The Community Structure of the European Network of Interlocking Directorates 2005–2010

The boards of directors at large European companies overlap with each other to a sizable extent both within and across national borders. This could have important economic, political and management consequences. In this work we study in detail the topological structure of the networks that arise from this phenomenon. Using a comprehensive information database, we reconstruct the implicit networks of shared directorates among the top 300 European firms in 2005 and 2010, and suggest a number of novel ways to explore the trans-nationality of such business elite networks. Powerful community detection heuristics indicate that geography still plays an important role: there exist clear communities and they have a distinct national character. Nonetheless, from 2005 to 2010 we observe a densification of the boards interlocks network and a larger transnational orientation in its communities. Together with central actors and assortativity analyses, we provide statistical evidence that, at the level of corporate governance, Europe is getting closer.     

The Structure of “N1, N6-Carbonyladenosine”

Abstract

Re-interpretation of the available data led to structural assignment of the title N¹, N⁶carbonyladenosine (1b) as N⁶,N⁶-carbonyldiadenosine (4b).     

The Structure of Anuran Podocyte—Determined by Ecology?

Abstract The podocytes of ten frog species with different habitat preference were investigated by scanning electron microscopy. The visceral epithelium within these species shows considerable variation in the branching mode of the cellular processes, in the number of pedicels and in the form of cell bodies. The presence of various podocyte cell forms within anurans of one family (e.g. within Ranidae and Discoglossidae) indicates that podocytic structure is not manifested phylogenetically. The complexity of processes and pedicel numbers are high in glomeruli of terrestrial and semiterrestrial frogs but low in aquatic and semiaquatic animals. Consequently, podocyte structure is (a) correlated with environmental conditions and (b) plays an important role in osmoregulation. Furthermore, since podocytes are suggested to serve as stabilizers of glomerular vessels, the cells of the visceral epithelium provide the structural basis for regulation of glomerular filtration rate, e.g. for glomerular intermittency.     

The Solution NMR Structure of 2′-O-Methyl CGCGCG RNA Duplex

Abstract

Complete assignments of nonexchangeable protons in ¹H NMR spectra of 2′-O-methyl-CGCGCG complemented by its analysis of ¹³C and ³¹P NMR spectra revealed A-RNA double helical structure in low salt solution.     

The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity?

The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.     

The Solution Structure of the C-Terminal Ig-like Domain of the Bacteriophage λ Tail Tube Protein

Immunoglobulin (Ig)-like domains are found frequently on the surface of tailed double-stranded DNA bacteriophages, yet their functional role remains obscure. Here, we have investigated the structure and function of the C-terminal Ig-like domain of gpV (gpV_C), the tail tube protein of phage λ. This domain has been predicted through sequence similarity to be a member of the bacterial Ig-like domain 2 (Big_2) family, which is composed of more than 1300 phage and bacterial sequences. Using trypsin proteolysis, we have delineated the boundaries of gpV_C and have shown that its removal reduces the biological activity of gpV by 100-fold; thus providing a definitive demonstration of a functional role for this domain. Determination of the solution structure of gpV_C by NMR spectroscopy showed that it adopts a canonical Ig-like fold of the I-set class. This represents the first structure of a phage-encoded Ig-like domain and only the second structure of a Big_2 domain. Structural and sequence comparisons indicate that the gpV_C structure is more representative of both the phage-encoded Big_2 domains and Big_2 domains in general than the other available Big_2 structure. Bioinformatics analyses have identified two conserved clusters of residues on the surface of gpV_C that may be important in mediating the function of this domain.     

The Effects of Lanthanoid on the Structure–Function of Lactate Dehydrogenase from Mice Heart

The activity of lactate dehydrogenase (LDH, EC1.1.1.27) is often changed upon inflammatory responses in animals. Lanthanoid (Ln) was shown to provoke various inflammatory responses both in rats and mice; however, the molecular mechanism by which Ln³⁺ exert its toxicity has not been completely understood, especially that we know little about the mechanism of the interaction between Ln with 4f electron shell and alternation valence and LDH. In this report, we investigated the mechanisms of LaCl₃, CeCl₃, and NdCl₃ on LDH activity in vivo and in vitro. Our results showed that La³⁺, Ce³⁺, and Nd³⁺ could significantly activate LDH in vivo and in vitro; the order of activation was Ce³⁺?>?Nd³⁺?>?La³⁺?>?control. The affinity of LDH for Ce³⁺ was higher than Nd³⁺ and La³⁺; the saturated binding sites for Ce³⁺ on the LDH protein were 1.2 and for La³⁺ and Nd³⁺ 1.55. Ln³⁺ caused the reduction of exposure degree of cysteine or tryptophan/tyrosine of LDH, the increase of space resistance, and the enhancement of α-helix in secondary structure of LDH, which was greatest in Ce³⁺ treatment, medium in Nd³⁺ treatment, and least in La³⁺ treatment. It implied that the changes of structure–function on LDH caused by Ln³⁺ were closely related to the characteristics of 4f electron shell and alternation valence in Ln.     

The Novel Three-Dimensional Structure of Native Human α2-Macroglobulin and Comparisons with the Structure of the Methylamine Derivative

A three-dimensional reconstruction of α₂-macro-globulin (α₂M) was computed from stain images. The structure appears to have point group symmetry 222 and, as also revealed by a tilt experiment, has the gross shape of a oval that displays a ∼90° twist in the body of the molecule. The reconstruction reveals a novel structure that consists of two Z-shaped components arranged in opposite orientation. These shapes are interconnected by two bridges at the elbow bends of the Z and by two arch-like features that join their ends. The molecule has dimensions of ∼190 × 125 × 120 Å that encloses a 90° twisted ellipsoidal shaped central cavity of 70 × 35 Å. The cavity has four small openings arranged in a staggered configuration that extend to the outside. Serial slices of α₂M and α₂M-methylamine show that the bodies of the structures appear to be twisted in the opposite orientation. It is proposed that the four thioester bonds in the native molecule are responsible for maintaining its twisted configuration and that their cleavage with methylamine results in the structure becoming twisted in the opposite orientation. A comparison of average images derived from unstained particles of monoclonal Fab-labeled α₂M and α₂M-methylamine is consistent with this proposal. This unusual change in the handedness of α₂M may have an important role in the encapsulation of the proteinase.     

The Higher Structure of Chromatin in the LCR of the β-Globin Locus Changes during Development

The β-globin locus control region (LCR) is able to enhance the expression of all globin genes throughout the course of development. However, the chromatin structure of the LCR at the different developmental stages is not well defined. We report DNase I and micrococcal nuclease hypersensitivity, chromatin immunoprecipitation analyses for histones H2A, H2B, H3, and H4, and 3C (chromatin conformation capture) assays of the normal and mutant β-globin loci, which demonstrate that nucleosomes at the DNase I hypersensitive sites of the LCR could be either depleted or retained depending on the stages of development. Furthermore, MNase sensitivity and 3C assays suggest that the LCR chromatin is more open in embryonic erythroblasts than in definitive erythroblasts at the primary- and secondary-structure levels; however, the LCR chromatin is packaged more tightly in embryonic erythroblasts than in definitive erythroblasts at the tertiary chromatin level. Our study provides the first evidence that the occupancy of nucleosomes at a DNase I hypersensitive site is a developmental stage-related event and that embryonic and adult cells possess distinct chromatin structures of the LCR.     

Structure of Bovine αs-Casein

The secondary structure of bovine α_s-casein and chemically modified α_s-casein in various solvents was investigated by infrared absorption spectrum and optical rotatory dispersion measurements. Amino groups of α_s-casein were either succinylated or acetylated, and carboxyl groups were either methylated or ethylated. Acetylated- and ethylated-α_s-caseins are insoluble in water. Water-soluble samples have unordered structure in water. In organic solvents, such as 2-chloroethanol and ethylene glycol, they have about 50% α-helical fraction. On the other hand, it was found that methylated-α_s-casein had two infrared absorption peaks centered at 1625 and 1643 cm^?1 in D₂O-CH₃OD mixed solvent. This fact may be connected with the presence of β-structure. In the case of solid film of this sample, cast from solution containing CH₃OH, the presence of β-structure was indicated, too. The authors attempted to explain the formation of β-structure in methylated-α_s-casein in terms of the electrostatic interactions due to the differences in the net charge between methylated and unmodified α_s-caseins.     

The Refined Crystal Structure of Toxic Shock Syndrome Toxin-1 at 2.07 Å Resolution

The pyrogenic toxin toxic shock syndrome toxin-1 fromStaphylococcus aureusis a causative agent of the toxic shock syndrome disease. It belongs to a family of proteins known as superantigens that cross-link major histocompatibility class II molecules and T-cell receptors leading to the activation of a substantial number of T cells. The crystal structure of this protein has been refined to 2.07 Å with anR_crystvalue of 20.4% for 51,240 reflections. The final model contains three molecules in the asymmetric unit with good stereochemistry and a root-mean-square deviation of 0.009 Å and 1.63° from ideality for bond lengths and bond angles, respectively. The overall fold is considerably similar to that of other known microbial superantigens (staphylococcal enterotoxins). However, a detailed structural analysis shows that toxic shock syndrome toxin-1 lacks several structural features that affect its specificity for Vβ elements of the T-cell receptor and also its recognition by major histocompatibility class II molecules.     

The Binding of Benzopyranes to Human Serum Albumin. A Structure–Affinity Study

The binding of several benzopyranes to serum albumin was studied by equilibrium dialysis at pH7.4 in a 67mM sodium phosphate buffer at 37°C. The equilibrium data were analyzed using a computer program for curve fitting. The binding isotherm for warfarin, 4-hydroxycoumarin, 4-chromanol, coumarin, 3-acetylcoumarin, and benzoic acid can be described by two stoichiometric dissociation constants. Elimination of the 4-hydroxyl group in the coumarin chemical structures decreases the binding affinity of the compounds on the primary binding site of serum albumin, with 4-chromanol the smallest ligand which binds to seroalbumin with high affinity. Thus, the affinity of 4-benzopyranol and the 4-hydroxybenzopyranones greater than that of benzopyranones. On the other hand, elimination of the 2-oxo group in the benzopyranone chemical structures decreases affinity for the secondary binding site.     

The Structure and Diversity of α1-Acid Glycoprotein/Orosomucoid Gene in Africans

Human orosomucoid (ORM), or α₁-acid glycoprotein, is known to be controlled by duplicated and triplicated genes on chromosome 9, encoding ORM1 and ORM2 proteins. In this study, the structure and diversity of the ORM gene were investigated in 16 Sub-Saharan Africans, who originated from widely dispersed locations in Africa. The duplicated ORM1-ORM2 gene was observed in all 16 samples. ORM1*S1(2), characterized by an ORM2 gene-specific sequence in intron 5, was common in Africans. Three Africans showed the duplication of the ORM1 gene. The organization of the triplicated ORM1A-ORM1B-ORM2 gene was established in two Africans. The recombination breakpoints resulting in the ORM1 duplication lay within a small genomic interval around exon 1 of the ORM1B gene. The duplication of the ORM2 gene reported previously was not detected in this population sample. Several single-nucleotide polymorphisms were observed in the ORM2 gene. The rearrangement of the ORM gene is likely to occur often in Africans.     

The Three-Dimensional Structure of Aspergillus niger Pectin Lyase B at 1.7-? Resolution

The three-dimensional structure of Aspergillus niger pectin lyase B (PLB) has been determined by crystallographic techniques at a resolution of 1.7 Å. The model, with all 359 amino acids and 339 water molecules, refines to a final crystallographic R factor of 16.5%. The polypeptide backbone folds into a large right-handed cylinder, termed a parallel β helix. Loops of various sizes and conformations protrude from the central helix and probably confer function. The largest loop of 53 residues folds into a small domain consisting of three antiparallel β strands, one turn of an α helix, and one turn of a 3₁₀ helix. By comparison with the structure of Erwinia chrysanthemi pectate lyase C (PelC), the primary sequence alignment between the pectate and pectin lyase subfamilies has been corrected and the active site region for the pectin lyases deduced. The substrate-binding site in PLB is considerably less hydrophilic than the comparable PelC region and consists of an extensive network of highly conserved Trp and His residues. The PLB structure provides an atomic explanation for the lack of a catalytic requirement for Ca²⁺ in the pectin lyase family, in contrast to that found in the pectate lyase enzymes. Surprisingly, however, the PLB site analogous to the Ca²⁺ site in PelC is filled with a positive charge provided by a conserved Arg in the pectin lyases. The significance of the finding with regard to the enzymatic mechanism is discussed.     

Structure of pulmonary surfactant membranes and films: The role of proteins and lipid–protein interactions

The pulmonary surfactant system constitutes an excellent example of how dynamic membrane polymorphism governs some biological functions through specific lipid–lipid, lipid–protein and protein–protein interactions assembled in highly differentiated cells. Lipid–protein surfactant complexes are assembled in alveolar pneumocytes in the form of tightly packed membranes, which are stored in specialized organelles called lamellar bodies (LB). Upon secretion of LBs, surfactant develops a membrane-based network that covers rapidly and efficiently the whole respiratory surface. This membrane-based surface layer is organized in a way that permits efficient gas exchange while optimizing the encounter of many different molecules and cells at the epithelial surface, in a cross-talk essential to keep the whole organism safe from potential pathogenic invaders.The present review summarizes what is known about the structure of the different forms of surfactant, with special emphasis on current models of the molecular organization of surfactant membrane components. The architecture and the behaviour shown by surfactant structures in vivo are interpreted, to some extent, from the interactions and the properties exhibited by different surfactant models as they have been studied in vitro, particularly addressing the possible role played by surfactant proteins. However, the limitations in structural complexity and biophysical performance of surfactant preparations reconstituted in vitro will be highlighted in particular, to allow for a proper evaluation of the significance of the experimental model systems used so far to study structure–function relationships in surfactant, and to define future challenges in the design and production of more efficient clinical surfactants.     

The Patterns of Secretory Structure and Their Relation to Hypericin Content in Hypericum

金丝桃属植物分泌结构的类型和金丝桃素含量的相关性 吕洪飞^1,2 沈宗根¹ 李景原¹ 胡正海^1**     

The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase Vo Proton Channel

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The 1.8 Å Resolution Structure of Hevamine,a Plant Chitinase/Lysozyme,and Analysis of the Conserved Sequence and Structure Motifs of Glycosyl Hydrolase Family 18

The three-dimensional structure of hevamine, a plant enzyme with chitinase and lysozyme activity, has been refined at 1.8 Å resolution to an R-factor of 14.9% and a freeR-factor of 19.6%. The final model consists of all 273 amino acid residues and 206 ordered water molecules. Two non-prolinecis-peptides were identified, involving Phe32 and Trp255, both of which are implicated in substrate binding.Other glycosyl hydrolase family 18 proteins with known three-dimen sional structure are bacterial chitinase A, endo-β-N-acetylglucosaminidase F₁, endo-β-N-acetylglucosaminidase H, and the two plant proteins concanavalin B and narbonin, which have no known enzymatic activity. All these structures contain a (βα)₈barrel fold, with the two family 18 consensus regions roughly corresponding to the third and fourth barrel strands. This confirms the grouping of these proteins into family 18, which was only based on weak and local sequence similarity. The substrate specificity of the enzymes is determined by the loops following the barrel strands that form the substrate binding site. All enzymes have an aspartic acid and a glutamic acid residue in positions identical with Asp 125 and the catalytic Glu127 of hevamine. The lack of chitinase activity of concanavalin B and narbonin can be explained by the absence of one of these carboxylate groups, and by differences in the loops that form the substrate-binding cleft in hevamine.