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DOE OSTI2017

Structural determinants for protein unfolding and translocation by the Hsp104 protein disaggregase

Here, the ring-forming Hsp104 ATPase cooperates with Hsp70 and Hsp40 molecular chaperones to rescue stress-damaged proteins from both amorphous and amyloid-forming aggregates. The ability to do so relies upon pore loops present in the first ATP-binding domain (AAA-1; loop-1 and loop-2) and in the second ATP-binding domain (AAA-2; loop-3) of Hsp104, which face the protein translocating channel and couple ATP-driven changes in pore loop conformation to substrate translocation. A hallmark of loop-1 and loop-3 is an invariable and mutational sensitive aromatic amino acid (Tyr 257 and Tyr 662 ) involved in substrate binding. However, the role of conserved aliphatic residues (Lys 256 , Lys 258 , and Val 663 ) flanking the pore loop tyrosines, and the function of loop-2 in protein disaggregation has not been investigated. Here we present the crystal structure of an N-terminal fragment of Saccharomyces cerevisiae Hsp104 exhibiting molecular interactions involving both AAA-1 pore loops, which resemble contacts with bound substrate. Corroborated by biochemical experiments and functional studies in yeast, we show that aliphatic residues flanking Tyr 257 and Tyr 662 are equally important for substrate interaction, and abolish Hsp104 function when mutated to glycine. Unexpectedly, we find that loop-2 is sensitive to aspartate substitutions that impair Hsp104 function and abolish protein disaggregation when loop-2 is replaced by four aspartate residues. Our observations suggest that Hsp104 pore loops have non-overlapping functions in protein disaggregation and together coordinate substrate binding, unfolding, and translocation through the Hsp104 hexamer.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A Study of the Interaction, Morphology, and Structure in Trypsin-Epigallocatechin-3-Gallate Complexes

Understanding the interaction between proteins and polyphenols is of significance to food industries. The aim of this research was to investigate the mode of aggregation for trypsin-EGCG (Epigallocatechin-3-gallate) complexes. For this, the complex was characterized by fluorescence spectroscopy, circular dichroism (CD) spectra, small-angel X-ray scattering (SAXS), and atomic force microscope (AFM) techniques. The results showed that the fluorescence intensity of trypsin-EGCG complexes decreased with increasing the concentration of EGCG, indicating that the interaction between trypsin and EGCG resulted in changes in the microenvironment around fluorescent amino acid residues. The results of CD analysis showed conformational changes in trypsin after binding with EGCG. The results from SAXS analysis showed that the addition of EGCG results in the formation of aggregates of trypsin-EGCG complexes, and increasing the concentration of EGCG resulted in larger aggregates. AFM images showed that the trypsin-EGCG complex formed aggregates of irregular ellipsoidal shapes with the size of about 200 × 400 × 200 nm, with EGCG interconnecting the trypsin particles. Overall, according to these results, it was concluded that the large aggregates of trypsin-EGCG complexes are formed from several small aggregates that are interconnected. The results of this study shed some light on the interaction between digestive enzymes and EGCG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

Despite an abundance of online databases providing access to chemical data, there is increasing demand for highquality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency’s (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifer (ID) mapping and downloading of multiple data streams in several diferent formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identifcation of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA’s DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user trafc over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a fexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Structure-guided design of pure orthosteric inhibitors of αIIbβ3 that prevent thrombosis but preserve hemostasis

A prevailing dogma is that inhibition of vascular thrombosis by antagonizing platelet integrin αIIbβ3 cannot be achieved without compromising hemostasis, thus causing serious bleeding and increased morbidity and mortality. It is speculated that these adverse outcomes result from drug-induced activating conformational changes in αIIbβ3 but direct proof is lacking. Here, we report the structure-guided design of peptide Hr10 and a modified form of the partial agonist drug tirofiban that act as “pure” antagonists of αIIbβ3, i.e., they no longer induce the conformational changes in αIIbβ3. Both agents inhibit human platelet aggregation but preserve clot retraction. Hr10 and modified tirofiban are as effective as partial agonist drugs in inhibiting vascular thrombosis in humanized mice, but neither causes serious bleeding, establishing a causal link between partial agonism and impaired hemostasis. Pure orthosteric inhibitors of αIIbβ3 may thus provide safer alternatives for human therapy, and valuable tools to probe structure–activity relationships in integrins.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Foldable semi-ladder polymers: novel aggregation behavior and high-performance solution-processed organic light-emitting transistors

A critical issue in developing high-performance organic light-emitting transistors (OLETs) is to balance the trade-off between charge transport and light emission in a semiconducting material. Although traditional materials for organic light-emitting diodes (OLEDs) or organic field-effect transistors (OFETs) have shown modest performance in OLET devices, design strategies towards high-performance OLET materials and the crucial structure–performance relationship remain unclear. Our research effort in developing cross-conjugated weak acceptor-weak donor copolymers for luminescent properties lead us to an unintentional discovery that these copolymers form coiled foldamers with intramolecular H-aggregation, leading to their exceptional OLET properties. An impressive external quantum efficiency (EQE) of 6.9% in solution-processed multi-layer OLET devices was achieved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Fiber Sorbents – A Versatile Platform for Sorption-Based Gas Separations

Increasing demand for high-purity fine chemicals and a drive for process intensification of large-scale separations have driven significant work on the development of highly engineered porous materials with promise for sorption-based separations. While sorptive separations in porous materials offer energy-efficient alternatives to longstanding thermal-based methods, the particulate nature of many of these sorbents has sometimes limited their large-scale deployment in high-throughput applications such as gas separations, for which the necessary high feed flow rates and gas velocities accrue prohibitive operational costs. These processability limitations have been historically addressed through powder shaping methods aimed at the fabrication of structured sorbent contactors based on pellets, beads or monoliths, commonly obtained as extrudates. These structures overcome limitations such as elevated pressure drops commonly recorded across powder adsorption beds but often accrue thermal limitations arising from elevated particle density and aggregation, which ultimately cap their maximum separation performance. Furthermore, the harsh mechanical strain to which powder particles are subjected during contactor fabrication, in the form of extrusion/compression forces, can result in partial pore occlusion and framework degradation, further limiting their performance. Here, we present the development of porous fiber sorbents as an alternative sorbent contactor design capable of addressing sorbent processability limitations while enabling an array of performance-maximizing heat integration capabilities. This new sorbent form factor leverages pre-existing know-how from hollow fiber spinning to produce fiber-shaped sorbent contactors through the phase inversion of known polymers in a process known as dry-jet/wet quenching. The process of phase inversion allows microporous sorbent particles to be latched onto a macroporous polymer matrix under mild processing conditions, thus making it compatible with soft porous materials prone to amorphization under traditional pelletization conditions. Sorbent fibers can be created with different geometries through control of the spinning apparatus and process, offering the possibility to produce monolithic and hollow fibers alike, the latter of which can be integrated with thermalization fluid flows. In this Account, we summarize our progress in the field of fiber sorbents from both design and application standpoints. We further guide the reader through the evolution of this field from the early inceptive work on zeolite hollow fibers to recent developments on MOF fibers. We highlight the versatile nature of fiber sorbents, both from the composition, fabrication and structure points of view, and further demonstrate how fiber sorbents offer alternative paths in tackling new and challenging chemical separation challenges like direct air capture (DAC), with a final perspective on the future of the field.

36 MATERIALS SCIENCE↗

DOE OSTI2017

All-Atom Molecular Dynamics Study of Water–Dodecane Interface in the Presence of Octanol

In this work, classical atomistic molecular dynamics (MD) simulations were performed to investigate the structural properties of octanol at water/dodecane interface. Multiple combinations of simulation conditions and force fields were employed in order to :obtain high fidelity interfacial structure. The analysis of noncovalent interactions shows that the convergence of interfacial octanol distribution requires a simulation time scale larger than 100 ns. Finite size effect diminishes with increasing dimension of simulation box both laterally and vertically. In the largest simulated systems with vanishing finite size effect, the additive CHARMM force field shows similar interfacial aggregation behavior with the DRUDE polarizable model. Self-assembly of octanol molecules at water/oil interface is observed, expected to reduce;the free energy barrier between water phase and oil phase. This work provides an MD simulation benchmark for structural study of complex liquid/liquid interface with cosurfactant reducing interfacial tension between two immiscible phases.

Qiao, Baofu↗

DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Abstract Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy‐bithiophene‐based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field‐effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non‐polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

Yu, Hang [Department of Physics and Centre for Pro↗

DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Predicting the mechanical response of oligocrystals with deep learning

In this study, we employ data-driven homogenization approaches to predict the particular mechanical evolution of polycrystalline aggregates with tens of individual crystals. In these oligocrystals the differences in stress response due to microstructural variation is pronounced. Shell-like structures produced by metal-based additive manufacturing and the like make the prediction of the behavior of oligocrystals technologically relevant. The predictions of traditional homogenization theories based on grain volumes are not sensitive to variations in local grain neighborhoods. Direct simulation of the local response with crystal plasticity finite element methods is more detailed, but the computations are expensive. To represent the stress-strain response of a polycrystalline sample given its initial grain texture and morphology we have designed a novel neural network that incorporates a convolution component to observe and reduce the information in the crystal texture field and a recursive component to represent the causal nature of the history information. This model exhibits accuracy on par with crystal plasticity simulations at minimal computational cost per prediction.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Identifying Cu( ii )–amyloid peptide binding intermediates in the early stages of aggregation by resonance Raman spectroscopy: a simulation study

The aggregation of amyloid beta (Aβ) peptides plays a crucial role in the pathology and etiology of Alzheimer's disease. Experimental evidence shows that copper ion is an aggregation-prone species with the ability to coordinately bind to Aβ and further induce the formation of neurotoxic Aβ oligomers. However, the detailed structures of Cu(II)–Aβ complexes have not been illustrated, and the kinetics and dynamics of the Cu(II) binding are not well understood. Two Cu(II)–Aβ complexes have been proposed to exist under physiological conditions, and another two might exist at higher pH values. By using ab initio simulations for the spontaneous resonance Raman and time domain stimulated resonance Raman spectroscopy signals, we obtained the characteristic Raman vibronic features of each complex. Finally, these signals contain rich structural information with high temporal resolution, enabling the characterization of transient states during the fast Cu–Aβ binding and interconversion processes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Filtering higher-order datasets

Many complex systems often contain interactions between more than two nodes, known as higher-order interactions, which can change the structure of these systems in significant ways. Researchers often assume that all interactions paint a consistent picture of a higher-order dataset's structure. In contrast, the connection patterns of individuals or entities in empirical systems are often stratified by interaction size. Ignoring this fact can aggregate connection patterns that exist only at certain scales of interaction. To isolate these scale-dependent patterns, we present an approach for analyzing higher-order datasets by filtering interactions by their size. We apply this framework to several empirical datasets from three domains to demonstrate that data practitioners can gain valuable information from this approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Enhanced Arsenic (III and V) Removal in Anoxic Environments by Hierarchically Structured Citrate/FeCO 3 Nanocomposites

Novel citrate/FeCO 3 nanocomposites (CF-NCs) were synthesized for effective arsenic (III and V) sorption with constant addition of Fe2+ into HCO 3 - solution in the presence of citrate. This paper is the first report on the formation of CF-NCs, and in this study we investigate the mechanisms of arsenic uptake by the sorbent under anoxic conditions through various solid- and liquid-phase spectroscopic methods, including X-ray absorption spectroscopy. In CF-NCs, citrate was found to be incorporated into the structure of siderite (up to 17.94%) through (Fe 2+ citrate) - complexes. The crystal morphology of rhombohedral siderite was changed into hierarchically nanostructured spherical aggregates composed of several sheet-like crystals, which improved the surface reactivity in the presence of sufficient citrate. Compared to pure siderite (15.2%), enhanced removal of As(III) in the range of 19.3% to 88.2% was observed, depending on the amount of incorporated citrate. The maximum sorption capacities of CF-NCs for As(III) and As(V) were 188.97 and 290.22 mg/g, respectively, which are much higher than those of previously reported siderite-based adsorbents. It was found that arsenic (III and V) sorption on CF-NCs occurred via bidentate corner-sharing surface complexation, predominantly without changes in the arsenic oxidation states. These results suggest that arsenic (III and V) can be attenuated by siderite in anoxic environments, and this attenuation can be even more effective when siderite is modified by incorporation of organic compounds such as citrate.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1974

Earth Observatory Satellite system definition study. Report no. 3: Design/cost tradeoff studies. Appendix A: EOS program WBS dictionary. Appendix B: EOS mission functional analysis

The work breakdown structure (WBS) dictionary for the Earth Observatory Satellite (EOS) is defined. The various elements of the EOS program are examined to include the aggregate of hardware, computer software, services, and data required to develop, produce, test, support, and operate the space vehicle and the companion ground data management system. A functional analysis of the EOS mission is developed. The operations for three typical EOS missions, Delta, Titan, and Shuttle launched are considered. The functions were determined for the top program elements, and the mission operations, function 2.0, was expanded to level one functions. Selection of ten level one functions for further analysis to level two and three functions were based on concern for the EOS operations and associated interfaces.

Source record↗

NASA NTRS1991

Formation of planetesimals

Formation of planetesimals is discussed. The following subject areas are covered: (1) nebular structure; (2) aerodynamics of the solid bodies in the nebula; (3) problems with gravitational instability; (4) particle growth by coagulation; properties of fractal aggregates; and (5) coagulation and settling of fractal aggregates.

Weidenschilling, Stuart J.↗

NASA NTRS2006

Zero to Integration in Eight Months, the Dawn Ground Data System Engineering Challange

The Dawn Project has presented the Ground Data System (GDS) with technical challenges driven by cost and schedule constraints commonly associated with National Aeronautics and Space Administration (NASA) Discovery Projects. The Dawn mission consists of a new and exciting Deep Space partnership among: the Jet Propulsion Laboratory (JPL), responsible for project management and flight operations; Orbital Sciences Corporation (OSC), spacecraft builder and responsible for flight system test and integration; and the University of California, at Los Angeles (UCLA), responsible for science planning and operations. As a cost-capped mission, one of Dawn s implementation strategies is to leverage from both flight and ground heritage. OSC's ground data system is used for flight system test and integration as part of the flight heritage strategy. Mission operations, however, are to be conducted with JPL s ground system. The system engineering challenge of dealing with two heterogeneous ground systems emerged immediately. During the first technical interchange meeting between the JPL s GDS Team and OSC's Flight Software Team, August 2003, the need to integrate the ground system with the flight software was brought to the table. This need was driven by the project s commitment to enable instrument engineering model integration in a spacecraft simulator environment, for both demonstration and risk mitigation purposes, by April 2004. This paper will describe the system engineering approach that was undertaken by JPL's GDS Team in order to meet the technical challenge within a non-negotiable eight-month schedule. Key to the success was adherence to an overall systems engineering process and fundamental systems engineering practices: decomposition of the project request into manageable requirements; definition of a structured yet flexible development process; integration of multiple ground disciplines and experts into a focused team effort; in-process risk management; and aggregation of the intermediate products to an integrated final product. In addition, this paper will highlight the role of lessons learned from the integration experience. The lessons learned from an early GDS deployment have served as the foundation for the design and implementation of the Dawn Ground Data System.

systems engineering↗

NASA NTRS2017

A Breccia of Ureilitic and C2 Carbonaceous Chondrite Materials from Almahata Sitta: Implications for the Regolith of Urelitic Asteroids

The Almahata Sitta (AhS) polymict ureilite is the first meteorite to originate from a spectrally classified asteroid (2008 TC3) [1-3], and provides an unprecedented opportunity to correlate properties of meteorites with those of their parent asteroid. AhS is also unique because its fragments comprise a wide variety of meteorite types. Of approximately140 stones studied to-date, ~70% are ureilites (carbon-rich ultramafic achondrites) and 30% are various types of chondrites [4,5]. None of these show contacts between ureilitic and chondritic lithologies. It has been inferred that 2008 TC3 was loosely aggregated, so that it disintegrated in the atmosphere and only its most coherent clasts fell as individual stones [1,3,5]. Understanding the structure and composition of this asteroid is critical for missions to sample asteroid surfaces. We are studying [6] the University of Khartoum collection of AhS [3] to test hypotheses for the nature of 2008 TC3. We describe a sample that consists of both ureilitic and chondritic materials.

Goodrich, C. A.↗

DOE OSTI2018

Structure of Lung-Mimetic Multilamellar Bodies with Lipid Compositions Relevant in Pneumonia

The hierarchical assembly of lipids, as modulated by composition and environment, plays a significant role in the function of biological membranes and a myriad of diseases. Elevated concentrations of calcium ions and cardiolipin (CL), an anionic tetra-alkyl lipid found in mitochondria and some bacterial cell membranes, have been implicated in pneumonia recently. However, their impact on the physicochemical properties of lipid assemblies in lungs and how it impairs alveoli function is still unknown. We use small- and wide-angle X-ray scattering (S/WAXS) and solid-state nuclear magnetic resonance (ssNMR) to probe the structure and dynamics of lung-mimetic multilamellar bodies (MLBs) in the presence of Ca 2+ and CL. We conjecture that CL overexpressed in the hypophase of alveoli strongly affects the structure of lung-lipid bilayers and their stacking in the MLBs. Specifically, S/WAXS data revealed that CL induces significant shrinkage of the water-layer separating the concentric bilayers in multilamellar aggregates. ssNMR measurements indicate that this interbilayer tightening is due to undulation repulsion damping as CL renders the glycerol backbone of the membranes significantly more static. In addition to MLB dehydration, CL promotes intrabilayer phase separation into saturated-rich and unsaturated-rich lipid domains that couple across multiple layers. Expectedly, addition of Ca 2+ screens the electrostatic repulsion between negatively charged lung membranes. Furthermore, when CL is present, addition of Ca 2+ results in an apparent interbilayer expansion likely due to local structural defects. Combining S/WAXS and ssNMR on systems with compositions pertinent to healthy and unhealthy lung membranes, we propose how alteration of the physiochemical properties of MLBs can critically impact the breathing cycle.

59 BASIC BIOLOGICAL SCIENCES↗