Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine
Abstract not provided
Pletnev, Vladimir Z.↗
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Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography
This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase
Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. In conclusion, as a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Sorting Stable versus Unstable Hypothetical Compounds: The Case of Multi-Functional ABX Half-Heusler Filled Tetrahedral Structures
Electronic structure theory has recently been used to propose hypothetical compounds in presumed crystal structures, seeking new useful functional materials. In some cases, such hypothetical materials are metastable, albeit with technologically useful long lifetimes. Yet, in other cases, suggested hypothetical compounds may be significantly higher in energy than their lowest-energy crystal structures or competing phases, making their synthesis and eventual device-stability questionable. By way of example, the focus here is on the family of 1:1:1 compounds ABX called 'filled tetrahedral structure' (sometimes called Half-Heusler) in the four groups with octet electron count: I-I-VI (e.g., CuAgSe), I-II-V (e.g., AgMgAs), I-III-IV (e.g., LiAlSi), and II-II-IV (e.g., CaZnSn). First-principles thermodynamics is used to sort the lowest-energy structure and the thermodynamic stability of the 488 unreported hypothetical ABX compounds, many of which were previously proposed to be useful technologically. It is found that as many as 235 of the 488 are unstable with respect to decomposition (hence, are unlikely to be viable technologically), whereas other 235 of the unreported compounds are predicted to be thermodynamically stable (hence, potentially interesting new materials). 18 additional materials are too close to determine. The electronic structures of these predicted stable compounds are evaluated, seeking potential new material functionalities.
36 MATERIALS SCIENCE↗
Nucleon spin structure at Jefferson Lab
In the past decade an extensive experimental program to measure the spin structure of the nucleon has been carried out in the three halls at Jefferson Lab. Using a longitudinally polarized beam scattering off longitudinally or transversely polarized {sup 3}He, NH{sub 3} and ND{sub 3} targets, the double spin asymmetries A{sub ||} and A{sub perpendicular} were measured, providing data of impressively high precision that gives a better understanding of the structure of the nucleon in the deep inelastic scattering and the valence quarks regions. The virtual photon asymmetries A{sub 1,2} and polarized structure functions g{sub 1,2} were also extracted for the proton, neutron and deuteron over large kinematic ranges, allowing the extraction of first moments and the testing of sum rules and duality.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Low temperature crystal structure and magnetic properties of RAl{sub 2}
Low temperature crystal structure and magnetic properties of RAl{sub 2} (R = Pr and Nd) have been studied using temperature dependent powder x-ray diffraction, magnetization, and heat capacity measurements. Unlike PrAl{sub 2}, NdAl{sub 2} retains cubic MgCu{sub 2}-type structure from room temperature down to 5 K, which is also confirmed from first principles electronic structure calculations. The magnetization measurements show both PrAl{sub 2} and NdAl{sub 2} order ferromagnetically at T{sub C} = 32 K and 77 K, respectively. However, the magnetization measurements show the former is a hard ferromagnet compared to the latter which is a soft ferromagnetic material. The magnetic entropy change obtained from heat capacity measurements at ΔH = 30 kOe for PrAl{sub 2} and NdAl{sub 2} are 3.15 J mol{sup −1} K{sup −1} and 1.18 J mol{sup −1} K{sup −1}, respectively.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structure and electronic properties of Cu nanoclusters supported on Mo{sub 2}C(001) and MoC(001) surfaces
The atomic structure and electronic properties of Cu{sub n} nanoclusters (n = 4, 6, 7, and 10) supported on cubic nonpolar δ-MoC(001) and orthorhombic C- or Mo-terminated polar β-Mo{sub 2} C(001) surfaces have been investigated by means of periodic density functional theory based calculations. The electronic properties have been analyzed by means of the density of states, Bader charges, and electron localization function plots. The Cu nanoparticles supported on β-Mo{sub 2} C(001), either Mo- or C-terminated, tend to present a two-dimensional structure whereas a three-dimensional geometry is preferred when supported on δ-MoC(001), indicating that the Mo:C ratio and the surface polarity play a key role determining the structure of supported clusters. Nevertheless, calculations also reveal important differences between the C- and Mo-terminated β-Mo{sub 2} C(001) supports to the point that supported Cu particles exhibit different charge states, which opens a way to control the reactivity of these potential catalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Isochronal annealing effects on local structure, crystalline fraction, and undamaged region size of radiation damage in Ga-stabilized δ-Pu
The effects on the local structure due to self-irradiation damage of Ga stabilized δ-Pu stored at cryogenic temperatures have been examined using extended x-ray absorption fine structure (EXAFS) experiments. Extensive damage, seen as a loss of local order, was evident after 72 days of storage below 15 K. The effect was observed from both the Pu and the Ga sites, although less pronounced around Ga. Isochronal annealing was performed on this sample to study the annealing processes that occur between cryogenic and room temperature storage conditions, where damage is mostly reversed. Damage fractions at various points along the annealing curve have been determined using an amplitude-ratio method, a standard EXAFS fitting, and a spherical crystallite model, and provide information complementary to the previous electrical resistivity- and susceptibility-based isochronal annealing studies. The use of a spherical crystallite model accounts for the changes in EXAFS spectra using just two parameters, namely, the crystalline fraction and the particle radius. Together, these results are discussed in terms of changes to the local structure around Ga and Pu throughout the annealing process and highlight the unusual role of Ga in the behavior of the lowest temperature anneals.
36 MATERIALS SCIENCE↗
The Impacts of Cation Stoichiometry and Substrate Surface Quality on Nucleation, Structure, Defect Formation, and Intermixing in Complex Oxide Heteroepitaxy–LaCrO3 on SrTiO3(001)
Our ability to design and fabricate electronic devices with reproducible properties using complex oxides is critically dependent on our ability to controllably synthesize these materials in thin-film form. Structure-property relationships are intimately tied to film and interface composition. Here we report on the effects of cation stoichiometry in LaCrO3 heteroepitaxial films prepared using molecular beam epitaxy. We show that LaCrO3 films grow pseudomorphically on SrTiO3(001) over an wide range of La-to-Cr atom ratios. However, the growth mode and structural quality are sensitive to the La-to-Cr ratio, with La-rich films being of considerably lower structural quality than Cr-rich films. Cation mixing occurs at the interface for all La-to-Cr ratios investigated, and is not quenched by deposition at ambient temperature. Indiffused La atoms occupy Sr sites in the substrate. The presence of defects in the SrTiO3 substrate is implicated in promoting La indiffusion by comparing the properties of LaCrO3/SrTiO3 with those of LaCrO3/Si, both prepared at ambient temperature. Additionally, pulsed laser deposition is shown to result in more extensive interfacial mixing than molecular beam epitaxy for deposition at ambient temperature on Si.
Environmental Molecular Sciences Laboratory↗
A novel optical polarization conversion structure designed by multi-layered thin film structures at the wavelength of 10.6 μm
Polarization conversion performance is one of the most important design contents of optical devices. At present, there are many ways to implement polarization conversion. However, they are mostly based on the form of split ring resonator or equivalent plasma, which are not conducive to the miniaturization of electromagnetic devices, particularly in the field of laser applications. In this paper, a novel optical polarization conversion structure has been designed by multi-layered PS/PTFE thin film structures at the wavelength of 10.6 μm based on the equivalent medium theory. Then it was verified that the proposed structure can effectively convert the linear polarized wave to circular polarized wave by the EM full-wave simulation. Compared with the current laser polarization manipulation devices, the proposed novel polarization converter has advantages of ultrathin thickness of structure, simple structure, good light transmission and no electromagnetic loss. Although the structural parameters in this paper are designed for EM wave the wavelength of 10.6 μm, the proposed design idea of the polarization conversion structure is also suitable for the electromagnetic wave at other wavelengths.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Structural insights into inhibitor binding to a fungal ortholog of aspartate semialdehyde dehydrogenase
Highlights: • Structure of an inhibitor bound to an essential fungal enzyme. • Effects of cofactor binding on oligomeric assembly. • Structure guided docking of a potent fungal enzyme inhibitor. • Structural comparison to related microbial enzymes. The aspartate pathway, uniquely found in plants and microorganisms, offers novel potential targets for the development of new antimicrobial drugs. Aspartate semialdehyde dehydrogenase (ASADH) catalyzes production of a key intermediate at the first branch point in this pathway. Several fungal ASADH structures have been determined, but the prior crystallization conditions had precluded complex formation with enzyme inhibitors. The first inhibitor-bound and cofactor-bound structures of ASADH from the pathogenic fungi Blastomyces dermatitidis have now been determined, along with a structural and functional comparison to other ASADH family members. The structure of this new ASADH is similar to the other fungal orthologs, but with some critical differences in the orientation of some active site functional groups and in the subunit interface region. The presence of this bound inhibitor reveals the first details about inhibitor binding interactions, and the flexible orientation of its aromatic ring provides helpful insights into the design of potentially more potent and selective antifungal compounds.
60 APPLIED LIFE SCIENCES↗
The relationship between Mn oxidation state and structure in triclinic and hexagonal birnessites
Abstract not provided
Ling, Florence T. (ORCID:0000000225763608)↗
Structural response of phyllomanganates to wet aging and aqueous Mn(II)
Abstract not provided
Hinkle, Margaret A. G.↗
Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer
The aldehyde dehydrogenase (ALDH) superfamily is a vast group of enzymes that catalyze the NAD + -dependent oxidation of aldehydes to carboxylic acids. ALDH16 is perhaps the most enigmatic member of the superfamily, owing to its extra C-terminal domain of unknown function and the absence of the essential catalytic cysteine residue in certain non-bacterial ALDH16 sequences. Herein we report the first production of recombinant ALDH16, the first biochemical characterization of ALDH16, and the first crystal structure of ALDH16. Recombinant expression systems were generated for the bacterial ALDH16 from Loktanella sp. and human ALDH16A1. Four high-resolution crystal structures of Loktanella ALDH16 were determined. Loktanella ALDH16 is found to be a bona fide enzyme, exhibiting NAD + -binding, ALDH activity, and esterase activity. In contrast, human ALDH16A1 apparently lacks measurable aldehyde oxidation activity, suggesting that it is a pseudoenzyme, consistent with the absence of the catalytic Cys in its sequence. The fold of ALDH16 comprises three domains: NAD+-binding, catalytic, and C-terminal. The latter is unique to ALDH16 and features a Rossmann fold connected to a protruding β-flap. The tertiary structural interactions of the C-terminal domain mimic the quaternary structural interactions of the classic ALDH superfamily dimer, a phenomenon we call “trans-hierarchical structural similarity.” ALDH16 forms a unique dimer in solution, which mimics the classic ALDH superfamily dimer-of-dimer tetramer. Small-angle X-ray scattering shows that human ALDH16A1 has the same dimeric structure and fold as Loktanella ALDH16. Finally, we suggest that the Loktanella ALDH16 structure may be considered to be the archetype of the ALDH16 family.
59 BASIC BIOLOGICAL SCIENCES↗
Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity
Not Available
Manjasetty, Babu A.↗
Three new homochiral coordination polymers involving two three-dimensional structural architectures: Syntheses, structures and magnetic properties
The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. -- Graphical abstract: The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. Highlights: • Three homochiral 3D coordination polymers were synthesized. • 1 and 2 are 3D structure with metal-D-cam helical chains pillared by pyrazine. • 3 shows a 3D homochiral framework involving 1D manganese-carboxylate chains. • Magnetic data analysis indicates that 1–3 exhibit weak antiferromagnetic coupling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗