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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies in this paper expand on those observations through protein structure, mutagenesis and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. Finally, MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Measuring the dynamic response of the thylakoid architecture in plant leaves by electron microscopy

The performance of the photosynthesis machinery in plants, including light harvesting, electron transport, and protein repair is controlled by structural changes of the thylakoid membrane system inside the chloroplasts. In particular, the structure of the stacked grana area of thylakoid membranes is highly dynamic, changing in response to different environmental cues such as light intensity. For example, the aqueous thylakoid lumen enclosed by thylakoid membranes in grana has been documented to swell in the presence of light. However, light-induced alteration of the stromal gap in the stacked grana (partition gap) and of the unstacked stroma lamellae have not been well characterized. Light-induced changes of the entire thylakoid membrane system including the lumen in both stacked and unstacked domains as well as the partition gap are presented here, and the functional implications are discussed. This structural analysis was made possible by development of a robust semi-automated image analysis method combined with optimized plant tissue fixation techniques for transmission electron microscopy generating quantitative structural results for the analysis of thylakoid ultrastructure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic bacteria that have been engineered to produce ethanol from the cellulose and hemicellulose fractions of biomass, respectively. Although engineered strains of T. saccharolyticum produce ethanol with a yield of 90% of the theoretical maximum, engineered strains of C. thermocellum produce ethanol at lower yields (~50% of the theoretical maximum). In the course of engineering these strains, a number of mutations have been discovered in their adhE genes, which encode both alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes. To understand the effects of these mutations, the adhE genes from six strains of C. thermocellum and T. saccharolyticum were cloned and expressed in Escherichia coli , the enzymes produced were purified by affinity chromatography, and enzyme activity was measured. In wild-type strains of both organisms, NADH was the preferred cofactor for both ALDH and ADH activities. In high-ethanol-producing (ethanologen) strains of T. saccharolyticum , both ALDH and ADH activities showed increased NADPH-linked activity. Interestingly, the AdhE protein of the ethanologenic strain of C. thermocellum has acquired high NADPH-linked ADH activity while maintaining NADH-linked ALDH and ADH activities at wild-type levels. When single amino acid mutations in AdhE that caused increased NADPH-linked ADH activity were introduced into C. thermocellum and T. saccharolyticum , ethanol production increased in both organisms. Structural analysis of the wild-type and mutant AdhE proteins was performed to provide explanations for the cofactor specificity change on a molecular level. This work describes the characterization of the AdhE enzyme from different strains of C. thermocellum and T. saccharolyticum . C. thermocellum and T. saccharolyticum are thermophilic anaerobes that have been engineered to make high yields of ethanol and can solubilize components of plant biomass and ferment the sugars to ethanol. In the course of engineering these strains, several mutations arose in the bifunctional ADH/ALDH protein AdhE, changing both enzyme activity and cofactor specificity. We show that changing AdhE cofactor specificity from mostly NADH linked to mostly NADPH linked resulted in higher ethanol production by C. thermocellum and T. saccharolyticum .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Quantitative Structure–Property Relationship (QSPR) Analysis of ZrO 2 -Containing Soda-Lime Borosilicate Glasses

Quantitative structure–property relationship (QSPR) analysis is a promising approach to correlate structural features with properties of glass materials that lack long-range order and usually have complex structures. By using carefully chosen descriptors based on structural models generated from molecular dynamics (MD) simulations, correlations with properties and insights on glass behaviors can be obtained. Zirconia can significantly alter glass properties including chemical durability, even in a small amount, and hence plays an important role in vitrification of nuclear waste where long-term chemical durability is desired. In this study, borosilicate glasses with the composition of xZrO 2 –(61 – x)SiO 2 –17B 2 O 3 –18Na 2 O–4CaO with x = 0, 1, 2, 4, 6, and 8 were simulated using classical MD simulations with the recently developed composition-dependent potentials. Short-range (e.g., bond distance and coordination numbers) and medium-range (e.g., Qn distribution, network connectivity, and ring-size distribution) structural features altered by ZrO 2 were obtained and analyzed. The use of a descriptor (Fnet descriptor) that combines short-range structural characteristics, from MD simulations, and the cation-oxygen single bond strength was found to provide excellent linear correlations with the density and initial dissolution rate of these glasses. Furthermore, the results show that by combining MD simulations and QSPR analysis the composition and structural effect on the properties of complex multicomponent glasses can be elucidated, thus suggesting that this is a promising approach for future glass research and new composition design.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Stoichiometry and mechanistic implications of the MacAB-TolC tripartite efflux pump

Highlights: • The exact stoichiometry of the MacAB-TolC pump was confirmed. • Structural comparison provides a mechanism for MacA-dependent MacB activation. • Improving understanding of the regulatory mechanisms of other efflux pumps. The MacAB-TolC tripartite efflux pump is involved in resistance to macrolide antibiotics and secretion of protein toxins in many Gram-negative bacteria. The pump spans the entire cell envelope and operates by expelling substances to extracellular space. X-ray crystal and electron microscopic structures have revealed the funnel-like MacA hexamer in the periplasmic space and the cylindrical TolC trimer. Nonetheless, the inner membrane transporter MacB still remains ambiguous in terms of its oligomeric state in the functional complex. In this study, we purified a stable binary complex using a fusion protein of MacA and MacB of Escherichia coli, and then supplemented MacA to meet the correct stoichiometry between the two proteins. The result demonstrated that MacB is a homodimer in the complex, which is consistent with results from the recent complex structure using cryo-electron microscopy single particle analysis. Structural comparison with the previously reported MacB periplasmic domain structure suggests a molecular mechanism for regulation of the activity of MacB via an interaction between the MacB periplasmic domain and MacA. Our results provide a better understanding of the tripartite pumps at the molecular level.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Luminescent MOFs comprising mixed tritopic linkers and Cd(II)/Zn(II) nodes for selective detection of organic nitro compounds and iodine capture

Two CPs ([Cd{sub 3}(BTC){sub 2}(TIB){sub 2}(H{sub 2}O){sub 4}].(H{sub 2}O){sub 2}){sub n} (1) and ([Zn{sub 3}(BTC){sub 2}(TIB){sub 2}].(H{sub 2}O){sub 6}){sub n} (2) composed of tripodal linkers BTC (1,3,5-benzenetricarboxylate) and TIB (1,3,5-tris(imidazol-1-ylmethyl)benzene) were synthesized via solvothermal route and structurally characterized. Single crystal structural analysis reveals 1 possesses a novel 3D framework structure, whereas 2 represents a previously established compound. Owing to the d{sup 10} configuration of metal nodes and robust 3D frameworks, 1 and 2 exhibit excellent fluorescence properties which have been exploited to sense organic nitro compounds in vapor phase. Compound 1 demonstrates selective sensing of nitromethane over structurally similar methanol with ca. 70 and 43% fluorescence quenching in case of former and later. Similarly, 58% fluorescence quenching was observed in case of nitrobenzene over the structurally resembling toluene for which 30% quenching was observed. Compound 2 did not show any preference for nitro compounds and exhibited comparable fluorescence quenching when exposed to the vapors of nitro or other geometrically resembling organic molecules. Furthermore, adsorption experiments revealed that 1 and 2 can uptake 2.74 and 14.14 wt% molecular iodine respectively in vapor phase which can be released in organic solvents such as hexane and acetonitrile. The maximal iodine uptake in case of 1 and 2 corresponds to 0.15 and 0.80 molecules of iodine per formula unit of respective frameworks. Comprehensive structural description, thermal stability and luminescence behavior for both CPs has also been presented. - Graphical abstract: Two 3D luminescent CPs comprising mixed tripodal ligands have been hydrothermally synthesized and structurally characterized. Iodine encapsulation capacity of synthesized CPs is evaluated and their fluorescence quenching in presence of small organic molecules is exploited for sensing of nitro organics. - Highlights: • Two 3D mixed ligand coordination polymers containing Cd and Zn center are prepared. • Crystal structure and thermal stability of synthesized CPs has been described. • Photoluminescence intensity of CPs was observed to vary in presence of organic vapors. • Photoluminescence quenching in case of Cd CP is exploited to selectively sense nitro organics. • These thermally stable robust CPs are also used for iodine adsorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Anion-induced structural transformation of a sulfate-incorporated 2D Cd(II)–organic framework

A Cd(II)–organic framework {[Cd_2(tpim)_4(SO_4)(H_2O)_2]·(SO_4)·21H_2O}{sub n} (1) was synthesized by reacting CdSO{sub 4}·8/3H{sub 2}O and 2,4,5-tri(4-pyridyl)imidazole (tpim) under hydrothermal conditions. A structural analysis showed that compound 1 adopts a layered structure in which the [Cd(tpim){sub 2}]{sub n} chains are linked by sulfate anions. These 2D layers are further packed into a 3D supramolecular framework via π–π interactions. The structure contains two types of SO{sub 4}{sup 2−} anions, i.e., bridging SO{sub 4}{sup 2−} and free SO{sub 4}{sup 2−} anions, the latter of which are included in the large channels of the framework. Compound 1 exhibits interesting anion exchange behavior. In the presence of SCN{sup −} anions, both the bridging and free SO{sub 4}{sup 2−} anions in 1 were completely exchanged by SCN{sup −} ligands to form a 1D species [Cd(tpim){sub 2}(SCN){sub 2}] (1A), in which the SCN{sup –} moieties function as a monodentate ligand. On the other hand, when compound 1 was ion exchanged with N{sub 3}{sup −} anions in aqueous solution, the bridging SO{sub 4}{sup 2−} moieties remained intact, and only the free guest SO{sub 4}{sup 2−} were replaced by N{sub 3}{sup −} anions. The gas adsorption behavior of the activated compound 1 was also investigated. - Highlights: • An interesting anion-induced structural transformation of a sulfate-incorporated 2D Cd(II)–organic framework is reported. • The sulfate-incorporated 2D layer compound exhibits very different anion exchange behavior with respect to SCN{sup −} and N{sub 3}{sup −}. • Both the bridging and free SO{sub 4}{sup 2−} anions in the 2D structure were completely exchanged by SCN{sup −} ligands, resulting in the formation of a 1D species. However, in the case of N{sub 3}{sup −} anions, only the free guest SO{sub 4}{sup 2−} in the structure was replaced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions

Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of $T$ = 4 and $T$ = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3–2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1’, α1’–α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral $T$ = 4 and $T$ = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Evidence for interfacial geometric interactions at metal–support interfaces and their influence on the electroactivity and stability of Pt nanoparticles

Supported metals are widely used as industrial catalysts wherein the supports affect catalytic performances remarkably through either electronic and/or geometric interactions with the metals, and/or providing interfacial synergistic sites. Herein, we observed evidence for interfacial geometric interactions (IGIs) at Pt–C interfaces through a combination of atomic-scale structural analysis, in situ X-ray absorption fine structure, and electrochemical measurements for Pt/C model systems. The IGI has a long-range attribute and affects Pt surface atoms not only at interfacial perimeters but also adjacent to interfaces. The affected Pt surface atoms are proposed to contribute enhanced activity and stability for the oxygen reduction reaction through retarding the formation of strongly adsorbed oxygenated intermediates. Our work provides some necessary information for a better understanding of support effects and catalytically active surface sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Magnetic and dielectric characterization of Co{sub 0.9}Ni{sub 0.1}Fe{sub 2}O{sub 4} prepared by hydroxide co-precipitation method

Co{sub 1–x} Ni{sub x}Fe{sub 2}O{sub 4} (where x=0.1) were prepared by using the hydroxide co-precipitation method. An obtained precipitate was sintered at 1100°C by microwave sintering technique. The structural analysis confirms the single-phase cubic spinel structure with Fd-3m space group. The magnetic characterization was carried out at temperature 300K.Saturation magnetisation and coercivity is 77.22 and 908 Oe. Irreversibility is observed between the ZFC and FC curves at 100 Oe. The variation in the dielectric constant and loss tangent are studied at room temperature with increasing frequency. Continues decrease in the the dielectric constant with increasing frequency shows inverse dependence on frequency. Morphological and elemental studies were done by using the scanning electron microscope with EDAX.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Low-resolution refinement tools in REFMAC5

Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening. Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Porous electrodes for spectroelectrochemistry and x-ray structure analyses

An electrochemical cell that allows for in-situ structural characterization of amorphous thin film materials during the course of electrolysis using high-energy X-ray scattering (>50 keV). The compact and versatile cell employs a three-electrode configuration and minimizes X-ray scattering contributions from the cell, reference and counter electrodes, as well as the working electrode support. A large surface area working electrode has a physically robust support and is largely transparent to X-rays. This design, which utilizes a three-dimensional working electrode, also greatly improves the intensity and quality of the scattered signal compared to a two-dimensional working electrode. The in-situ cell can be used not only to investigate structural evolution during electrolysis using X-ray scattering (e.g. pair distribution function), but also to perform electrochemical potential-dependent structural analysis by extended X-ray absorption fine structure.

Kwon, Gihan↗
DOE OSTI2016

University of Nevada, Reno Graduate Certificate in Nuclear Packaging

This paper describes a new Graduate Certificate in Nuclear Packaging (GCNP). Nuclear materials are currently used for large-scale production of electricity without greenhouse gas generation, advanced medical treatments, food sterilization, and sophisticated measurement technologies. In order to benefit from these uses, nuclear materials packaging must be developed, manufactured, inspected, and maintained for storage, transfer, transport, and disposal that protect the public and the environment. The U.S. Department of Energy (DOE) Packaging Certification Program (PCP) originally offered the following ten, one-day to ten-day training courses. 1. Methods for Reviewing Safety Analysis Reports for Packages and Performing Confirmatory Analysis; 2. Welding Criteria for Shipping Containers; 3. Structural Analysis and Acceptance Criteria; 4. Quality Assurance (QA) for Radioactive Material Packaging Training; 5. Application of the American Society of Mechanical Engineers (ASME) Code to Radioactive Material Transportation Packaging; 6. ARG-US Radio Frequency Identification (RFID) System for Management of Nuclear and Radioactive Materials; 7. Packaging Operations and Maintenance; 8. Packaging Leakage Test Training; 9. Management of SARP Preparation; 10. Transport Security of Radioactive Material. These courses were designed in accordance with DOE standards. They were taught at a rigorous graduate-university level by experienced technical staff who are coordinated by Argonne, Lawrence Livermore, and Savannah River National Laboratories. The courses were taught at these Laboratories or nearby locations. The PCP courses are attended by personnel from government agencies, national laboratories, and the nuclear industry, from both inside and outside the United States. Students in these classes have generally earned undergraduate or higher degrees. These courses are designed to assist student with specialized job duties, and may provide them a competitive advantage when seeking employment or promotion in the nuclear packaging and other related fields. (authors)

36 MATERIALS SCIENCE↗
DOE OSTI2022

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer

Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗