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Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine
Abstract not provided
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.
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.
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.
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.
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.
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.
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.
The relationship between Mn oxidation state and structure in triclinic and hexagonal birnessites
Abstract not provided
Structural response of phyllomanganates to wet aging and aqueous Mn(II)
Abstract not provided
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.
Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity
Not Available
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.
The crystal structures of Ni{sub 3+x}Sn{sub 4}Zn and Ni{sub 6+x}Sn{sub 8}Zn and their structural relations to Ni{sub 3+x}Sn{sub 4}, NiSn and Ni{sub 5−δ}ZnSn{sub 4}
The crystal structures of two new compounds were determined from single-crystal X-ray diffraction measurements: Ni{sub 3+x}Sn{sub 4}Zn, (x~1.35, a=7.110(2) Å, b=4.123(1) Å, c=10.346(3) Å, β=90.23(2)°, space group I2/m, Z=2. R1=0.025, wR2=0.059 for 748 unique reflections, 35 variable parameters) and Ni{sub 6+x}Sn{sub 8}Zn, x~1.35 (a=12.379(3) Å, b=4.095(1) Å, c=12.155(3) Å, β=116.25(3)°, space group C2/m, Z=2. R1=0.026, wR2=0.052 for 1346 unique reflections, 60 variable parameters). In addition, a structural refinement was performed for Ni{sub 3+x}Sn{sub 4}, x~0.13 (a=12.264(3) Å, b=4.066(1) Å, c=5.223(2) Å, β=104.85(3)°, space group C2/m, Z=2. R1=0.019, wR2=0.046 for 617 unique reflections, 29 variable parameters). The three compounds show pronounced similarities among each other as well as to the crystal structures of surrounding binary Ni–Sn and ternary Ni–Sn–Zn compounds. In particular, the two new compounds form a homologous series with Ni{sub 3+x}Sn{sub 4}, x~0.13. They contain “Ni{sub 4}Sn{sub 4}” and “Ni{sub 2}Sn{sub 4}” building blocks which by different interconnection build up the distinct structures. Topological relations with NiSn and Ni{sub 5−δ}Sn{sub 4}Zn, δ~0.25 are evident. - Graphical abstract: Projection of the structure of Ni{sub 6+x}ZnSn{sub 8}, x~1.35 and constituent building blocks. Display Omitted - Highlights: • The crystal structures of Ni{sub 6+x}Sn{sub 8}Zn and Ni{sub 3+x}Sn{sub 4}Zn were determined using single crystal XRD. • Topological relations to Ni–Sn and Ni–Sn–Zn compounds were established and discussed. • Common structural units were identified and their interconnection patterns described.
The crystal structure, electronic, and magnetic properties of NaPd{sub 3}Ge{sub 2}
Highlights: • Correct crystal structure of NaPd{sub 3}Ge{sub 2} is solved by single crystal X-ray diffraction. • NaPd{sub 3}Ge{sub 2} is found to crystallize in the ErRh{sub 3}Si{sub 2} structure type. • NaPd{sub 3}Si{sub 2}, NaPd{sub 3}Ge{sub 2} and NaPd{sub 3}Sn{sub 2} are found to be metals down to 2 K. • All three compounds show a weak diamagnetic response down to 2 K. • Trend of p-block atom dimer breaking as function of size. - Abstract: Crystals of NaPd{sub 3}X{sub 2}, (X = Si, Ge, Sn) were synthesized and their crystal structures investigated by single crystal X-ray diffraction. The previously reported structures of NaPd{sub 3}Si{sub 2} and NaPd{sub 3}Sn{sub 2} were confirmed. NaPd{sub 3}Ge{sub 2} was found to have a different unit cell from that originally reported; therefore the structure was solved. It is an orthorhombically distorted version of the hexagonal CeCo{sub 3}Be{sub 2}-type structure, in space group Imma, with cell parameters a = 7.244(1) Å, b = 9.938(1) Å, c = 5.767(2) Å. The originally reported cell is explained through triple twinning of the true cell. The structure of NaPd{sub 3}Ge{sub 2} fits the trend of decreasing X–X dimerization as a function of increasing period from Si–Sn. All three compounds are metals showing weak diamagnetism with increasing resistivity from NaPd{sub 3}Si{sub 2}–NaPd{sub 3}Sn{sub 2}; no superconductivity is observed down to 2 K.