Estimation of ^{3}J_{HN\hbox{-}H\alpha} and ^{3}J_{H\alpha\hbox{-}H\beta} coupling constants from heteronuclear TOCSY spectra

(3)J proton-proton coupling constants bear information on the intervening dihedral angles. Methods have been developed to derive this information from NMR spectra of proteins. Using series expansion of the time dependent density matrix, and exploiting the simple topology of amino acid spin-systems, formulae for estimation of (3)J(HN-Halpha) and (3)J(Halpha-Hbeta) from HSQC-TOCSY spectra are derived. The results obtained on a protein entailing both alpha-helix and beta-sheet secondary structure elements agree very well with J-coupling constants computed from the X-ray structure. The method compares well with existing methods and requires only 2D spectra which would be typically otherwise recorded for structural studies.     

Coupling of secondary active transport with\Delta \tilde \mu _{H^ + }

Most nutrients and ions in bacteria, yeasts, algae, and plants are transported uphill at the expense of a gradient of the electrochemical potential of protons deltamu-H+ (a type of secondary active transport). Diagnosis of such transports rests on the determination of the transmembrane electrical potential difference deltapsi and the difference of pH at the two membrane sides. The behavior of kinetic parameters K(T) (the half-saturation constant) and J(max), (the maximum rate of transport) upon changing driving ion concentrations and electrical potentials may be used to determine the molecular details of the transport reaction. Equilibrium accumulation ratios of driven solutes are expected to be in agreement with the deltapsi and deltapH measured independently, as well as with the Haldane-type expression involving K(T) and J(max). Different stoichiometries of H+/solute, as well as intramembrane effects of pH and deltapsi, may account for some of the observed inconsistencies.     

Evidence that the intrinsic membrance protein LHCII in thylakoids is necessary for maintaining localized\Delta \tilde \mu _{H^ + } energy coupling

This work tested the hypothesis that thylakoid localized proton-binding domains, suggested to be involved in localized -driven ATP formation, are maintained with the involvement of several membrane proteins, including the LHCII (Laszlo, J. A., Baker, G. M., and Dilley, R. A. (1984) Biochim. Biophys. Acta 764, 160–169), which comprises about 50% of the total thylakoid protein. The concept we have in mind is that several membrane proteins cooperate to shield a localized proton diffusion pathway from direct contact with the lumen, thus providing a physical barrier to H⁺ equilibration between the sequestered domains and the lumen. A barely mutant,chlorina f ₂, that lacks Chl b and does not accumulate some of the LHCII proteins, was tested for its capacity to carry out localized-proton gradient-dependent ATP formation. Two previously developed assays permit clear discrimination between localized and delocalized gradient-driven ATP formation. Those assays include the effect of a permeable buffer, pyridine, on the number of single-turnover flashes needed to reach the energetic threshold for ATP formation and the more recently developed assay for lumen pH using 8-hydroxy-1,3,6-pyrene trisulfonic acid as a lumenally loaded pH-sensitive fluorescent probe. By those two criteria, the wild-type barley thylakoids revealed either a localized or a delocalized energy coupling mode under low- or high-salt storage conditions, respectively. Addition of Ca⁺⁺ to the high-salt storage medium caused those thylakoids to maintain a localized energy-coupling response, as previously observed for pea thylakoids. In contrast, thechlorina f ₂ mutant thylakoids had an active delocalized energy coupling activity but did not show localized energy coupling under any conditions, and added Ca⁺⁺ to the thylakoid storage medium did not alter the delocalized energy coupling mode. One interpretation of the results is that the absence of the LHCII polypeptides produces a leaky pathway for protons which allows the gradient to equilibrate with the lumen under all conditions. Another interpretation is possible but seems less likely, that being that the absence of the LHCII polypeptides in some way causes the proposed Ca⁺⁺ -gated H⁺ flux site on the membrane sector (CF₀) of the energy coupling complex to lose its gating function.     

Study on the Interaction Between {\mathrm{Cu}}{\left( {{\mathrm{phen}}} \right)}^{{2 + }}_{3} and Bovine Serum Albumin by Spectroscopic Methods

In this work, the interaction between ${\text{Cu}}\left( {{\text{phen}}} \right)_3^{\,\,2 + } In this work, the interaction between Cu(phen)(2+)(3) and bovine serum albumin (BSA) was investigated by fluorescence spectroscopy combined with UV-vis absorption and circular dichroism (CD) spectroscopic techniques under physiological conditions. The fluorescence data proved that the fluorescence quenching of BSA by Cu(phen)(2+)(3) was the result of the Cu(phen)(2+)(3) -BSA complex formation. The binding constants (K (a)) between Cu(phen)(2+)(3) and BSA at four different temperatures were calculated according to the modified Stern-Volmer equation. The enthalpy change (DeltaH) and entropy change (DeltaS) were calculated to be 10.74 kJ mol(-1) and 54.35 J mol(-1) K(-1), respectively, which indicated that electrostatic interactions played a major role in the formation of Cu(phen)(2+)(3) -BSA complex. The distance r between the donor (BSA) and acceptor[Cu(phen)(2+)(3)] was obtained to be 3.55 nm based on F?rster's energy transfer theory. The synchronous fluorescence and CD spectroscopy results showed that the polarity of the residues increased and the lost of the alpha-helix content of BSA (from 59.84 to 53.70%). These indicated that the microenvironment and conformation of BSA were changed in the presence of Cu(phen)(2+)(3).     

Specificity of xenoreactive anti-Gal{alpha}1-3Gal IgM for {alpha}-galactosyl ligands

The transplantation of organs from lower animals such as pigsinto humans is prevented by a severe rejection reaction initiatedby complement fixing xenoreactive natural antibodies. Most anti-pigxenoreactive natural antibodies in humans are thought to recognizeGal     

Towards superconductivity in hydrides: computational studies of two hypothetical ternary compounds, {\text{Yb}}^{{{\text{II}}}} {\text{BeH}}_{4} and {\text{Cs}}_{3} {\text{Yb}}^{{{\text{III}}}} {\text{H}}_{6}

Two examples of novel, as yet unsynthesized ternary lanthanide hydrides--Yb(II)BeH4 and Cs3Yb(III)H6--are investigated computationally. Their unprecedented electronic structure is discussed and the potential superconductivity of Cs3Yb(III)H6 explored. Methods of synthesis are postulated for both compounds.     

The human V pre B gene is located on chromosome 22 near a cluster of {\text{V}}_{\lambda _1 } gene segments

The chromosomal location of the human V _pre B gene was determined by Southern blotting analysis of restriction enzyme-digested DNAs from a panel of 17 mouse-human somatic cell hybrids. The pattern of hybridization of a V_preB-specific probe in conjunction with earlier analysis of several marker genes allowed the following conclusions: 1) V _pre B is on human chromosome 22 within band 22q11.2 distal to the bcr-like gene, bcr-2 and proximal to the bcr-like gene, bcr-4. 2) V_preB has been localized relative to several constitutional and tumor-specific breakpoints within 22q 11.2, segregates in hybrids retaining 22q^–chromosomes with some but not with all members of the subgroup of the V genes, and is amplified with these genes in K562 cells. 3) The order of the loci on chromosome 22 is centromerebcr-2, V _preB, .     

Cloning,characterization and expression of \emph{OsFMO}_{{\mathbf{(}\emph{t}\mathbf{)}}} in rice encoding a flavin monooxygenase

Flavin monooxygenases (FMO) play a key role in tryptophan (Trp)-dependent indole-acetic acid (IAA) biosynthesis in plants and regulate plant growth and development. In this study, the full-length genomic DNA and cDNA of OsFMO _(t), a FMO gene that was originally identified from a rolled-leaf mutant in rice, was isolated and cloned from wild type of the rolled-leaf mutant. OsFMO _(t) was found to have four exons and three introns, and encode a protein with 422 amino acid residues that contains two basic conserved motifs, with a ‘G×G××G’ characteristic structure. OsFMO_(t) showed high amino acid sequence identity with FMO proteins from other plants, in particular with YUCCA from Arabidopsis, FLOOZY from Petunia, and OsYUCCA1 from rice. Our phylogenetic analysis showed that OsFMO_(t) and the homologous FMO proteins belong to the same clade in the evolutionary tree. Overexpression of OsFMO _(t) in transformed rice calli produced IAA-excessive phenotypes that showed browning and lethal effects when exogenous auxins such as naphthylacetic acid (NAA) were added to the medium. These results suggested that the OsFMO_(t) protein is involved in IAA biosynthesis in rice and its overexpression could lead to the malformation of calli. Spatio-temporal expression analysis using RT-PCR and histochemical analysis for GUS activity revealed that expression of OsFMO _(t) was totally absent in the rolled-leaf mutant. However, in the wild type variety, this gene was expressed at different levels temporally and spatially, with the highest expression observed in tissues with fast growth and cell division such as shoot apexes, tender leaves and root tips. Our results demonstrated that IAA biosynthesis regulated by OsFMO _(t) is likely localized and might play an essential role in shaping local IAA concentrations which, in turn, is critical for regulating normal growth and development in rice.     

Column Chromatographic Separation of Chlorophyllide {alpha} and Pheophorbide {alpha}

Chlorophyllide a, pheophorbide a, chlorophyll a and pheophytina were separated in a short time by anion-exchange chromatographywith a short column of DEAE-Sepharose CL-6B. (Received February 16, 1984; Accepted April 13, 1984)     

Endor characterization and D2O exchange in the \begin{array}{*{20}c} {\mathop Z\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array} /{\kern 1pt} \begin{array}{*{20}c} {\mathop D\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array} radical in photosystem II

The early suggestion by Lozier and Butler (Photochem. Photobiol. 17, 133–137 (1973)) that EPR Signal II arises from radicals associated with the water-splitting process in PSII has been confirmed and extended over the intervening years. Recent work has identified the Signal II radicals, \(\begin{array}{*{20}c} {\mathop D\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array}\) and \(\begin{array}{*{20}c} {\mathop Z\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array}\) , with plastosemiquinone cation species. In the experiments presented here we have used ENDOR spectroscopy and D₂O/H₂O exchange to characterize these paramagnets in more detail. The ENDOR matrix region, which arises from protons which interact weakly with the unpaired electron spin, is well-resolved at 4 K and at least seven resonances are apparent. A number of hyperfine couplings in the 3–8 MHz range are observed and are suggested to arise from methyl or hydroxyl protons which occur as substituents on the plastosemiquinone cation ring or from amino acid protons hydrogen-bonded to the 1,4-hydroxyl groups. Orientation selection experiments are consistent with these possibilities. D₂O/H₂O exchange shows that the D⁺/Z⁺ site is accessible to solvent. However, the exchange occurs slowly and is not complete even after 72 hours which suggests that the free radicals are functionally isolated from solvent water.     

{Omega}-oxidation of {alpha}-chlorinated fatty acids: identification of {alpha}-chlorinated dicarboxylic acids

Myeloperoxidase-derived HOCl targets tissue- and lipoprotein-associated plasmalogens to generate α-chlorinated fatty aldehydes, including 2-chlorohexadecanal. Under physiological conditions, 2-chlorohexadecanal is oxidized to 2-chlorohexadecanoic acid (2-ClHA). This study demonstrates the catabolism of 2-ClHA by ω-oxidation and subsequent β-oxidation from the ω-end. Mass spectrometric analyses revealed that 2-ClHA is ω-oxidized in the presence of liver microsomes with initial ω-hydroxylation of 2-ClHA. Subsequent oxidation steps were examined in a human hepatocellular cell line (HepG2). Three different α-chlorinated dicarboxylic acids, 2-chlorohexadecane-(1,16)-dioic acid, 2-chlorotetradecane-(1,14)-dioic acid, and 2-chloroadipic acid (2-ClAdA), were identified. Levels of 2-chlorohexadecane-(1,16)-dioic acid, 2-chlorotetradecane-(1,14)-dioic acid, and 2-ClAdA produced by HepG2 cells were dependent on the concentration of 2-ClHA and the incubation time. Synthetic stable isotope-labeled 2-ClHA was used to demonstrate a precursor-product relationship between 2-ClHA and the α-chlorinated dicarboxylic acids. We also report the identification of endogenous 2-ClAdA in human and rat urine and elevations in stable isotope-labeled urinary 2-ClAdA in rats subjected to intraperitoneal administration of stable isotope-labeled 2-ClHA. Furthermore, urinary 2-ClAdA and plasma 2-ClHA levels are increased in LPS-treated rats. Taken together, these data show that 2-ClHA is ω-oxidized to generate α-chlorinated dicarboxylic acids, which include α-chloroadipic acid that is excreted in the urine.     

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.     

Delay decomposition approach to $$\mathcal {H}_{\infty }$$ filtering analysis of genetic oscillator networks with time-varying delays

In this paper, the \(\mathcal {H}_{\infty }\) filtering problem is treated for N coupled genetic oscillator networks with time-varying delays and extrinsic molecular noises. Each individual genetic oscillator is a complex dynamical network that represents the genetic oscillations in terms of complicated biological functions with inner or outer couplings denote the biochemical interactions of mRNAs, proteins and other small molecules. Throughout the paper, first, by constructing appropriate delay decomposition dependent Lyapunov–Krasovskii functional combined with reciprocal convex approach, improved delay-dependent sufficient conditions are obtained to ensure the asymptotic stability of the filtering error system with a prescribed \(\mathcal {H}_{\infty }\) performance. Second, based on the above analysis, the existence of the designed \(\mathcal {H}_{\infty }\) filters are established in terms of linear matrix inequalities with Kronecker product. Finally, numerical examples including a coupled Goodwin oscillator model are inferred to illustrate the effectiveness and less conservatism of the proposed techniques.     

{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