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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human

Significance Telomerase synthesizes the telomeric DNA at the 3′ ends of chromosomes and maintains genome integrity. Telomerase RNA (TR) provides the template for telomere-repeat synthesis within a template/pseudoknot (t/PK) domain that is essential for activity. We investigated the structure and dynamics of the t/PK from medaka fish, which contain the smallest vertebrate TR, using NMR and modeling. Despite differences in length, sequence, and predicted secondary structure with human TR, the remarkable similarities between subdomains, including one newly identified in medaka, reveal a conserved architecture for vertebrate t/PK. Combining our model of the full-length pseudoknot and information from the 9-Å structure of Tetrahymena telomerase, we propose models for the interaction of medaka and human t/PK with telomerase reverse transcriptase, providing insight into function.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Comparison of different fractal dimension measuring algorithms for RE-TM M-O films

Noise in magneto-optical recording devices is discussed. In general, it appears that either the divider technique or amplitude spectrum technique may be used interchangeably to measure the fractal dimension (D) in the domain wall structure of ideal images. However, some caveats must be observed for best results. The divider technique is attractive for its simplicity and relatively modest computation requirements. However, it is sensitive to noise, in that noise pixels that touch the domain boundary are interpreted as being part of the boundary, skewing the measurement. Also, it is not useful in measuring nucleation-dominated films or domains that have significant amounts of structure within the interior of the domain wall. The amplitude spectrum method is more complex, and less intuitive than the divider method, and somewhat more expensive to implement computationally. However, since the camera noise tends to be white, the noise can be avoided in the measurement of D by avoiding that portion of the curve that is flat (due to the white noise) when the least squares line is fit to the plot. Also, many image processing software packages include a Fast Fourier Transformation (FFT) facility, while the user will most likely have to write his own edge extraction routine for the divider method. The amplitude spectrum method is a true two dimensional technique that probes the interior of the domain wall, and in fact, can measure arbitrary clusters of domains. It can also be used to measure grey-level images, further reducing processing steps needed to threshold the image.

Bernacki, Bruce E.↗
DOE OSTI2013

Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Development of a Nonlinear Time Domain Methodology (Part I)

The ASCE 4-2014 (draft) provides guidance in Appendix B for nonlinear time-domain soil structure interaction (NLSSI) analysis. To accommodate widespread use of NLSSI, it is necessary to develop a methodology, or a set of steps, that produce reasonable results. An NLSSI methodology opens the door to explore additional seismic behaviour at nuclear facilities such as 1) gapping and sliding, 2) inclined seismic waves coupled with gapping and sliding of foundations atop soil, 3) inclined seismic waves coupled with gapping and sliding of deeply embedded structures, 4) soil dilatancy, 5) surface waves, 4) buoyancy, 5) concrete cracking and 6) seismic isolation. This paper documents the NLSSI methodology. At a high level these steps include 1) define soil site parameters, 2) calibrate site-specific nonlinear soil constitutive model, 3) verify performance of time domain absorbing boundaries, 4) build free field soil site, 5) build 3D soil site model using the appropriate parameters 6) define design concrete material properties and develop appropriate concrete constitutive model, 7) build structural model, 8) define appropriate contact and/or friction behaviour, 9) build combined soil-structure model and run time domain models and 10) compare with SHAKE/SASSI results at increasing levels of ground motion. This paper will describe the NLSSI methodology, discuss important NLSSI considerations, and discuss its potential implementation in industry. A second paper, which is Part II, “Development of a Nonlinear Time Domain Methodology Results,” provides results comparing in-structure response from NLSSI with the linear frequency-domain program, SASSI.

42 ENGINEERING↗
DOE OSTI2014

Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO

Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed a+b fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Crystal structure of the kinase and UBA domains of SNRK reveals a distinct UBA binding mode in the AMPK family

Highlights: • The UBA domain of SNRK binds between the N- and C-lobes of the kinase domain. • The UBA binding mode in SNRK is similar to yet different from AMPK. • Structural analyses suggested an inhibitory function of SNRK UBA domain. Sucrose non-fermenting (Snf1)-related kinase (SNRK) is a novel member of the AMP-activated protein kinase (AMPK) family and is involved in many metabolic processes. Here we report the crystal structure of an N-terminal SNRK fragment containing kinase and adjacent ubiquitin-associated (UBA) domains. This structure shows that the UBA domain binds between the N- and C-lobes of the kinase domain. The mode of UBA binding in SNRK largely resembles that in AMPK and brain specific kinase (BRSK), however, unique interactions play vital roles in stabilizing the KD-UBA interface of SNRK. We further propose a potential role of the UBA domain in the regulation of SNRK kinase activity. This study provides new insights into the structural diversities of the AMPK kinase family.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana

Vernalization is a pivotal stage for some plants involving many epigenetic changes during cold exposure. In Arabidopsis, an essential step in vernalization for further flowering is successful silence the potent floral repressor Flowering Locus C (FLC) by repressing histone mark. AtVal1 is a multi-function protein containing five domains that participate into many recognition processes and is validated to recruit the repress histone modifier PHD-PRC2 complex and interact with components of the ASAP complex target to the FLC nucleation region through recognizing a cis element known as CME (cold memory element) by its plant-specific B3 domain. Here, we determine the crystal structure of the B3 domain in complex with Sph/RY motif in CME. Our structural analysis reveals the specific DNA recognition by B3 domain, combined with our in vitro experiments, we provide the structural insight into the important implication of AtVAL1-B3 domain in flowering process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction

NLRP12 is a NOD-like receptor that plays multiple roles in both inflammation and tumorigenesis. Despite the importance, little is known about its mechanism of action at the molecular level. Here, we report the crystal structure of NLRP12 PYD domain at 1.70 Å fused with an maltose-binding protein (MBP) tag. Interestingly, the PYD domain forms a dimeric configuration through a disulfide bond in the crystal. The possible biological significance is discussed in the context of ROS induced NF-κB activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2

Export of LDL-derived cholesterol from lysosomes requires the cooperation of the integral membrane protein Niemann–Pick C1 (NPC1) and a soluble protein, Niemann–Pick C2 (NPC2). Mutations in the genes encoding these proteins lead to Niemann–Pick disease type C (NPC). NPC2 binds to NPC1’s second (middle), lumenally oriented domain (MLD) and transfers cholesterol to NPC1’s N-terminal domain (NTD). Here, we report the 2.4-Å resolution crystal structure of a complex of human NPC1–MLD and NPC2 bearing bound cholesterol-3-O-sulfate. NPC1–MLD uses two protruding loops to bind NPC2, analogous to its interaction with the primed Ebola virus glycoprotein. Here, docking of the NPC1–NPC2 complex onto the full-length NPC1 structure reveals a direct cholesterol transfer tunnel between NPC2 and NTD cholesterol binding pockets, supporting the “hydrophobic hand-off” cholesterol transfer model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural and magnetic properties of CoTeMo⁢O 6

Here, we have conducted a comprehensive investigation into the magnetic properties of the chiral multiferroic material CoTeMo⁢O 6 . In contrast with the previous claim of canted antiferromagnetic order with ferromagnetic components [Y. Doi et al., J. Solid State Chem. 182, 3232 (2009)], our investigation reveals an antiferromagnetic ground state with compensated moments, providing an interesting platform for exploring exotic material properties. Through careful measurements of magnetization under a series of applied fields, we demonstrate that there exist two sequential field-induced magnetic transitions in CoTeMo⁢O 6 , with one occurring at 𝐻 𝑐⁢1 =460 Oe along the 𝑎 axis, and the other at 𝐻 𝑐⁢2 =1.16 T with the field along the 𝑏 axis. The values of 𝐻 𝑐⁢1 and 𝐻 𝑐⁢2 exhibit strong angular dependence and diverge with different rates as the applied field is rotated 90 ° within the 𝑎⁢𝑏 plane. This reflects the distinct nature of these transitions, which is further supported by the different critical behavior of 𝐻 𝑐⁢1 and 𝐻 𝑐⁢2 , characterized by the values of 𝛾, in the function of 𝐻 𝑐 =𝐻 0 ⁡(1−𝑇/𝑇 𝑐 ) 𝛾 . Furthermore, we have demonstrated that there exist structural and magnetic twin domains in CoTeMo⁢O 6 that strongly affect the experimental measurement of their macroscopic properties. Intriguingly, these twin domains can be related to the orthorhombicity/chirality of the crystal structure with the space group 𝑃⁢2 1 ⁢2 1⁢ 2. We further explored the magnetic and structural domains with uniaxial pressure and polarized light microscopy. Our results suggest that CoTeMo⁢O 6 could be used as a unique platform for investigating the intriguing physics involving intertwined degrees of freedom. The tunability of the underlying domain distribution and its strong anisotropy could also be useful for developing functional devices and applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Micro- and nanodomain imaging in uniaxial ferroelectrics: Joint application of optical, confocal Raman, and piezoelectric force microscopy

The application of the most effective methods of the domain visualization in model uniaxial ferroelectrics of lithium niobate (LN) and lithium tantalate (LT) family, and relaxor strontium-barium niobate (SBN) have been reviewed in this paper. We have demonstrated the synergetic effect of joint usage of optical, confocal Raman, and piezoelectric force microscopies which provide extracting of the unique information about formation of the micro- and nanodomain structures. The methods have been applied for investigation of various types of domain structures with increasing complexity: (1) periodical domain structure in LN and LT, (2) nanodomain structures in LN, LT, and SBN, (3) nanodomain structures in LN with modified surface layer, (4) dendrite domain structure in LN. The self-assembled appearance of quasi-regular nanodomain structures in highly non-equilibrium switching conditions has been considered.

36 MATERIALS SCIENCE↗
NASA NTRS1988

A frequency domain identification scheme for flexible structure control

The authors present a novel method called time-varying transfer function estimation (TTFE) in which time-domain parameters are computed through identification in the frequency domain. The method is particularly well suited for flexible structure control problems. An example of a flexible manipulator system is presented for which a self-tuning control law with frequency shaping is derived and demonstrated.

Tzes, Anthony P.↗
NASA NTRS1993

Structural system reliability under multiple failure modes

This paper describes a computational method for system reliability estimation of propulsion structures. The failure domain of the entire structural system is computed through the union of failure regions for various critical system failure modes. The effect of non-critical progressive damage is incorporated through structural reanalysis, resulting in the construction of several linear segments to approximately cover the system failure domain. An adaptive damage imposition scheme is outlined for the sake of computational efficiency. The proposed method is used to construct the system survival cdf (cumulative distribution function) of a two-rotor system.

Mahadevan, S.↗
DOE OSTI2015

Crystal structure of the FLT3 kinase domain bound to the inhibitor quizartinib (AC220)

More than 30% of acute myeloid leukemia (AML) patients possess activating mutations in the receptor tyrosine kinase FMS-like tyrosine kinase 3 or FLT3. A small-molecule inhibitor of FLT3 (known as quizartinib or AC220) that is currently in clinical trials appears promising for the treatment of AML. Here, we report the co-crystal structure of the kinase domain of FLT3 in complex with quizartinib. FLT3 with quizartinib bound adopts an “Abl-like” inactive conformation with the activation loop stabilized in the “DFG-out” orientation and folded back onto the kinase domain. This conformation is similar to that observed for the uncomplexed intracellular domain of FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop. The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients. This co-complex further provides a structural rationale for quizartinib-resistance mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural and biochemical studies of the extracellular domain of Myelin protein zero-like protein 1

Highlights: • Structure of the extracellular domain of human MPZL1 is reported. • MPZL1 shows remarkably truncated strand G than that of its homologous family member MPZ. • Asn50 is a major glycosylation site important for MPZL1 binding ConA. • Dimeric interfaces of MPZL1 are maintained by hydrogen bonds between Ser86 and Val145. Myelin protein zero-like protein 1 (MPZL1) is a member of the immunoglobulin superfamily, and is also a receptor of concanavalin A (ConA). MPZL1 is upregulated in hepatocellular carcinoma (HCC) and accelerates migration of HCC cells. However, function of MPZL1 as a receptor of ConA and its role in HCC development are largely unknown. To elucidate the functional basis, we have determined the crystal structure of the extracellular domain of MPZL1 at 2.7 Å resolution. Overall, it folds like a typical immunoglobulin variable-like domain that is much like MPZ. Unexpectedly, we found Asn50 is a unique glycosylation site and the glycosylation mediates its interaction with ConA. Furthermore, we also found that MPZL1 exists as a homodimer in the crystal, in which hydrogen bonds between Ser86 and Val145 play an important role. Our results demonstrate that glycosylation of Asn50 is essential for its function as a receptor of ConA. We propose that dimerization of MPZL1 participates in control of its signal transmission in cell adhesion.

60 APPLIED LIFE SCIENCES↗