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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Protein Surface Printer for Exploring Protein Domains

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

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

Nanocomposite structure of two-line ferrihydrite powder from total scattering

Ferrihydrite is one of the most important iron-containing minerals on Earth. Yet determination of its atomic-scale structure has been frustrated by its intrinsically poor crystallinity. The key difficulty is that physically-different models can appear consistent with the same experimental data. Using X-ray total scattering and a nancomposite reverse Monte Carlo approach, we evaluate the two principal contending models—one a multi-phase system without tetrahedral iron(III), and the other a single phase with tetrahedral iron(III). Our methodology is unique in considering explicitly the complex nanocomposite structure the material adopts: namely, crystalline domains embedded in a poorly-ordered matrix. The multi-phase model requires unphysical structural rearrangements to fit the data, whereas the single-phase model accounts for the data straightforwardly. Hence the latter provides the more accurate description of the short- and intermediate-range order of ferrihydrite. We discuss how this approach might allow experiment-driven (in)validation of complex models for important nanostructured phases beyond ferrihydrite.

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

Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules

In Saccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside the Saccharomycetaceae family are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure of ScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyond Saccharomycetaceae, e.g. in Schizosaccharomyces pombe or human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix αC in the zf-C3HC and Rsm1 modules, and an extra helix αAB' in the Rsm1 module. Conservation of key residues responsible for its distinct features identifies S. pombe Rsm1 and Homo sapiens NIPA/ZC3HC1 as structural orthologs of ScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function of ScPml39 in S. cerevisiae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Optical high-order harmonic generation as a structural characterization tool

Structural characterization is essential to material engineering, but few tools can detect structural properties in the time domain. High harmonic generation (HHG) emerges as a new frontier that touches the heart of condensed-matter physics from the symmetry to quantum geometrical nature of electrons, but its capability in structural characterization has not been materialized. Here, we establish a crucial connection between the symmetry of a material and the helicity of light. We employ monolayer MoS 2 as an example. In this work, we show that a linearly polarized laser pulse used in experiments is not ideal for structural characterization because it only generates in-plane anisotropy. It is the circularly polarized laser field that is capable of producing four distinctive HHG signals from the four phases of MoS 2 . This finally links the laser helicity to the crystal structure. The results are generic and are not affected by the Berry curvature, the interband or intraband contribution. Our study unleashes the power of HHG as a structural characterization tool for technologically important materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Novel Z-DNA binding domains in giant viruses

Z-nucleic acid structures play vital roles in cellular processes and have implications in innate immunity due to their recognition by Zα domains containing proteins (Z-DNA/Z-RNA binding proteins, ZBPs). Although Zα domains have been identified in six proteins, including viral E3L, ORF112, and I73R, as well as, cellular ADAR1, ZBP1, and PKZ, their prevalence across living organisms remains largely unexplored. In this study, we introduce a computational approach to predict Zα domains, leading to the revelation of previously unidentified Zα domain-containing proteins in eukaryotic organisms, including non-metazoan species. Our findings encompass the discovery of new ZBPs in previously unexplored giant viruses, members of the Nucleocytoviricota phylum. Through experimental validation, we confirm the Zα functionality of select proteins, establishing their capability to induce the B-to-Z conversion. Additionally, we identify Zα-like domains within bacterial proteins. While these domains share certain features with Zα domains, they lack the ability to bind to Z-nucleic acids or facilitate the B-to-Z DNA conversion. Our findings significantly expand the ZBP family across a wide spectrum of organisms and raise intriguing questions about the evolutionary origins of Zα-containing proteins. Moreover, our study offers fresh perspectives on the functional significance of Zα domains in virus sensing and innate immunity and opens avenues for exploring hitherto undiscovered functions of ZBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life

Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Two VHH Antibodies Neutralize Botulinum Neurotoxin E1 by Blocking Its Membrane Translocation in Host Cells

Botulinum neurotoxin serotype E (BoNT/E) is one of the major causes of human botulism, which is a life-threatening disease caused by flaccid paralysis of muscles. After receptor-mediated toxin internalization into motor neurons, the translocation domain (HN) of BoNT/E transforms into a protein channel upon vesicle acidification in endosomes and delivers its protease domain (LC) across membrane to enter the neuronal cytosol. It is believed that the rapid onset of BoNT/E intoxication compared to other BoNT serotypes is related to its swift internalization and translocation. We recently identified two neutralizing single-domain camelid antibodies (VHHs) against BoNT/E1 termed JLE-E5 and JLE-E9. Here, we report the crystal structures of these two VHHs bound to the LCHN domain of BoNT/E1. The structures reveal that these VHHs recognize two distinct epitopes that are partially overlapping with the putative transmembrane regions on HN, and therefore could physically block membrane association of BoNT/E1. This is confirmed by our in vitro studies, which show that these VHHs inhibit the structural change of BoNT/E1 at acidic pH and interfere with BoNT/E1 association with lipid vesicles. Therefore, these two VHHs neutralize BoNT/E1 by preventing the transmembrane delivery of LC. Furthermore, structure-based sequence analyses show that the 3-dimensional epitopes of these two VHHs are largely conserved across many BoNT/E subtypes, suggesting a broad-spectrum protection against the BoNT/E family. In summary, this work improves our understanding of the membrane translocation mechanism of BoNT/E and paves the way for developing VHHs as diagnostics or therapeutics for the treatment of BoNT/E intoxication.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Modeling and simulation of earthquake soil structure interaction excited by inclined seismic waves

Presented is an application of wave potential formulation (WPF) together with domain reduction method (DRM) to modeling earthquake soil structure interaction (ESSI) behavior in horizontally layered ground under inclined incident seismic waves. Wave potential formulation is used to develop a spatially varying, inclined seismic wave field from incident Primary (P) and Secondary (S) waves that propagate through layered ground. Developed seismic wave field is then used to develop effective forces for Domain Reduction Method that are then used for analyzing ESSI response of a soil structure system. Developed methodology, called WPF-DRM, is verified using analytic solution for a free field response of layered ground subjected to inclined incident waves. Developed WPF-DRM methodology is illustrated through analysis of an ESSI response of a deeply embedded structure, a small modular reactor (SMR) subjected to incident S wave polarized in vertical plane (SV) with variation in inclinations and frequencies. Presented example highlights the influences of incident wave inclination and frequency on ESSI response of analyzed SMR.

58 GEOSCIENCES↗
DOE OSTI2021

Explicit structural topology optimization using boundary element method‐based moving morphable void approach

Abstract This article presents an explicit topology optimization approach using boundary element method based moving morphable void (MMV). Structural analysis in the conventional MMV approach is performed on a fixed mesh over the entire design domain. However, in the proposed method structural boundaries are described using B‐splines and discretized with boundary elements making explicit representation of the boundaries possible. In this regard, the proposed approach has following merits: a) the use of weak material, which is often adopted to mimic voids can be completely avoided; b) exact and explicit description of voids in MMV allows the capture of tiny structural features in a robust and effective way; c) numerical instabilities stemming from the use of fixed meshes can be naturally avoided. Several numerical examples are provided to demonstrate the effectiveness of the proposed approach.

Zhang, Weisheng↗
DOE OSTI2023

Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis

Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α) 8 -barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with k cat = 6.0 ± 0.6 s –1 and K m = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA

Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.

Yeoh, Zoe C. (ORCID:0000000226949068)↗
DOE OSTI2024

Picosecond volume expansion drives a later-time insulator–metal transition in a nano-textured Mott insulator

There is significant technological interest in developing ever faster switching between different electronic and magnetic states of matter. Manipulating properties at terahertz rates requires accessing the intrinsic timescales of both electrons and associated phonons, which is possible with short-pulse photoexcitation. However, in many Mott insulators, the electronic transition is accompanied by the nucleation and growth of percolating domains of the changed lattice structure, leading to empirical timescales dominated by slowly coarsening dynamics. Here, in this study, we use time-resolved X-ray diffraction and reflectivity measurements to show that the photoinduced insulator-to-metal transition in an epitaxially strained Mott insulating thin film occurs without observable domain formation and coarsening effects, allowing the study of the intrinsic electronic and lattice dynamics. Above a fluence threshold, the initial electronic excitation drives a fast lattice rearrangement, which is followed by a slower electronic evolution into a metastable nonequilibrium state. Microscopic model calculations based on time-dependent dynamical mean-field theory and semiclassical lattice dynamics explain the threshold behaviour and elucidate the delayed onset of the electronic phase transition. This work highlights the importance of combined electronic and structural studies in unravelling the physics of dynamic transitions and the timescales of photoinduced processes. During a photoinduced phase transition, electronic rearrangements are usually faster than lattice ones. Time-resolved measurements now show that the insulator-to-metal transition in a thin-film Mott insulator is preceded by lattice reconfiguration.

36 MATERIALS SCIENCE↗