Structural plasticity of the selectivity filter in a nonselective ion channel
Explore the source record for details and available documents.
Roy, Raktim N.↗
SEARCH · Search NASA
Results for “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.
The seventh blind test of crystal structure prediction: structure ranking methods
A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.
Chemistry↗
Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response
The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin–antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate–latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novel TA system involved in Mycobacterium tuberculosis latency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.
Bajaj, R. Alexandra↗
Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms
Explore the source record for details and available documents.
Radka, Christopher D.↗
Structure Prediction from Neutron Scattering Profiles: A Data Sciences Approach
Explore the source record for details and available documents.
Computer Science↗
Ab initio GGA+U investigations of the structural, electronic, and magnetic properties of Cd 1-x Mn x Te alloy
The structural, electronic and magnetic properties of Cd 1-x Mn x Te alloy in the zinc-blende (ZB) phase within the framework of spin-polarized density functional theory using the generalized gradient approximation (GGA) are studied. In particular, we employ GGA+U SIC method that gives a better description of systems with strong Coulomb correlations of the d-electrons. First, we discuss implementation of GGA+U method to the ground state calculations of pure CdTe and ferromagnetic MnTe. The alloy is modelled at some selected compositions by ordered structures described in terms of periodically repeated supercells for the compositions x = 0.25, 0.5, and 0.75. The compositional dependence of the lattice constant, electronic band structure and partial densities of states of ferromagnetic Cd 1-x Mn x Te alloy are studied. We estimate the spin-exchange splitting energies produced by the Mn 3d-states and determine the exchange constants for the conduction and valence bands of the alloy. The energy positions of the occupied and unoccupied Mn 3d-bands in the electronic structure of ferromagnetic Cd 1-x Mn x Te alloy are also presented. Our calculations using GGA+U SIC approach agree well with the available experimental data and other calculations.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase
The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.
Science & Technology - Other Topics↗
Effect of Cr Spacer on Structural and Magnetic Properties of Fe/Gd Multilayers
Here, we analyze the role of a thin Cr spacer between Fe and Gd layers on the structure and magnetic properties of a [Fe(35 Å)/Cr(t Cr )/Gd(50 Å)/Cr(t Cr )] 12 superlattice. Samples without the Cr spacer (t Cr = 0) and with a thin spacer (t Cr = 4 Å) are investigated using X-ray diffraction, polarized neutron and resonance X-ray magnetic reflectometry, static magnetometry, magneto-optical Kerr effect, and ferromagnetic resonance techniques. Magnetic properties are studied experimentally in a wide temperature range 4–300 K and analyzed theoretically using numerical simulation on the basis of the mean-field model. We show that a reasonable agreement with the experimental data can be obtained considering temperature dependence of the effective field parameter in gadolinium layers. In conclusion, the analysis of the experimental data shows that besides a strong reduction of the antiferromagnetic coupling between Fe and Gd, the introduction of Cr spacers into Fe/Gd superlattice leads to modification of both structural and magnetic characteristics of the ferromagnetic layers.
36 MATERIALS SCIENCE↗
Synthesis, structure, electronic characterization, and halogenation of gold(III) phlorin complexes
The metalation chemistry of the phlorin, which is a non-aromatic tetrapyrrole macrocycle containing a single sp 3 -hybridized meso-carbon has remained underdeveloped, as compared to that of more traditional tetrapyrroles such as porphyrins, corroles and phthalocyanines. There have been few prior efforts to prepare metallophlorins, and those that have been reported have relied on either reduction or nucleophilic attack of parent metalloporphyrins, rather than direct metalation of freebase phlorin constructs. In this work, an alternate synthetic approach for preparation of gold(III) phlorin complexes that involves the first direct metalation of two different freebase phlorin derivatives (3H(Phl tBu ) and 3H(Phl F )) with AuBr 3 to produce the stable and fully isolable gold(III) phlorin complexes Au(Phl tBu ) and Au(Phl F ) is reported. The first structural characterization of a metallophlorin bearing geminal dimethyl substituents at the sp 3 -hybridized meso-carbon via X-ray crystallography is also reported. In addition to the preparation of Au(Phl tBu ) and Au(Phl F ), the UV-vis absorption and redox properties of these two gold(III) phlorins in comparison to those of their freebase homologues is also detailed. Notably, the metallophlorins are characterized by panchromatic absorbance profiles and intense and broad bands that span the long-visible and into the near-IR regions, as well as two fully reversible oxidation and reduction waves as probed by cyclic voltammetry. Lastly, the chlorination of Au(Phl tBu ) using PhI(Cl 2 ) was probed and it was found that this regioslective reaction generates monochlorinated (Au(Phl tBu Cl)) and dichlorinated (Au(Phl tBu Cl 2 )) products, which were both structurally characterized by X-ray crystallography.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Vertical Structure of Radiative Heating Rates of the MJO during DYNAMO
The vertical structure of radiative heating rates over the region of the tropi-cal Indian Ocean associated with the MJO during the DYNAMO/ARM MJO Investigation Experiment is presented. The mean and variability of heating rates during active, suppressed, and disturbed phases are determined from the Paci?c Northwest National Laboratory combined remote sensing retrieval (CombRet) from Gan Island, Maldives (0.69? S, 73.15? E). TOA and surface ?uxes from the CombRet product are compared with collocated three-hourly CERES SYN1deg Ed4A satellite retrievals. The ?uxes are correlated in time with correlation coef?cients around 0.9, yet CombRet time-mean OLR is 15 W m-2 larger. Previous work has suggested that CombRet under-samples high clouds, due to attenuation by low-level clouds and reduced instrument sensitivity with altitude. However, mean OLR differs between CombRet and CERES for all values of OLR, not just the lowest values corresponding to widespread high clouds. The discrepancy peaks for mid-range OLR, sugges-tive of precipitating, towering cumulus convective clouds, rather than strati-form cirrus clouds. Biases in the cloud-top height of thick clouds substantially contribute to the overestimate of OLR by CombRet. CombRet data is used to generate composite shortwave and longwave atmospheric heating rate pro-?les as a function of the local OLR. Though there is considerable variability in CombRet not directly related to OLR, the time-height structure of mean heating rate composites generated using OLR as the interpolant is broadly representative of tropical convective variability on intraseasonal time scales.
Shell, Karen M.↗
Coupling of regional geophysics and local soil-structure models in the EQSIM fault-to-structure earthquake simulation framework
Accurate understanding and quantification of the risk to critical infrastructure posed by future large earthquakes continues to be a very challenging problem. Earthquake phenomena are quite complex and traditional approaches to predicting ground motions for future earthquake events have historically been empirically based whereby measured ground motion data from historical earthquakes are homogenized into a common data set and the ground motions for future postulated earthquakes are probabilistically derived based on the historical observations. This procedure has recognized significant limitations, principally due to the fact that earthquake ground motions tend to be dictated by the particular earthquake fault rupture and geologic conditions at a given site and are thus very site-specific. Historical earthquakes recorded at different locations are often only marginally representative. There has been strong and increasing interest in utilizing large-scale, physics-based regional simulations to advance the ability to accurately predict ground motions and associated infrastructure response. However, the computational requirements for simulations at frequencies of engineering interest have proven a major barrier to employing regional scale simulations. In a U.S. Department of Energy Exascale Computing Initiative project, the EQSIM application development is underway to create a framework for fault-to-structure simulations. This framework is being prepared to exploit emerging exascale platforms in order to overcome computational limitations. This article presents the essential methodology and computational workflow employed in EQSIM to couple regional-scale geophysics models with local soil-structure models to achieve a fully integrated, complete fault-to-structure simulation framework. Here, the computational workflow, accuracy and performance of the coupling methodology are illustrated through example fault-to-structure simulations.
97 MATHEMATICS AND COMPUTING↗
Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA
Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.
59 BASIC BIOLOGICAL SCIENCES↗
Structural color from a coupled nanowire pair beyond the bonding and antibonding model
Optical resonances in nanostructures can be harnessed to produce a wide range of structural colors. Conversely, the analysis of structural colors has been used to clarify the nature of optical resonances. Here, we show that silicon nanowire (NW) pairs can display a wide range of structural colors by controlling their radiative coupling. This is accomplished by exciting a series of Fabry–Pérot-like modes where light is repeatedly scattered between two NWs. These modes are beyond the expectation from the conventional chemical bonding model under a quasi-electrostatic approximation, in which only bonding and antibonding modes can be formed in a pair system through modal hybridization. The additional eigenmodes found in a two-resonator system originate from the nonlinear, frequency-dependent coupling strength derived from the radiative nature of low- Q resonators. The Fabry–Pérot modes can be tuned across the entire visible frequency range by varying the distance between two NWs, leading to what we believe is a new type of universal building blocks that can provide structural color within a subwavelength footprint. The presented results pave the way toward the design and usage of highly tunable resonances that exploit the radiative coupling of high-index nanostructures.
Li, Qitong↗
Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics
Triosephosphate isomerase (TPI) deficiency is a poorly understood disease characterized by hemolytic anemia, cardiomyopathy, neurologic dysfunction, and early death. TPI deficiency is one of a group of diseases known as glycolytic enzymopathies, but is unique for its severe patient neuropathology and early mortality. The disease is caused by missense mutations and dysfunction in the glycolytic enzyme, TPI. Previous studies have detailed structural and catalytic changes elicited by disease-associated TPI substitutions, and samples of patient erythrocytes have yielded insight into patient hemolytic anemia; however, the neuropathophysiology of this disease remains a mystery. This study combines structural, biochemical, and genetic approaches to demonstrate that perturbations of the TPI dimer interface are sufficient to elicit TPI deficiency neuropathogenesis. The present study demonstrates that neurologic dysfunction resulting from TPI deficiency is characterized by synaptic vesicle dysfunction, and can be attenuated with catalytically inactive TPI. Collectively, our findings are the first to identify, to our knowledge, a functional synaptic defect in TPI deficiency derived from molecular changes in the TPI dimer interface.
59 BASIC BIOLOGICAL SCIENCES↗
Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study
The structural analysis of catechol 1,2 dioxygenase from Stutzerimonas frequens GOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfC12DO and its homologous isoA C12DO from Acinetobacter radioresistens under low ionic strength conditions. In some cases, tetramers were also reported, such as for the Rodococcus erythropolis C12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a putative candidate for bioremediation applications in polluted soils or waters.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Chemistry of Akdalaite, Al[subscript 10]O[subscript 14](OH)[subscript 2], the Isostructural Aluminum Analogue of Ferrihydrite
Abstract not provided
Parise, John B.↗
Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses
The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.
58 GEOSCIENCES↗
The Morphology and Structure of Stellar Populations in the Fornax Dwarf Spheroidal Galaxy from Dark Energy Survey Data
Using deep wide-field photometry 3 yr data (Y3) from the Dark Energy Survey (DES), we introduce a panoramic study of the Fornax dwarf spheroidal galaxy. The data discussed here—a small subset of the full survey—uniformly cover a region of 25 deg 2 centered on the galaxy to a depth of g ~ 23.5. We use these data to study the structural properties of Fornax, overall stellar population, and its member stars in different evolutionary phases. We also search for possible signs of tidal disturbance. Fornax is found to be significantly more spatially extended than what early studies suggested. No statistically significant distortions or signs of tidal disturbances were found down to a surface brightness limit of ~32.1 mag arcsec -2 . Yet, there are hints of shell-like features located ~20'–40' from the center of Fornax that may be stellar debris from past merger events. We also find that intermediate-age and young main-sequence populations show different orientation at the galaxy center and have many substructures. The deep DES Y3 data allow us to characterize the age of those young stellar substructures with great accuracy, both those previously known and those newly identified as possible overdensities in this work, on the basis of their color–magnitude diagram morphology. We find that the youngest overdensities are all found on the eastern side of Fornax, where the Fornax field population itself is slightly younger than in the west. In summary, the high-quality DES Y3 data reveal that Fornax has many rich structures and provide insights into its complex formation history.
79 ASTRONOMY AND ASTROPHYSICS↗