Syntheses, structures and properties of copper(II) complexes containing N-(2-hydroxybenzyl)-amino amide ligands

Four copper(II) complexes containing the reduced Schiff base ligands, namely, N-(2-hydroxybenzyl)-glycinamide (Hsglym) and N-(2-hydroxybenzyl)-l-alaninamide (Hsalam) have been synthesized and characterized. The crystal structures of [Cu₂(sglym)₂Cl₂] (1), [Cu₂(salam)₂(NO₃)₂] · H₂O (3), [Cu₂(salam)₂(NO₃)(H₂O)](NO₃) · 1.5H₂O (4), [Cu₂(salam)₂](ClO₄)₂ · 2H₂O (5) show that the Cu(II) atoms are bridged by two phenolato oxygen atoms in the dimers. The sglym ligand bonded to Cu(II) in facial manner while salam ligand prefers to bind to Cu(II) in meridonal geometry. Variable temperature magnetic studies of 3 showed it is antiferromagnetic. These Cu(II) complexes and [Cu₂(sglym)₂(NO₃)₂] (2), exhibit very small catecholase activity as compared to the corresponding complexes containing acid functional groups.     

Chlorophyll a is the crucial redox sensor and transmembrane signal transmitter in the cytochrome b6f complex. Components and mechanisms of state transitions from the hydrophobic mismatch viewpoint

The cytochrome (cyt) b₆f complex is involved in the transmembrane redox signaling that triggers state transitions in cyanobacteria and chloroplasts. However, the components and molecular mechanisms are still unclear. In an attempt to solve this long-standing problem, we first focused on the unknown role of a single chlorophyll a (Chla) in cyt b₆f with a new approach based on Chla structural properties. Various b₆f X-ray crystal structures were analyzed to identify their differences, which correlate with differences in Chla molecular volume. We found that the distance of the Rieske [2Fe-2S] cluster to Chla correlates with the distance between a pair of residues at the Q_o-site and the distance between a pair of residues at the opposite membrane side. These correlations were accompanied by the rotation of a key peripheral residue and by changes in the hydrophobic thickness of cyt b₆f. Parallel analysis of cyt bc₁ crystal structures allowed us to conclude that Chla acts as the crucial redox sensor and transmembrane signal transmitter in b₆f for changes in the plastoquinone pool redox state. The hydrophobic mismatch induced by the changed hydrophobic thickness of cyt b₆f is the driving force for the structural reorganizations of the photosynthetic apparatus during induction and the progression of state transitions in cyanobacteria and chloroplasts. A mechanism for LHCII kinase activation in chloroplasts is also proposed. Our understanding of the dynamic structural changes in bc-complexes during turnover at the Q_o-site and state transitions is augmented by the time-sequence ordering of 56 bc crystal structures.     

Comparison of native and non‐native ubiquitin oligomers reveals analogous structures and reactivities

Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post‐translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non‐enzymatic methods to synthesize Ub chains of well‐defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non‐native linkages; however, few studies have examined the extent to which non‐native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non‐native linkages. Using small‐angle X‐ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non‐native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady‐state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non‐native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non‐native linkages can serve as surrogate substrates for explorations of Ub function.     

Comparative analyses of quaternary arrangements in homo‐oligomeric proteins in superfamilies: Functional implications

A comprehensive analysis of the quaternary features of distantly related homo‐oligomeric proteins is the focus of the current study. This study has been performed at the levels of quaternary state, symmetry, and quaternary structure. Quaternary state and quaternary structure refers to the number of subunits and spatial arrangements of subunits, respectively. Using a large dataset of available 3D structures of biologically relevant assemblies, we show that only 53% of the distantly related homo‐oligomeric proteins have the same quaternary state. Considering these homologous homo‐oligomers with the same quaternary state, conservation of quaternary structures is observed only in 38% of the pairs. In 36% of the pairs of distantly related homo‐oligomers with different quaternary states the larger assembly in a pair shows high structural similarity with the entire quaternary structure of the related protein with lower quaternary state and it is referred as “Russian doll effect.” The differences in quaternary state and structure have been suggested to contribute to the functional diversity. Detailed investigations show that even though the gross functions of many distantly related homo‐oligomers are the same, finer level differences in molecular functions are manifested by differences in quaternary states and structures. Comparison of structures of biological assemblies in distantly and closely related homo‐oligomeric proteins throughout the study differentiates the effects of sequence divergence on the quaternary structures and function. Knowledge inferred from this study can provide insights for improved protein structure classification and function prediction of homo‐oligomers. Proteins 2016; 84:1190–1202. © 2016 Wiley Periodicals, Inc.     

Types of interfaces for homodimer folding and binding

Homodimers have a role in catalysis and regulation through the formation of stable interfaces. These interfaces are formed through different folding mechanisms such as 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI). Therefore, it is of interest to understand folding mechanism using structural features at the interfaces. Several studies have documented the significance of structural features for the understanding of homodimer folding mechanisms. However, the known features provide limited information for understanding homodimer folding mechanisms. Hence, we created an extended dataset of 47 homodimers (twenty eight 2S, twelve 3SMI and seven 3SDI) to examine the types of interfaces in protein homodimers. 2S are usually small sized, 3SMI are often medium sized and 3SDI often exist as large sized proteins. The ratio of interface to total (I/T) residue is large in 2S and small in 3SMI and 3SDI. Hence, we used I/T measure to group 2S, 3SMI and 3SDI into categories with large I/T (≫ 50%), moderate I/T (50 - 25%) and small I/T (≪ 25%) interfaces. The grouping is further sub-grouped based on the type of physical interaction visualized at the interface using representations in two dimensions (2D). 2D representation of the interface shows eight different forms of interactions in these homodimers. 2S homodimers frequently have large I/T and thus, utilize the entire protein structure in the formation of the interface where the individual subunits are heavily inter communicated with each other. This is not true in the case of 3SMI and 3SDI. 3SMI subunits usually interact with each other at the interface with a gentle touch-like contact and hence, they have low I/T ratio. 3SDI are often quite different in interaction compared to 3SMI and their subunits do deeply interact at the interface with only one part of the surface and hence also having low I/T ratio.     

Supramolecular salts containing the anionic [Ge(C2O4)3] complex and heteroaromatic amines

The crystalline compounds (Hbipy)₂[Ge(C₂O₄)₃] (1) and (Hphen)₂[Ge(C₂O₄)₃] · 2(H₂O) (2) [Hbipy⁺ is the 2,2′-bipyridinium cation (C₁₀H₉N₂), and Hphen⁺ is the 1,10′-phenathrolinium cation (C₁₂H₉N₂)] were isolated from mild hydrothermal syntheses and their structures were elucidated from single-crystal X-ray diffraction. The two compounds were further characterised by vibrational spectroscopy (FT-IR and FT-Raman), thermogravimetric analysis (TGA) and CHN elemental composition. Compounds 1 and 2 comprise the tris(oxalato-O,O′)germanate dianion complex, [Ge(C₂O₄)₃]²⁻, which co-crystallises with Hbipy⁺ (in 1), or Hphen⁺ and water molecules (in 2). In 1, the germanium oxalate anionic complex, [Ge(C₂O₄)₃]²⁻, and the Hbipy⁺ organic residues interact mutually via N-H?O hydrogen bonding interactions, leading to supramolecular discrete hydrogen-bonded units which are further interconnected via π-π stacking. Compound 2, on the other hand, exhibits a more complex hydrogen bonding network due to the presence of the water molecules of crystallisation which, along with π-π stacking between neighbouring Hphen⁺ residues, mediate the crystal packing.     

Effect of outer sphere anions on the structure and color of nitrosylpentaamminechromium complex

Three kinds of crystalline compounds containing the nitrosylpentaamminechromium complexes [Cr(NO)(NH₃)₅]²⁺(A) were obtained: chloride ACl₂ (red-orange), chloride perchlorate ACl(ClO₄) (brown), and perchlorate A(ClO₄)₂ (green). The cause of the color change of the complex A with the change of outer sphere anions was sought using X-ray structural data of ACl₂, ACl(ClO₄), and A(ClO₄)₂. Crystal data: ACl₂, orthorhombic, space group Cmcm, a=10.0236 (9) Å, b=9.098 (3) Å, c=10.357(1) Å, V=944.5 (5) ų, Z=4; ACl(ClO₄), tetragonal, space group P4/nmm, a=7.6986 (8) Å, c=9.9566(8) Å, V=590.1 (1) Å^3,Z=2; A(ClO₄)₂, orthorhombic, space group Pnma, a=15.760 (2) Å, b=11.480(2) Å, c=7.920 (2) Å, V=1432.9 (4) ų, Z=4. The complex cation in ACl₂ has a distorted octahedral structure with a linear CrNO moiety. The short CrN (nitrosyl) distance of 1.692 (7) Å indicates the presence of multiple bonding between the chromium atom and the nitrogen atom in the nitrosyl group. The interatomic distances and angles within the complex cations hardly change with the change of the counter anions, while the distances between the complex cations in each crystal increase in the order ACl₂<ACl(ClO₄)<A(ClO₄)₂. The bulky perchlorate anions seems to separate the complex cations, while smaller chloride anions are not large enough to separate them. The distance (3.213(5) Å) between O(NO) and N(NH₃ in the adjacent complex cation) is rather short in the crystal of ACl₂, and there are six hydrogen bonds, where the NO group is surrounded by four NH₃ ligands. The distance (4.002(5) Å) between O(NO) and N(NH₃) is much longer in the crystal of A(ClO₄)₂, indicating the presence of no hydrogen bonding. In the crystal of ACl(ClO₄) the distance (3.452(4) Å) between O(NO) and N(NH₃) is in between those of ACl₂ and A(ClO₄)₂. The presence of hydrogen bonding between O(NO) and N(NH₃ in the adjacent complex cation) seems to cause the color change with the change of outer sphere anions.     

集球藻对盐胁迫的生理适应及细胞结构变化

盐胁迫是影响荒漠区土壤藻类生存的重要环境因子。集球藻是一种广泛分布于生物土壤结皮中的球状绿藻, 能够积累红色素(如虾青素)和油滴, 显示出其独特的生理特性和潜在的应用价值。目前对集球藻的生理、细胞结构以及色素积累的研究非常匮乏。以从荒漠生物结皮中分离的一种集球藻为材料, 在实验室条件下研究盐胁迫对集球藻生物量、光合活性、膜脂过氧化产物丙二醛含量、细胞可溶性蛋白质含量和可溶性糖含量以及细胞结构的影响。研究结果表明, 与对照处理相比, 盐胁迫导致集球藻生物量和光合活性的显著降低, 细胞可溶性蛋白和可溶性糖呈现一定的积累。同时盐处理导致集球藻膜脂丙二醛含量大量增加, SOD和CAT 活性升高。研究还表明, 对照处理下细胞结构完整, 细胞器形态清晰, 生长后期有大量脂肪体积累。在盐处理下藻体细胞形态结构出现阶段性破坏特征和脂肪体以及淀粉粒的积累, 此外细胞器结构模糊和消失, 细胞出现质壁分离和空泡化等。研究为更好地揭示集球藻在盐胁迫环境中的生理适应特性、微结构特征以及色素积累机制具有重要的科学意义, 并为该藻的基础和应用研究提供实验资料。       

Synthesis, characterization and X-ray structure of [Pd(SO4)(dppp)] · H2O, a catalyst for the CO-ethene copolymerization [dppp = 1,3-bis(diphenylphosphino)propane]

The title complex has been synthesized by first reacting dppp with Pd(AcO)₂ in acetone and then with NaHSO₄ in water. It has been characterized by IR, NMR and X-ray diffraction studies. The ³¹P NMR spectrum in DMSO shows a singlet at 16.62 ppm indicating that the two P atoms are equivalent and that the sulfate anion is weakly coordinating. The X-ray structure shows that the Pd atom is surrounded in an almost regular square planar environment by the two P atoms and by two O atoms of the sulfate anion and that the neutral complex is accompanied by a water molecule of crystallization. The Pd-P distances (2.217(1) and 2.233(1)) and the P-Pd-P angle (90.78(3)°) are close to those found in other complexes where the chelating diphosphine is the same. Also the Pd-O distances and the O-Pd-O bond angle are comparable to those of other relevant chelating ligands.In MeOH, the title complex, in combination with H₂SO₄, catalyses the CO-ethene copolymerization. The productivity reaches a maximum upon increasing the H₂SO₄/Pd ratio up to ca. 470 (7650 g of polyketone/g Pd h at 90 °C and 45 atm, CO/ethene 1/1). The viscosity of the polyketone passes through a maximum of 0.95 dL/g in m-cresol when the above ratio is ca. 100. It has been proposed that acid promotes the copolymerization process by destabilizing the β- and γ-chelates intermediates involved in chain growing process, thus favoring the insertion of the monomers. At relatively high acid concentration the lowering of productivity and viscosity suggests that the sulfate anion competes with the monomers for the coordination to the metal center.In H₂O-CH₃COOH as a solvent the productivity strongly depends on the H₂O/CH₃COOH ratio, as it passes through a maximum of 12 000 g polymer/g Pd h in the presence of ca. 60% of H₂O. The productivity is significantly lower than that found when the acetate and chloride analogues are used (27 000 g polyketone/g Pd · h). Thus, it is likely that the sulfate anion assists significantly the copolymerization process even though the concentration of CH₃COOH/CH₃COO⁻ is much preponderant.