Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “DOMAIN STRUCTURE”

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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Control of Directed Self-Assembly in Block Polymers by Polymeric Topcoats

The morphology of a block copolymer thin film is particularly sensitive to its boundary conditions. Lithographic applications of block polymers in the microelectronics and memory device industries require formation of morphologies with perpendicularly oriented domains. Current fabrication targets envisage the creation of dense arrays of structures with domain sizes in the sub-10 nanometer regime. Such length scales can be reached by resorting to block polymers with highly incompatible blocks (and a large Flory-Huggings parameter, x). High-x values, however, generally lead to large differences in the surface energies of the corresponding blocks, thereby interfering with formation of the sought after perpendicularly oriented domains. In this work, a theoretically informed coarse grain model is used to introduce a topcoat strategy that enables control of the orientation of block copolymer domains in highly incompatible block polymer materials. A systematic study of a wide range of polymeric material combinations is presented, and the conditions leading to optimal assembly of perpendicular morphologies are clearly identified. We consider the effect of molecular weight, block polymer film thickness and architecture, and degree of incompatibility. Our results are summarized in the form of generic phase diagrams that should serve as a guide for experimental deployment of the top-coat strategy put forth in this work.

Ramírez-Hernández, Abelardo↗
DOE OSTI2015

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. In this paper, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed and the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. Finally, the open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1992

The structure of the gamma-domain for H-infinity Riccati solutions

The authors investigated some properties of the solutions to H-infinity Riccati equations which play a key role in the state approach to H-infinity optimization problem. The structure of the gamma-domain for the Riccati solutions has been described. There are two kinds of lower bounds for the solutions to exist and to be positive semidefinite respectively. A quadratically convergent algorithm for computing the lower bound is discussed.

Li, X. P.↗
DOE OSTI2024

The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of nonflowering plants retain immune-related functions through translineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to nonflowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable with motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CC MAEPL in the nonflowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CC MAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent nonflowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ~500 million years ago.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Frequency- and Time-Domain Methods in Soil-Structure Interaction Analysis

Soil-structure interaction (SSI) analysis in the nuclear industry is currently performed using linear codes that function in the frequency domain. There is a consensus that these frequency-domain codes give reasonably accurate results for low-intensity ground motions that result in almost linear response. For higher intensity ground motions, which may result in nonlinear response in the soil, structure or at the vicinity of the foundation, the adequacy of frequency-domain codes is unproven. Nonlinear analysis, which is only possible in the time domain, is theoretically more appropriate in such cases. These methods are available but are rarely used due to the large computational requirements and a lack of experience with analysts and regulators. This paper presents an assessment of the linear frequency-domain code, SASSI, which is widely used in the nuclear industry, and the time-domain commercial finite-element code, LS-DYNA, for SSI analysis. The assessment involves benchmarking the SSI analysis procedure in LS-DYNA against SASSI for linearly elastic models. After affirming that SASSI and LS-DYNA result in almost identical responses for these models, they are used to perform nonlinear SSI analyses of two structures founded on soft soil. An examination of the results shows that, in spite of using identical material properties, the predictions of frequency- and time-domain codes are significantly different in the presence of nonlinear behavior such as gapping and sliding of the foundation.

42 ENGINEERING↗
DOE OSTI2021

Disorder-induced time effect in the antiferromagnetic domain state of Fe 1+ y Te

Herein we report on temperature-dependent soft X-ray absorption spectroscopy (XAS) measurements utilizing linearly polarized synchrotron radiation to probe magnetic phase transitions in iron-rich Fe 1+y Te (y ≈ 0.12). X-ray magnetic linear dichroism (XMLD) signals, which sense magnetic ordering processes at surfaces, start to increase monotonically below the Néel temperature T N = 57 K. This increase is due to a progressive bicollinear antiferromagnetic (AFM) alignment of Fe spins of the monoclinic Fe 1+y Te parent phase. This AFM alignment was achieved by a [1 0 0]-oriented biasing field favoring a single-domain state during cooling across T N . Our specific heat and magnetization measurements confirm the bulk character of this AFM phase transition. On longer time scales, however, we observe that the field-biased AFM state is highly unstable even at the lowest temperature of T = 3 K. After switching off the biasing field, the XMLD signal decays exponentially with a time constant τ = 1506 s. The initial XMLD signal is restored only upon repeating a cycle consisting of heating and field-cooling through T N . We explain the time effect by a gradual formation of a multi-domain state with 90° rotated AFM domains, promoted by structural disorder, facilitating the motion of twin-domains. Significant disorder in our Fe 1+y Te sample is evident from our X-ray diffraction and specific heat data. The stability of magnetic phases in Fe-chalcogenides is an important material property, since the Fe(Te 1-x Se x ) phase diagram shows magnetism intimately connected with superconductivity.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Spiky electric and magnetic field structures in flux rope experiments

Magnetic flux ropes are structures that are common in the corona of the sun and presumably all stars. They can be thought of as the building blocks of solar structures. They have been observed in Earth’s magnetotail and near Mars and Venus. When multiple flux ropes are present magnetic field line reconnection, which converts magnetic energy to other forms, can occur when they collide. The structure of multiple magnetic ropes, the interactions between multiple ropes, and their topological properties such as helicity and writhing have been studied theoretically and in laboratory experiments. In this paper, we report on spiky potential and magnetic fields associated with the ropes. We show that the potential structures are chaotic for a range of their temporal half-widths and the probability density function (PDF) of their widths resembles the statistical distribution of crumpled paper. The spatial structure of the magnetic spikes is revealed using a correlation counting method. Computer simulation suggests that the potential structures are the nonlinear end result of an instability involving relative drift between ions and electrons.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1989

A frequency domain analysis for damped space structures

A method is presented for the analysis of damped structural systems in which the structural components are represented by impedance models and analyzed in the frequency domain. Methods are presented to assemble and condense system impedance matrices, and then to identify approximate mass, stiffness, and damping matrices for systems whose impedances are complicated functions of frequency. Formulas are derived for determination of approximate values for system natural frequencies and damping using frequency domain quantities. The sensitivities of these approximate values to system parameter changes are analyzed. The implementation of these analysis tools is discussed and applied to a simple mechanical system.

Hagood, Nesbitt W.↗
DOE OSTI2018

Structure of a lipid-bound viral membrane assembly protein reveals a modality for enclosing the lipid bilayer

Cellular membranes are maintained as closed compartments, broken up only transiently during membrane reorganization or lipid transportation. However, open-ended membranes, likely derived from scissions of the endoplasmic reticulum, persist in vaccinia virus-infected cells during the assembly of the viral envelope. A group of viral membrane assembly proteins (VMAPs) were identified as essential for this process. To understand the mechanism of VMAPs, we determined the 2.2-Å crystal structure of the largest member, named A6, which is a soluble protein with two distinct domains. The structure of A6 displays a novel protein fold composed mainly of alpha helices. The larger C-terminal domain forms a unique cage that encloses multiple glycerophospholipids with a lipid bilayer-like configuration. The smaller N-terminal domain does not bind lipid but negatively affects lipid binding by A6. Mutations of key hydrophobic residues lining the lipid-binding cage disrupt lipid binding and abolish viral replication. Furthermore, our results reveal a protein modality for enclosing the lipid bilayer and provide molecular insight into a viral machinery involved in generating and/or stabilizing open-ended membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Atypical Response Regulator ChxR from Chlamydia trachomatis Is Structurally Poised for DNA Binding

ChxR is an atypical two-component signal transduction response regulator (RR) of the OmpR/PhoB subfamily encoded by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Despite structural homology within both receiver and effector domains to prototypical subfamily members, ChxR does not require phosphorylation for dimer formation, DNA binding or transcriptional activation. Thus, we hypothesized that ChxR is in a conformation optimal for DNA binding with limited interdomain interactions. To address this hypothesis, the NMR solution structure of the ChxR effector domain was determined and used in combination with the previously reported ChxR receiver domain structure to generate a full-length dimer model based upon SAXS analysis. Small-angle scattering of ChxR supported a dimer with minimal interdomain interactions and effector domains in a conformation that appears to require only subtle reorientation for optimal major/ minor groove DNA interactions. SAXS modeling also supported that the effector domains were in a head-to-tail conformation, consistent with ChxR recognizing tandem DNA repeats. The effector domain structure was leveraged to identify key residues that were critical for maintaining protein - nucleic acid interactions. In combination with prior analysis of the essential location of specific nucleotides for ChxR recognition of DNA, a model of the full-length ChxR dimer bound to its cognate cis-acting element was generated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Atomic layer epitaxy of kagome magnet Fe 3 Sn 2 and Sn-modulated heterostructures

Magnetic materials with kagome crystal structure exhibit rich physics, such as frustrated magnetism, skyrmion formation, topological flat bands, and Dirac/Weyl points. Until recently, most studies on kagome magnets have been performed on bulk crystals or polycrystalline films. Here, we report the atomic layer molecular beam epitaxy synthesis of high-quality thin films of topological kagome magnet Fe 3 Sn 2 . The structural and magnetic characterization of Fe 3 Sn 2 on epitaxial Pt(111) identifies highly ordered films with c-plane orientation and an in-plane magnetic easy axis. Studies on the local magnetic structure by anomalous Nernst effect imaging reveal in-plane oriented micrometer size domains. Superlattice structures consisting of Fe 3 Sn 2 and Fe 3 Sn are also synthesized by atomic layer molecular beam epitaxy, demonstrating the ability to modulate the sample structure at the atomic level. The realization of high-quality films by atomic layer molecular beam epitaxy opens the door to explore the rich physics of this system and investigate novel spintronic phenomena by interfacing Fe 3 Sn 2 with other materials.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Crystal structure studies of NADP{sup +} dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain

Highlights: • We determined the structure of isocitrate dehydrogenase with citrate and cofactor. • The structure reveals a unique novel terminal domain involved in dimerization. • Clasp domain shows significant difference, and catalytic residues are conserved. • Oligomerization of the enzyme is quantized with subunit-subunit interactions. • Novel domain of this enzyme is classified as subfamily of the type IV. - Abstract: NADP{sup +} dependent isocitrate dehydrogenase (IDH) is an enzyme catalyzing oxidative decarboxylation of isocitrate into oxalosuccinate (intermediate) and finally the product α-ketoglutarate. The crystal structure of Thermus thermophilus isocitrate dehydrogenase (TtIDH) ternary complex with citrate and cofactor NADP{sup +} was determined using X-ray diffraction method to a resolution of 1.80 Å. The overall fold of this protein was resolved into large domain, small domain and a clasp domain. The monomeric structure reveals a novel terminal domain involved in dimerization, very unique and novel domain when compared to other IDH’s. And, small domain and clasp domain showing significant differences when compared to other IDH’s of the same sub-family. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDH’s. Also, helices/beta sheets are absent in the small domain, when compared to other IDH’s of the same sub family. The overall TtIDH structure exhibits closed conformation with catalytic triad residues, Tyr144-Asp248-Lys191 are conserved. Oligomerization of the protein is quantized using interface area and subunit–subunit interactions between protomers. Overall, the TtIDH structure with novel terminal domain may be categorized as a first structure of subfamily of type IV.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Crystal Structure of USP7 Ubiquitin-like Domains with an ICP0 Peptide Reveals a Novel Mechanism Used by Viral and Cellular Proteins to Target USP7

Herpes simplex virus-1 immediate-early protein ICP0 activates viral genes during early stages of infection, affects cellular levels of multiple host proteins and is crucial for effective lytic infection. Being a RING-type E3 ligase prone to auto-ubiquitination, ICP0 relies on human deubiquitinating enzyme USP7 for protection against 26S proteasomal mediated degradation. USP7 is involved in apoptosis, epigenetics, cell proliferation and is targeted by several herpesviruses. Several USP7 partners, including ICP0, GMPS, and UHRF1, interact through its C-terminal domain (CTD), which contains five ubiquitin-like (Ubl) structures. Despite the fact that USP7 has emerged as a drug target for cancer therapy, structural details of USP7 regulation and the molecular mechanism of interaction at its CTD have remained elusive. Here, we mapped the binding site between an ICP0 peptide and USP7 and determined the crystal structure of the first three Ubl domains bound to the ICP0 peptide, which showed that ICP0 binds to a loop on Ubl2. Sequences similar to the USP7-binding site in ICP0 were identified in GMPS and UHRF1 and shown to bind USP7-CTD through Ubl2. In addition, co-immunoprecipitation assays in human cells comparing binding to USP7 with and without a Ubl2 mutation, confirmed the importance of the Ubl2 binding pocket for binding ICP0, GMPS and UHRF1. Therefore we have identified a novel mechanism of USP7 recognition that is used by both viral and cellular proteins. Our structural information was used to generate a model of near full-length USP7, showing the relative position of the ICP0/GMPS/UHRF1 binding pocket and the structural basis by which it could regulate enzymatic activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure of the eukaryotic protein O-mannosyltransferase Pmt1–Pmt2 complex

In eukaryotes, a nascent peptide entering the endoplasmic reticulum (ER) is scanned by two Sec61 translocon-associated large membrane machines for protein N-glycosylation and protein O-mannosylation, respectively. While the structure of the eight-protein oligosaccharyltransferase complex has been determined recently, the structures of mannosyltransferases of the PMT family, which are an integral part of ER protein homeostasis, are still unknown. In this paper we report cryo-EM structures of the Saccharomyces cerevisiae Pmt1–Pmt2 complex bound to a donor and an acceptor peptide at 3.2-Å resolution, showing that each subunit contains 11 transmembrane helices and a lumenal β-trefoil fold termed the MIR domain. The structures reveal the substrate recognition model and confirm an inverting mannosyl-transferring reaction mechanism by the enzyme complex. Furthermore, we found that the transmembrane domains of Pmt1 and Pmt2 share a structural fold with the catalytic subunits of oligosaccharyltransferases, confirming a previously proposed evolutionary relationship between protein O-mannosylation and protein N-glycosylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites

The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the T H 1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. Here, the data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation

Enteroviruses use a type I Internal Ribosome Entry Site (IRES) structure to facilitate protein synthesis and promote genome replication. Type I IRES elements require auxiliary host proteins to organize RNA structure for 40S ribosomal subunit assembly. Heterogeneous nuclear ribonucleoprotein A1 stimulates enterovirus 71 (EV71) translation in part through specific interactions with its stem loop II (SLII) IRES domain. Here, we determined a conjoined NMR-small angle x-ray scattering structure of the EV71 SLII domain and a mutant that significantly attenuates viral replication by abrogating hnRNP A1 interactions. Native SLII adopts a locally compact structure wherein stacking interactions in a conserved 5'-AUAGC-3' bulge preorganize the adjacent helices at nearly orthogonal orientations. Mutating the bulge sequence to 5'-ACCCC-3' ablates base stacking in the loop and globally reorients the SLII structure. Biophysical titrations reveal that the 5'-AUAGC-3' bulge undergoes a conformational change to assemble a functional hnRNP A1–RNA complex. Importantly, IRES mutations that delete the bulge impair viral translation and completely inhibit replication. Furthermore, this work provides key details into how an EV71 IRES structure adapts to hijack a cellular protein, and it suggests that the SLII domain is a potential target for antiviral therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗