Three-dimensional EM structure of the ectodomain of integrin {alpha}V{beta}3 in a complex with fibronectin

Integrins are alphabeta heterodimeric cell surface receptors that mediate transmembrane signaling by binding extracellular and cytoplasmic ligands. The ectodomain of integrin alphaVbeta3 crystallizes in a bent, genuflexed conformation considered to be inactive (unable to bind physiological ligands in solution) unless it is fully extended by activating stimuli. We generated a stable, soluble complex of the Mn(2+)-bound alphaVbeta3 ectodomain with a fragment of fibronectin (FN) containing type III domains 7 to 10 and the EDB domain (FN7-EDB-10). Transmission electron microscopy and single particle image analysis were used to determine the three-dimensional structure of this complex. Most alphaVbeta3 particles, whether unliganded or FN-bound, displayed compact, triangular shapes. A difference map comparing ligand-free and FN-bound alphaVbeta3 revealed density that could accommodate the RGD-containing FN10 in proximity to the ligand-binding site of beta3, with FN9 just adjacent to the synergy site binding region of alphaV. We conclude that the ectodomain of alphaVbeta3 manifests a bent conformation that is capable of stably binding a physiological ligand in solution.     

When being straight bends rules: a rationale for the linear FeNO unit in the low-spin square-pyramidal {FeNO}7 tetracyanonitrosylferrate(2-) anion

All low-spin S=1/2 heme-NO complexes feature FeNO angles of about 140 degrees . In contrast, the square-pyramidal [Fe(CN)(4)(NO)](2-) complex features an exactly linear {FeNO}(7) unit. We have sought here to determine a possible, simple molecular orbital (MO) rationale for these structural variations. A DFT-based (DFT=density functional theory) MO analysis shows that the linearity of the latter stems from the greater pyramidalization of the Fe center, relative to nitrosylheme, which results in significant differences in d orbital hybridization. Thus, the singly occupied molecular orbital (SOMO) of [Fe(CN)(4)(NO)](2-) , while primarily Fe dz2-based, also has a significant amount of 4p(z) character, which makes it less stereochemically active, accounting for the linearity of the FeNO unit.     

Density functional theory studies on a designed photoactive {FeNO} nitrosyl and the corresponding photoinactive {FeNO} species: Insight into the origin of NO photolability

Density functional theory (DFT) and time-dependent DFT (TDDFT) studies on a photoactive {FeNO}⁶ nitrosyl [(PaPy₃)Fe(NO)](ClO₄)₂ (1) and the corresponding light-insensitive {FeNO}⁷ species [(PaPy₃)Fe(NO)](ClO₄) (2) have been carried out to determine the origin of NO photolability of 1. The iron center in these two nitrosyls formally exists in 2+ oxidation state and the difference in π-accepting ability of NO⁺ in 1 versus NO in 2 greatly affects the extent of NO photolability of these two nitrosyls. Low energy transitions from the carboxamido/π(FeNO) to the FeNO antibonding molecular orbitals lead to release of NO from 1 upon exposure to visible light. The decreased π-accepting ability of the NO moiety in 2 does not favor such transitions; instead transitions from orbitals centered at the FeNO unit to the π_py orbitals of the ligand frame become more favorable and the photolability of NO is lost in 2.     

The unexpected reactions of [RuCl3(2mqn)NO] (H2mqn=2-methyl-8-quinolinol) with 2-chloro-8-quinolinol (H2cqn) and of [RuCl(2cqn)(2mqn)NO] on photoirradiation

The reaction of [RuCl₃(2mqn)NO]⁻ (H2mqn=2-methyl-8-quinolinol) with 2-chloro-8-quinolinol (H2cqn) afforded cis-1 [RuCl(2cqn)(2mqn)NO] (the oxygen of 2cqn is trans to the NO) (complex 1), cis-1 [RuCl(2cqn)(2mqn)NO] (the oxygen of 2mqn is trans to the NO) (complex 2) and a 1:1 mixture of cis-2 [RuCl(2cqn)(2mqn)NO] (the oxygen of 2mqn is trans to the NO) and cis-2 [RuCl(2cqn)(2mqn)NO] (the oxygen of 2cqn is trans to the NO) (complex 3). The reaction was compared with that of [RuCl₃(2mqn)NO]⁻ with 8-quinolinol (Hqn) or 5-chloro-8-quinolinol (H5cqn). Photoirradiation reaction of complex 1 at room temperature in deaerated CH₂Cl₂ in the presence of NO gave trans-[RuCl(2cqn)(2mqn)NO] (the Cl is trans to the NO) and complex 2 with recovery of complex 1. The reaction was contrasted with that of cis-1 [RuCl(qn)(2mqn)NO] or cis-1 [RuCl(5cqn)(2mqn)NO]. The crystal structure of complex 1 was determined by X-ray diffraction. The reactions were examined under consideration of atomic charge of the phenolato oxygen in 8-quinolinol and its derivatives calculated at the restricted Hartree-Fock/6-311G** level.     

Proton NMR study of triantennary complex type N-linked glycan chains: assignment of proton chemical shifts of the {beta}-Man residue in a basic unit of the triantennary glycan chain having a GlcNAc{beta}1->6Man{alpha}1->6Man{beta}->sequence

The chemical shifts of ring protons of the ß-Man residuein a triantennary complex type N-linked glycan chain havinga GlcNAcß1     

Characterization and adaptive evolution of {alpha}-tubulin genes in the Miscanthus sinensis complex (Poaceae)

To investigate the organization of and mode of selection in the α-tubulin genes, full-length α-tubulin genes were cloned from four intraspecific taxa of Miscanthus sinensis and its close relatives M. floridulus and M. condensatus using standard polymerase chain reaction (PCR) and rapid amplification of genomic ends (RAGE)-PCR strategies. Genealogical analysis of angiosperms recovered a monophyletic group of Miscanthus α-tubulin genes, which is homologous to the tua5 locus of maize. Two clusters of nearly equal frequency revealed paraphyly within each Miscanthus taxon. Between-cluster recombination was frequent. Additional evidence for co-occurrence of two haplotypes within individuals and a large-scale crossover all suggested a likely allelic relationship between the Miscanthus clusters. Given a long between-species divergence time in Miscanthus, wide occurrence of the trans-species polymorphisms in α-tubulin genes and the approximately equal frequency of each allelic type make it extremely unlikely that α-tubulin diversity has been maintained under neutrality. Balancing selection may have contributed to such an apportioning of genetic variability as well as to high levels of genetic variation in α-tubulin and higher substitution rates at synonymous sites of exons than at intron bases of M. sinensis. In addition, certain effects of demographic oscillation may have distorted the scenario of a functional locus operating under balancing selection.     

Predicting the impact of changing CO(2) on crop yields: some thoughts on food

Recent breakthroughs in CO(2) fumigation methods using free-air CO(2) enrichment (FACE) technology have prompted comparisons between FACE experiments and enclosure studies with respect to quantification of the effects of projected atmospheric CO(2) concentrations on crop yields. On the basis of one such comparison, it was argued that model projections of future food supply (some of which are based on older enclosure data) may have significantly overestimated the positive effect of elevated CO(2) concentration on crop yields and, by extension, food security. However, in the comparison, no effort was made to differentiate enclosure study methodologies with respect to maintaining projected CO(2) concentration or to consider other climatic changes (e.g. warming) that could impact crop yields. In this review, we demonstrate that relative yield stimulations in response to future CO(2) concentrations obtained using a number of enclosure methodologies are quantitatively consistent with FACE results for three crops of global importance: rice (Oryza sativa), soybean (Glycine max) and wheat (Triticum aestivum). We suggest, that instead of focusing on methodological disparities per se, improved projections of future food supply could be achieved by better characterization of the biotic/abiotic uncertainties associated with projected changes in CO(2) and climate and incorporation of these uncertainties into current crop models.     

Crystal structure of staphylococcal enterotoxin G (SEG) in complex with a mouse T-cell receptor {beta} chain

Superantigens (SAgs) are bacterial or viral toxins that bind MHC class II (MHC-II) molecules and T-cell receptor (TCR) in a nonconventional manner, inducing T-cell activation that leads to inflammatory cytokine production, which may result in acute toxic shock. In addition, the emerging threat of purpura fulminans and community-associated meticillin-resistant Staphylococcus aureus emphasizes the importance of a better characterization of SAg binding to their natural ligands that may allow the development of reagents to neutralize their action. The three-dimensional structure of the complex between a mouse TCR β chain (mVβ8.2) and staphylococcal enterotoxin G (SEG) at 2.0 Å resolution revealed a binding site that does not conserve the “hot spots” present in mVβ8.2-SEC2, mVβ8.2-SEC3, mVβ8.2-SEB, and mVβ8.2-SPEA complexes. Analysis of the mVβ8.2-SEG interface allowed us to explain the higher affinity of this complex compared with the others, which may account for the early activation of T-cells bearing mVβ8.2 by SEG. This mode of interaction between SEG and mVβ8.2 could be an adaptive advantage to bestow on the pathogen a faster rate of colonization of the host.     

{alpha}-Galactosyl (Gal{alpha}1-3Gal{beta}1-4GlcNAc-R) epitopes on human cells: synthesis of the epitope on human red cells by recombinant primate {alpha}1,3galactosyltransferase expressed in E.coli

Developing methods for in vitro synthesis of the carbohydratestructure Gal     

Purification of a DNA-binding protein from a multi-protein complex associated with DNA polymerase-{alpha} in pea (Pisum sativum)

DNA polymerase-     

Vascular endothelial growth factor A (VEGF-A) induces endothelial and cancer cell migration through direct binding to integrin {alpha}9{beta}1: identification of a specific {alpha}9{beta}1 binding site

Integrin α9β1 mediates accelerated cell adhesion and migration through interactions with a number of diverse extracellular ligands. We have shown previously that it directly binds the vascular endothelial growth factors (VEGF) A, C, and D and contributes to VEGF-induced angiogenesis and lymphangiogenesis. Until now, the α9β1 binding site in VEGF has not been identified. Here, we report that the three-amino acid sequence, EYP, encoded by exon 3 of VEGF-A is essential for binding of VEGF to integrin α9β1 and induces adhesion and migration of endothelial and cancer cells. EYP is specific for α9β1 binding and neither requires nor activates VEGFR-2, the cognate receptor for VEGF-A. Following binding to EYP, integrin α9β1 transduces cell migration through direct activation of the integrin signaling intermediates Src and focal adhesion kinase. This interaction is biologically important because it mediates in vitro endothelial cell tube formation, wound healing, and cancer cell invasion. These novel findings identify EYP as a potential site for directed pharmacotherapy.     

Formation of {Cu2(III)(mu-O)2}2+ core due to dioxygen reactivity of a copper(I) complex supported by a new hybrid tridentate ligand: reaction with exogenous substrates

Reaction of a Cu(I) complex of a hybrid tridentate ligand, encompassing [2-(pyridin-2-yl)ethyl]amine and dimethyl-substituted ethylalkylamine with dioxygen, generates in acetone at -80 degrees putative bis(mu-oxo)dicopper(III) intermediate. Structural characterization of a PPh(3)-adduct of a mononuclear Cu(I) complex of this new ligand has been achieved. This ligand coordinates in a facial mode utilizing three N-atoms (-CH(2)CH(2)-Py, -CH(2)CH(2)NMe(2), and -NCH(2)Ph). Reactivity of bis(mu-oxo)dicopper(III) intermediate toward exogenous substrates (2,4-di(tert-butyl)phenol and 2,4,6-tri(tert-butyl)phenol) has also been investigated.     

Synthesis, characterization and cytotoxic activity of substituted benzyl iminoether Pt(II) complexes of the type cis- and trans-[PtCl2{E-N(H)=C(OMe)CH2-C6H4-p-R}2] (R=Me, OMe, F). X-ray structure of trans-[PtCl2{E-N(H)=C(OMe)CH2-C6H4-p-F}2

New substituted benzyl iminoether derivatives of the type cis- and trans-[PtCl(2){E-N(H)C(OMe)CH(2)-C(6)H(4)-p-R}(2)] (R=Me (1a, 2a), OMe (3a, 4a), F (5a, 6a)) have been synthesized and characterized by elemental analyses, FT-IR spectroscopy and NMR techniques. The iminoether ligands are in the E configuration, which is stable in solution and in the solid state, as confirmed by the (1)H NMR data. Complex trans-[PtCl(2){E-N(H)C(OMe)CH(2)-C(6)H(4)-p-F}(2)] (6a) was also characterized by an X-ray diffraction study. Complexes 1a-6a have been tested against a panel of human tumor cell lines in order to evaluate their cytotoxic activity. cis-Isomers were significant more potent than the corresponding trans-isomers against all tumor cell lines tested; moreover, complexes 1a and 5a showed IC(50) values from about 2-fold to 6-fold lower than those exhibited by cisplatin, used as reference platinum anticancer drug.     

Unique genomic structure and expression of the mouse {alpha}2,8-sialyltransferase (ST8Sia III) gene

The mouse Sia     

Synthesis,spectral and magnetical characterization of monomeric [Cu(2-NO2bz)2(3-pyme)2(H2O)2] and polymeric [Cu{3,5-(NO2)2bz}2(3-pyme)2]n

Two new complexes of composition [Cu(2-NO₂bz)₂(3-pyme)₂(H₂O)₂] (1) and/or [Cu{3,5-(NO₂)₂bz}₂(3-pyme)₂] (2) (3-pyme = 3-pyridylmethanol, ronicol or 3-pyridylcarbinol, 2-NO₂bz = 2-nitrobenzoate and 3,5-(NO₂)₂bz = 3,5-dinitrobenzoate) have been prepared and studied by elemental analysis, electronic, infrared and EPR spectroscopy, magnetic susceptibility measurements and the structure of both complexes has been solved. Complex (1) shows an unusual molecular type of structure consisting of the [Cu(2-NO₂bz)₂(3-pyme)₂(H₂O)₂] molecules held together by hydrogen bonds and van der Waals interactions. Complex (2) exhibits a polymeric chain-like structure [Cu{3,5-(NO₂)₂bz}₂(3-pyme)₂]_n with copper atoms doubly bridged by two 3-pyridylmethanol molecules and the polymeric molecules are held together by van der Waals interactions. Complex (1) exhibits a magnetic moment μ_eff = 1.84 B.M. at 300 K that remains nearly constant within the temperature region (5–300 K). Further cooling results in lowering the magnetic moment to μ_eff = 1.82 B.M. at 1.8 K. The magnetic susceptibility temperature dependence obeys Curie–Weiss law with Curie constant of 0.423 cm³ K mol⁻¹ and with Weiss constant of −0.06 K. The magnetic moment of (2) exhibits a small increase with a decrease in the temperature (μ_eff = 1.80 B.M. at 300 K and μ_eff = 1.85 B.M. at 1.8 K) with Curie constant of 0.409 cm³ K mol⁻¹ and with Weiss constant of +1.1 K, which can indicate a very weak ferromagnetic interaction between the copper atoms within the chain. Applying the molecular field model resulted in obtaining zJ′ values −0.08 cm⁻¹ for complex (1), and −0.07 cm⁻¹ for complex (2), respectively, that could characterize intermolecular and interchain interactions transmitted through π–π stacking.     

N-{2-(4-methoxyphenyltelluro)ethyl}morpholine (L1) and its platinum(II) and ruthenium(II) complexes. Synthesis and crystal structure of L1 and trans-[PtCl2(L1)2]

The first tellurated derivative of morpholine, N-{2-(4-methoxyphenyltelluro)ethyl}morpholine (L¹) has been synthesized by reacting in situ generated ArTe⁻ with 4-(2-chloroethyl)morpholine hydrochloride under N₂ atmosphere. The compound L¹ gives molecular ion peak at m/z 351 and is characterized structurally. The donor atoms N and Te in compound L¹ are rightly oriented for its ligation in bidentate mode. The TeC(alkyl) is 0.02 Å longer than TeC(aryl). The complexes of ligand L¹ having composition [PtCl₂(L¹)₂] (1) and [RuCl₂(p-cymene)L¹] (2) have been synthesized. The compound 1 has been characterized structurally. The Pt has a square planar geometry in complex 1 and two molecules of ligand L¹ bonded through Te alone are trans to each other (PtTe=2.583(2) Å). The ¹³C{¹H} NMR spectrum of complex 1 is as expected. The ¹H NMR spectrum of single crystals of complex 1 shows multiplication of signals, which is supported by HETCOR experiments. The complex 2 also has ligand L¹ in a monodentate coordination mode, bonded through Te alone. This is supported by deshielded CH₂Te and ArCTe signals in ¹H and ¹³C{¹H} NMR spectra of complex 2 with respect to those of free ligand L¹. The HETCOR spectrum of complex 2 has been used to authenticate the assignments of CH₂Te group, as its two protons appear to be magnetically non-equivalent.     

Inhibitory and enhancing effects of NO on H(2)O(2) toxicity: dependence on the concentrations of NO and H(2)O(2)

Nitric oxide (NO) has been shown to both enhance hydrogen peroxide (H(2)O(2)) toxicity and protect cells against H(2)O(2) toxicity. In order to resolve this apparent contradiction, we here studied the effects of NO on H(2)O(2) toxicity in cultured liver endothelial cells over a wide range of NO and H(2)O(2) concentrations. NO was generated by spermine NONOate (SpNO, 0.001-1 mM), H(2)O(2) was generated continuously by glucose/glucose oxidase (GOD, 20-300 U/l), or added as a bolus (200 microM). SpNO concentrations between 0.01 and 0.1 mM provided protection against H(2)O(2)-induced cell death. SpNO concentrations >0.1 mM were injurious with low H(2)O(2) concentrations, but protective at high H(2)O(2) concentrations. Protection appeared to be mainly due to inhibition of lipid peroxidation, for which SpNO concentrations as low as 0.01 mM were sufficient. SpNO in high concentration (1 mM) consistently raised H(2)O(2) steady-state levels in line with inhibition of H(2)O(2) degradation. Thus, the overall effect of NO on H(2)O(2) toxicity can be switched within the same cellular model, with protection being predominant at low NO and high H(2)O(2) levels and enhancement being predominant with high NO and low H(2)O(2) levels.     

Part 3: synthesis and biological evaluation of some analogs of the antitumor agents, 2-{4-[(7-chloro-2-quinoxalinyl)oxy]phenoxy}propionic acid, and 2-{4-[(7-bromo-2-quinolinyl)oxy]phenoxy}propionic acid

2-{4-[(7-Chloro-2-quinoxalinyl)oxy]phenoxy}propionic acid (X469) and 2-{4-[(7-bromo-2-quinolinyl)oxy]phenoxy}propionic Acid (SH80) are among the most highly and broadly active antitumor agents to have been developed in our laboratories. However, the mechanism(s) of action of these agents remain to be elucidated, which prompted our continued endeavor to delineate a pharmacophoric pattern, from which a putative target might be deduced. Herein, we provide additional evidence that intact quinoxaline and quinoline rings in XK469 and SH80, respectively, are fundamental to the activities of these structures against transplanted tumors in mice. The consequence of further modification of the heterocyclic ring system in XK469 and SH80, leading to [1,8]naphthyridine; pyrrolo[1,2-a]; imidazo[1,2-a]; and imidazo[1,5-a] derivatives, all deprive the parent structures of antitumor activity. Introduction of CH3, CF3, CH3O, CO2H, or C6H5 substituents at C4 of the quinoline ring of SH80 led to weakly active antitumor agents. Similarly, the phenanthridine analog of SH80 manifested only modest cytotoxicity. Lastly, XK469 and SH80 are both significantly more active than the corresponding regioisomeric structures, 2-{4-[(7-halo-4-quinolinyl)oxy]phenoxy)propionic acids.     

The {beta}-amylase genes of grasses and a phylogenetic analysis of the Triticeae (Poaceae)

There are two forms of β-amylase in the Triticeae crop plants wheat, barley, and rye: an endosperm-specific form encoded by two or three closely linked genes, and a tissue-ubiquitous form encoded by a single gene. Both rice and corn have one ubiquitously expressed form encoded by a single gene. This study focuses on two phylogenetic analyses of β-amylase gene sequences. First, a phylogenetic analysis of coding sequences from wheat, barley, rye, rice, and corn was expected to clarify the relationship between the endosperm-specific and tissue-ubiquitous forms of the protein. Instead, it illustrates possible effects of distant outgroups, based on conflicting patterns of character state variation consistent with different root positions. Next, a broad sample of the monogenomic Triticeae was included in a phylogenetic analysis based on sequences from a portion of the tissue-ubiquitous β-amylase gene. The results were compared to existing Triticeae gene trees, among which extensive conflict had been noted in the past. One additional gene tree has not completely clarified the complexity of the group, but has shed additional light on reticulate phylogenetic patterns within the tribe, including relationships involving Eremopyrum, Thinopyrum, and the Triticum/Aegilops group.     

Reduction-induced inhibition and Mn(II) release from the photosystem II oxygen-evolving complex by hydroquinone or NH2OH are consistent with a Mn(III)/Mn(III)/Mn(IV)/Mn(IV) oxidation state for the dark-adapted enzyme

Hydroxylamine and hydroquinone were used to probe the oxidation states of Mn in the oxygen-evolving complex of dark-adapted intact (hydroxylamine) and salt-washed (hydroquinone) photosystem II. These preparations were incubated in the dark for 24 h in the presence of increasing reductant/photosystem II ratios, and the loss of oxygen evolution activity and of Mn(II) was determined for each incubation mixture. Monte Carlo simulations of these data yielded models that provide insight into the structure, reactivity, and oxidation states of the manganese in the oxygen-evolving complex. Specifically, the data support oxidation states of Mn(III)(2)/Mn(IV)(2) for the dark stable S(1) state of the O(2)-evolving complex. Activity and Mn(II) loss data were best modeled by assuming an S(1) --> S(-)(1) conversion of intermediate probability, a S(-)(1) --> S(-)(3) reaction of high probability, and subsequent step(s) of low probability. This model predicts that photosystem II Mn clusters that have undergone an initial reduction step become more reactive toward a second reduction, followed by a slower third reduction step. Analysis of the Mn(II) release parameters used to model the data suggests that the photosystem II manganese cluster consists of three Mn atoms that exhibit a facile reactivity with both reductants, and a single Mn that is reducible but sterically trapped at or near its binding site. Activity assays indicate that intact photosystem II centers reduced to S(-)(1) can evolve oxygen upon illumination, but that these centers are inactive in preparations depleted of the extrinsic 23 and 17 kDa polypeptides. Finally, it was found that a substantial population of the tyrosine D radical is reduced by hydroxylamine, but a smaller population reacts with hydroquinone over the course of a 24 h exposure to the reductant.