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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Comparison of γZ-structure function models

The γZ-box is an important contribution to the proton's weak charge. The γZ-box is calculated dispersively and depends on γZ-structure functions, F{sub 1,2,3}{sup γZ}(x,Q{sup 2}). At present there is no data for these structure functions and they must be modeled by modifying existing fits to electromagnetic data. Each group that has studied the γZ-box used different modifications. The results of the PVDIS experiment at Jefferson Lab may provide a first test of the validity of each group's models. I present details of the different models and their predictions for the PVDIS result.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2011

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Structural phase transitions in EuFe[subscript 2]As[subscript 2] superconductor at low temperatures and high pressures

The crystal structure of EuFe{sub 2}As{sub 2} has been studied up to a pressure of 35 GPa and down to a temperature of 8 K using temperature dependent x-ray diffraction in a diamond anvil cell at a synchrotron source. At 4.3 GPa, we have detected a structural phase transition from a high temperature tetragonal phase with I4/mmm space group to a low temperature orthorhombic phase with Fmmm space group around 120 K. With the application of pressure at a low temperature of 10 K, the orthorhombic phase is suppressed and a phase change to a collapsed tetragonal phase with I4/mmm space group is observed at 11 GPa. This collapsed tetragonal phase is similar to the one observed at ambient temperature and pressure above 8.5 GPa. We have shown that the collapsed tetragonal phase of EuFe{sub 2}As{sub 2} has the same pressure-volume (P-V) equation of state at ambient temperature and at 10 K, implying that the high pressure phase of EuFe{sub 2}As{sub 2} has a negligible thermal expansion coefficient.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Improved quasiparticle self-consistent electronic band structure and excitons in β – LiGaO 2

The band structure of β–LiGaO 2 is calculated using the quasiparticle self-consistent QSGWˆ method where the screened Coulomb interaction Wˆ is evaluated including electron-hole interaction ladder diagrams and G is the one-electron Green's function. Improved convergence compared to previous calculations leads to a significantly larger band gap of about 7.0 eV. However, exciton binding energies are found to be large and lead to an exciton gap of about 6.0 eV if also a zero-point-motion correction of about –0.4 eV is included. Furthermore, these results are in excellent agreement with recent experimental results on the onset of absorption. Besides the excitons observed thus far, the calculations indicate the existence of a Rydberg-like series of exciton excited states, which is however modified from the classical Wannier exciton model by the anisotropies of the material and the more complex mixing of Bloch states in the excitons resulting from the Bethe-Salpeter equation. The exciton fine structure and the exciton wave functions are visualized and analyzed in various ways.

36 MATERIALS SCIENCE↗
DOE OSTI2010

Structure functions for light nuclei

We discuss the nuclear EMC effect with particular emphasis on recent data for light nuclei including {sup 2}H, {sup 3}He, {sup 4}He, {sup 9}Be, {sup 12}C, and {sup 14}N. In order to verify the consistency of available data, we calculate the {chi}{sup 2} deviation between different data sets. We find a good agreement between the results from the NMC, SLAC E139, and HERMES experiments. However, our analysis indicates an overall normalization offset of about 2% in the data from the recent JLab E03-103 experiment with respect to previous data for nuclei heavier than {sup 3}He. We also discuss the extraction of the neutron/proton structure function ratio F{sub 2}{sup n}/F{sub 2}{sup p} from the nuclear ratios {sup 3}He/{sup 2}H and {sup 2}H/{sup 1}H. Our analysis shows that the E03-103 data on {sup 3}He/{sup 2}H require a renormalization of about 3% in order to be consistent with the F{sub 2}{sup n}/F{sub 2}{sup p} ratio obtained from the NMC experiment. After such a renormalization, the {sup 3}He data from the E03-103 and HERMES experiments are in a good agreement. Finally, we present a detailed comparison between data and model calculations, which include a description of the nuclear binding, Fermi motion, and off-shell corrections to the structure functions of bound proton and neutron, as well as the nuclear pion and shadowing corrections. Overall, a good agreement with the available data for all nuclei is obtained.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T{sub 6} bovine insulin derivatives

The level of structural detail around the metal sites in Ni{sup 2+} and Cu{sup 2+} T{sub 6} insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu{sup 2+} sites in Cu insulin was followed by XANES spectroscopy. Using synchrotron radiation (SR), the crystal structures of T{sub 6} bovine insulin complexed with Ni{sup 2+} and Cu{sup 2+} were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni{sup 2+} with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu{sup 2+} as a result of the Jahn–Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu{sup 2+} is sensitive towards photoreduction when exposed to SR. During the reduction of Cu{sup 2+} to Cu{sup +}, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent radiation damage was carried out by solid embedment of Cu insulin in a saccharose matrix. At 100 K the photoreduction was suppressed by ∼15%, and it was suppressed by a further ∼30% on cooling the samples to 20 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Synthesis, structural characterization, and electronic structure of the novel Zintl phase Ba 2 ZnP 2

The novel Zintl phase dibarium zinc diphosphide (Ba 2 ZnP 2 ) was synthesized for the first time. This was accom­plished using the Pb flux technique, which allowed for the growth of crystals of adequate size for structural determination via single-crystal X-ray diffraction methods. The Ba 2 ZnP 2 com­pound was determined to crystallize in a body-centered ortho­rhom­bic space group, Ibam (No. 72). Formally, this crystallographic arrangement belongs to the K 2 SiP 2 structure type. Therefore, the structure can be best described as infinite [ZnP 2 ] 4– polyanionic chains with divalent Ba 2+ cations located between the chains. All valence electrons are partitioned, which conforms to the Zintl–Klemm concept and suggests that Ba 2 ZnP 2 is a valence-precise com­position. In conclusion, the electronic band structure of this new com­pound, com­puted with the aid of the TB–LMTO–ASA code, shows that Ba 2 ZnP 2 is an intrinsic semiconductor with a band gap of ca 0.6 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Simulation of the electronic structure of simple oxides BeO and SiO{sub 2} and complex oxides Be{sub 2}SiO{sub 4} and Be{sub 2}Si{sub x}Ge{sub 1-x}O{sub 4} with the phenacite structure

The ab initio numerical calculations of the electronic structure of simple oxides BeO and SiO{sub 2} and complex oxides Be{sub 2}SiO{sub 4} and Be{sub 2}Si{sub x}Ge{sub 1-x}O{sub 4} with the phenacite structure have been performed using the electron density functional theory. The calculations indicate that the main feature of the systems under investigation is the presence of oxygen states in both the valence and conduction bands. The splitting of the bottom of the conduction band has been revealed in the electronic structure of the Be{sub 2}Si{sub x}Ge{sub 1-x}O{sub 4} system. The splitting width is about 1.5 eV. The main contribution to the formation of a narrow subband of the conduction band comes from the 2s and 2p states of oxygen and the 4d state of germanium. Microscopic models of the spatial localization of the electron density on lower energy states of the conduction band of oxide crystals have been developed using the Wannier function technique. The reflection spectra of BeO, SiO{sub 2}, and Be{sub 2}SiO{sub 4} have been analyzed. The reported calculations of the electronic structure imply the exciton nature of the 9.7-eV reflection peak in the Be{sub 2}SiO{sub 4} crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

Crystal Structure of BamB from Pseudomonas aeruginosa and Functional Evaluation of Its Conserved Structural Features

The assembly of β-barrel Outer Membrane Proteins (OMPs) in the outer membrane is essential for Gram-negative bacteria. The process requires the β-Barrel Assembly Machine (BAM), a multiprotein complex that, in E. coli, is composed of the OMP BamA and four lipoproteins BamB-E. Whereas BamA and BamD are essential, deletion of BamB, C or E produce membrane permeability defects. Here we present the high-resolution structure of BamB from Pseudomonas aeruginosa. This protein can complement the deletion of bamB in E. coli indicating that they are functionally equivalent. Conserved structural features include an eight-bladed β-propeller fold stabilized by tryptophan docking motifs with a central pore about 8 Å in diameter at the narrowest point. This pore distinguishes BamB from related b-propellers, such as quinoprotein dehydrogenases. However, a double mutation designed to block this pore was fully functional indicating that the opening is not essential. Two loops protruding from the bottom of the propeller are conserved and mediate binding to BamA. Conversely, an additional loop only present in E. coli BamB is not required for function. A cluster of highly conserved residues in a groove between blades 6 and 7 is crucial for proper BamB folding or biogenesis. It has been proposed that BamB may bind nascent OMPs by β-augmentation to its propeller outer strands, or recognize the aromatic residue signature at the C-terminus of OMPs. However, Isothermal Titration Calorimetry experiments and structural analysis do not support these proposals. The structural and mutagenesis analysis suggests that the main function of BamB is to bind and modulate BamA, rather than directly interact with nascent OMPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structural characteristics of lipocalin allergens: Crystal structure of the immunogenic dog allergen Can f 6

Lipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central β-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space

Glycine, the simplest amino acid, is also the most polymorphous. Herein, we report the structure determination of an unknown phase of glycine which was firstly reported by Pyne and Suryanarayanan in 2001. To date, the new phase has only been prepared at 208 K as nanocrystals within ice. Through computational crystal structure prediction and powder X-ray diffraction methods, we identified this elusive phase as glycine dihydrate (GDH), representing a first report on a hydrated glycine structure. The structure of GDH has important implications for the state of glycine in aqueous solution, and the mechanisms of glycine crystallization. GDH may also be the form of glycine that comes to Earth from extraterrestrial sources.

amino acid↗
DOE OSTI2012

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.

59 BASIC BIOLOGICAL SCIENCES↗