploration of the solar system is an ambitious goal. Future human missions to Mars or other planets will require the cooperation of many nations to be feasible. Exploration goals and concepts have been gathered by the International Space Exploration Coordination Group (ISECG) at a very high level, representing the overall goals and strategies of each participating space agency. The Global Exploration Roadmap published by ISECG states that international partnerships are part of what drives the the mission scenarios. It states "Collaborations will be established at all levels (missions, capabilities, technologies), with various levels of interdependency among the partners." To make missions with interdependency successful, technologists and system experts need to share information early, before agencies have made concrete plans and binding agreements. This paper provides an overview of possible ways of integrating NASA, ESA, and JAXA work into a conceptual roadmap of life support and environmental monitoring capabilities for future exploration missions. Agencies may have immediate plans as well as long term goals or new ideas that are not part of official policy. But relationships between plans and capabilities may influence the strategies for the best ways to achieve partner goals. Without commitments and an organized program like the International Space Station, requirements for future missions are unclear. Experience from ISS has shown that standards and an early understanding of requirements are an important part of international partnerships. Attempting to integrate systems that were not designed together can create many problems. Several areas have been identified that could be important to discuss and understand early: units of measure, cabin CO2 levels, and the definition and description of fluids like high purity oxygen, potable water and residual biocide, and crew urine and urine pretreat. Each of the partners is exploring different kinds of technologies. Different specific parameters may important to define or explore possible ranges depending on the system concepts. Early coordination between technology developers can create new possibilities for collaboration, and provide input to determine what combined options may provide the best overall system architecture.

Anderson, Molly↗
DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)

The high morbidity and mortality associated with SARS-CoV-2 infection, the etiological agent of COVID-19, has had a major impact on global public health. Significant progress has been made in the development of an array of vaccines and biologics, however, the emergence of SARS-CoV-2 variants and breakthrough infections are an ongoing major concern. Furthermore, there is an existing paucity of small-molecule host and virus-directed therapeutics and prophylactics that can be used to counter the spread of SARS-CoV-2, and any emerging and re-emerging coronaviruses. Here, we describe herein our efforts to address this urgent need by focusing on the structure-guided design of potent broad-spectrum inhibitors of SARS-CoV-2 3C-like protease (3CL pro or Main protease), an enzyme essential for viral replication. The inhibitors exploit the directional effects associated with the presence of a gem-dimethyl group that allow the inhibitors to optimally interact with the S4 subsite of the enzyme. Several compounds were found to potently inhibit SARS-CoV-2 and MERS-CoV 3CL proteases in biochemical and cell-based assays. Specifically, the EC50 values of aldehyde 1c and its corresponding bisulfite adduct 1d against SARS-CoV-2 were found to be 12 and 10 nM, respectively, and their CC50 values were >50 μM. Furthermore, deuteration of these compounds yielded compounds 2c/2d with EC50 values 11 and 12 nM, respectively. Replacement of the aldehyde warhead with a nitrile (CN) or an α-ketoamide warhead or its corresponding bisulfite adduct yielded compounds 1g, 1e and 1f with EC50 values 60, 50 and 70 nM, respectively. High-resolution cocrystal structures have identified the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and, furthermore, have illuminated the mechanism of action of the inhibitors. Overall, the high Safety Index (SI) (SI=CC50/EC50) displayed by these compounds suggests that they are well-suited to conducting further preclinical studies.

3-Chymotrypsin-like protease (3CLpro)↗
DOE OSTI2022

Citrus FRIGIDA cooperates with its interaction partner dehydrin to regulate drought tolerance

SUMMARY Drought is a major environmental stress that severely affects plant growth and crop productivity. FRIGIDA ( FRI ) is a key regulator of flowering time and drought tolerance in model plants. However, little is known regarding its functions in woody plants, including citrus. Thus, we explored the functional role of the citrus FRI ortholog ( CiFRI ) under drought. Drought treatment induced CiFRI expression. CiFRI overexpression enhanced drought tolerance in transgenic Arabidopsis and citrus, while CiFRI suppression increased drought susceptibility in citrus. Moreover, transcriptomic profiling under drought conditions suggested that CiFRI overexpression altered the expression of numerous genes involved in the stress response, hormone biosynthesis, and signal transduction. Mechanistic studies revealed that citrus dehydrin likely protects CiFRI from stress‐induced degradation, thereby enhancing plant drought tolerance. In addition, a citrus brassinazole‐resistant (BZR) transcription factor family member ( CiBZR1 ) directly binds to the CiFRI promoter to activate its expression under drought conditions. CiBZR1 also enhanced drought tolerance in transgenic Arabidopsis and citrus. These findings further our understanding of the molecular mechanisms underlying the CiFRI ‐mediated drought stress response in citrus.

Xu, Yuan‐Yuan↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks

Abstract Protein catalysis and allostery require the atomic-level orchestration and motion of residues and ligand, solvent and protein effector molecules. However, the ability to design protein activity through precise protein–solvent cooperative interactions has not yet been demonstrated. Here we report the design of 14 membrane receptors that catalyse G protein nucleotide exchange through diverse engineered allosteric pathways mediated by cooperative networks of intraprotein, protein–ligand and –solvent molecule interactions. Consistent with predictions, the designed protein activities correlated well with the level of plasticity of the networks at flexible transmembrane helical interfaces. Several designs displayed considerably enhanced thermostability and activity compared with related natural receptors. The most stable and active variant crystallized in an unforeseen signalling-active conformation, in excellent agreement with the design models. The allosteric network topologies of the best designs bear limited similarity to those of natural receptors and reveal an allosteric interaction space larger than previously inferred from natural proteins. The approach should prove useful for engineering proteins with novel complex protein binding, catalytic and signalling activities.

Chemistry↗