bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the ligandin site of maize glutathione S-transferase I
Authors: AXARLI Irine A. , RIGDEN Daniel J. , LABROU Nikolaos E.
Published: September 2004

Cytosolic GSTs (glutathione S-transferases) are a major reserve of high-capacity binding proteins and exhibit ligand-binding properties for a large variety of compounds. In the present study, the binding of two non-substrate anthraquinone dyes VBAR (Vilmafix Blue A-R) and CB3GA (Cibacron Blue 3GA) to maize (Zea mays) GST I was investigated. The results showed that the enzyme was specifically and irreversible inactivated by VBAR with a Kd of 35.5±2.2 μM and a k3 of 0.47 min−1. Proteolytic cleavage of the VBAR-modified enzyme and subsequent separation of peptides gave only one modified peptide. Sequencing of the modified peptide revealed the target site of VBAR reaction to be Lys41. CB3GA binds reversibly to GST I and behaves as a competitive inhibitor towards CDNB (1-chloro-2,4-dinitrobenzene) and glutathione. CB3GA binding to GST I is accompanied by a characteristic spectral change in the absorption at positive maximum (670 nm) which exhibited a hyperbolic dependence on dye concentration with a Kd of 12.1±0.5 μM. Site-directed mutagenesis of selected residues (Trp12, Phe35, Lys41, Asn49, Gln53, Ser67 and Ile118) was employed, and the mutated enzymes were assessed for CB3GA binding. These results, together with molecular-modelling studies, established that the ligandin-binding site of GST I is located mainly in the hydrophobic binding site. The ability of VBAR to specifically inactivate GST I was exploited further to demonstrate the specific binding of several plant hormones and flavonoids to GST I. The inactivation of other GST isoenzymes by VBAR was also investigated, and it was concluded that VBAR may have wide applicability as an affinity label for probing structure–function relationships of GST isoenzymes.
The nuclear bile acid receptor FXR is activated by PGC-1α in a ligand-dependent manner
Authors: KANAYA Eiko , SHIRAKI Takuma , JINGAMI Hisato
Published: September 2004

The nuclear bile acid receptor FXR (farnesoid X receptor) is one of the key factors that suppress bile acid biosynthesis in the liver. PGC-1α [PPARγ (peroxisome-proliferator-activated receptor γ) co-activator-1α] is known to control energy homoeostasis in adipose tissue, skeletal muscle and liver. We performed cell-based reporter assays using the expression system of a GAL4–FXR chimaera, the ligand-binding domain of FXR fused to the DNA-binding domain of yeast GAL4, to find the co-activators for FXR. We found that the transcriptional activation of a reporter plasmid by a GAL4–FXR chimaera was strongly enhanced by PGC-1α, in a ligand-dependent manner. Transcriptional activation of the SHP (small heterodimer partner) gene by the FXR–RXRα (retinoid X receptor α) heterodimer was also enhanced by PGC-1α in the presence of CDCA (chenodeoxycholic acid). Co-immunoprecipitation and pull-down studies using glutathione S-transferase–PGC-1α fusion proteins revealed that the ligand-binding domain of FXR binds PGC-1α in a ligand-influenced manner both in vivo and in vitro. Furthermore, our studies revealed that SHP represses its own transcription, and the addition of excess amounts of PGC-1α can overcome the inhibitory effect of SHP. These observations indicate that PGC-1α mediates the ligand-dependent activation of FXR and transcription of SHP gene.
Mammalian and Drosophila cells adhere to the laminin α4 LG4 domain through syndecans, but not glypicans
Authors: YAMASHITA Hironobu , GOTO Akira , KADOWAKI Tatsuhiko , KITAGAWA Yasuo
Published: September 2004

We have previously shown that the LG4 (laminin G-like) domain of the laminin α4 chain is responsible for the significantly higher affinity of the α4 chain to heparin than found for other α chains [Yamaguchi, Yamashita, Mori, Okazaki, Nomizu, Beck and Kitagawa (2000) J. Biol. Chem. 275, 29458–29465]; four basic residues were identified to be essential for this activity [Yamashita, Beck and Kitagawa (2004) J. Mol. Biol. 335, 1145–1149]. By creating GST (glutathione S-transferase)-fused LG1, LG2, LG4 and LG5 proteins, we found that only LG4 is active for the adhesion of human HT1080 cells, human umbilical vein endothelial cells and Drosophila haemocytes Kc167 with a half-saturating concentration of 20 μg/ml. Adhesion was counteracted by treatment of the cells with heparin, heparan sulphate and heparitinase I. Upon mutating the four basic residues essential for heparin binding within LG4, the adhesion activity was abolished. Pull-down experiments using glutathione beads/GST-fusion proteins indicate a direct interaction of LG4 with syndecan-4, which might be the major receptor for cell adhesion. Neither the release of glypican-1 by treating human cells with phosphatidylinositol-specific phospholipase C nor targeted knockdown of dally or dally-like protein impaired the cell-adhesion activity. As the LG4–LG5 domain of the α4 chain is cleaved in vivo from the main body of laminin-8 (α4β1γ1), we suggest that the heparan sulphate proteoglycan-binding activity of LG4 is significant in modulating the signalling of Wnt, Decapentaplegic and fibroblast growth factors.
Solubility–insolubility interconversion of sophoragrin, a mannose/glucose-specific lectin in Sophora japonica (Japanese pagoda tree) bark, regulated by the sugar-specific interaction
Authors: UEDA Haruko , FUKUSHIMA Hisako , HATANAKA Yasumaru , OGAWA Haruko
Published: September 2004

Sophoragrin, a mannose/glucose-specific lectin in Sophora japonica (Japanese pagoda tree) bark, was the first lectin found to show self-aggregation that is dependent on the sugar concentration accompanying the interconversion between solubility and insolubility [Ueno, Ogawa, Matsumoto and Seno (1991) J. Biol. Chem. 266, 3146–3153]. The interconversion is regulated by the concentrations of Ca2+ and specific sugars: mannose, glucose or sucrose. The specific glycotopes for sophoragrin were found in the sophoragrin subunit and an endogenous galactose-specific lectin, B-SJA-I (bark S. japonica agglutinin I), and the lectin subunit that binds to the glycotope was identified by photoaffinity glycan probes. Remarkably, the insoluble polymer of sophoragrin is dissociated by interaction with B-SJA-I into various soluble complexes. Based on these results, self-aggregation of sophoragrin was shown to be a unique homopolymerization due to the sugar-specific interaction. An immunostaining study indicated that sophoragrin localizes mainly in vacuoles of parenchymal cells coincidently with B-SJA-I. These results indicate that sophoragrin can sequester endogenous glycoprotein ligands via sugar-specific interactions, thus providing new insights into the occurrence and significance of the intravacuolar interaction shown by a legume lectin.
Transient kinetics of the reaction catalysed by magnesium protoporphyrin IX methyltransferase
Authors: SHEPHERD Mark , HUNTER C. Neil
Published: September 2004

Magnesium protoporphyrin IX methyltransferase (ChlM), an enzyme in the chlorophyll biosynthetic pathway, catalyses the transfer of a methyl group to magnesium protoporphyrin IX (MgP) to form magnesium protoporphyrin IX monomethyl ester (MgPME). S-Adenosyl-L-methionine is the other substrate, from which a methyl group is transferred to the propionate group on ring C of the porphyrin macrocycle. Stopped-flow techniques were used to characterize the binding of porphyrin substrate to ChlM from Synechocystis PCC6803 by monitoring tryptophan fluorescence quenching on a millisecond timescale. We concluded that a rapid binding step is preceded by a slower isomerization of the enzyme. Quenched-flow techniques have been employed to characterize subsequent partial reactions in the catalytic mechanism. A lag phase has been identified that has been attributed to the formation of an intermediate. Our results provide a greater understanding of this catalytic process which controls the relative concentrations of MgP and MgPME, both of which are implicated in signalling between the plastid and nucleus in plants.
Highly sensitive intramolecularly quenched fluorogenic substrates for renin based on the combination of L-2-amino-3-(7-methoxy-4-coumaryl)propionic acid with 2,4-dinitrophenyl groups at various positions
Authors: PASCHALIDOU Katherine , NEUMANN Ulf , GERHARTZ Bernd , TZOUGRAKI Chryssa
Published: September 2004

The development of renin inhibitors for the treatment of hypertension requires highly sensitive substrates to evaluate potency and to characterize the mechanism of tight-binding inhibitors. A series of intramolecularly quenched fluorogenic renin substrates, based on the N-terminal tetradecapeptide sequence of human angiotensinogen (hTDP), was synthesized using a solid-phase technique. Incorporation of the fluorescent amino acid L-Amp [L-2-amino-3-(7-methoxy-4-coumaryl)propionic acid] and the DNP (2,4-dinitrophenyl) group at various positions resulted in >90% quenching efficiency and strong product fluorescence. Shortening the hTDP sequence to an octapeptide from histidine in P5 to histidine in P3′ (substrate 3) resulted in an acceptable kcat/Km (41000 M−1·s−1) and further systematic variation gave substrate 9, DNP-Lys-His-Pro-Phe-His-Leu-Val-Ile-His-L-Amp, with a kcat/Km value of 350000 M−1·s−1 and 94% quenching efficiency. The free side chain of lysine, replacing the isoleucine residue at P6 position in the angiotensinogen sequence, contributed to the increased value for kcat. The pH dependence of kcat/Km for renin and substrate 9 showed that the optimal pH is at pH 6–7. It also showed two titrating groups on the acidic side of the pH optimum, and one titrating group with a pKa of 7.8 on the alkaline side. The combination of good kinetic and spectroscopic properties resulted in a >20-fold improvement in the sensitivity of renin assay, compared with the commercial substrate Arg-Glu(EDANS)-Ile-His-Pro-Phe-His-Leu-Val-Ile-His-Thr-Lys(DABCYL)-Arg {where EDANS is 5-[(2-aminoethyl)amino]naphthalene-1-sulphonic acid and DABCYL is 4-(4-dimethylaminophenylazo)benzoic acid} (kcat/Km=268000 M−1· s−1, quenching efficiency <80%). The detection limit in a microplate renin assay was 60 pM, making substrate 9 well suited for the evaluation of inhibitors at picomolar concentrations.
Insertion of the amyloid precursor protein into lipid monolayers: effects of cholesterol and apolipoprotein E
Authors: LAHDO Raghda , de LA FOURNIÈRE-BESSUEILLE Laurence
Published: September 2004

APP (amyloid precursor protein), together with Chol (cholesterol) and ApoE (apolipoprotein E), has been linked to Alzheimer's disease. We have examined the hypothesis that interaction of APP with the lipid membranes is modulated by Chol and ApoE. Insertion of APP into lipid monolayers was first evidenced as an increase in the surface pressure. APP injected into a subphase induced a substantial increase in the surface pressure of monolayers prepared from PC (L-α-phosphatidylcholine), Chol, SPM (sphingomyelin) and PS (L-α-phosphatidylserine), the major lipids present in the plasma membranes of brain cells. At a given initial pressure, the insertion of APP into expanded monolayers is higher than that in condensed monolayers, in the order Chol>PC>SPM>PS. The membrane insertion capacity of APP was also measured from surface pressure versus area (π–A) isotherms of APP–lipid monolayers. The increase in the mean area per molecule in protein–lipid monolayers, in the order PC>Chol>PS>SPM, provides further evidence for protein–lipid interactions. These interactions occurred at optimum salt levels and optimum pH values close to physiological conditions (150 mM NaCl and pH 7.4). In addition, ApoE4 affected the insertion of APP into lipid films. APP–ApoE complexes showed a decreased ability to penetrate lipid monolayers at a constant area. APP–ApoE complexes expanded the π–A isotherm of a Chol monolayer to a lesser extent than APP alone. These experiments demonstrate the roles of Chol and ApoE in the modulation of membrane insertion of APP.
Caenorhabditis elegans triple null mutant lacking UDP-N-acetyl-D-glucosamine:α-3-D-mannoside β1,2-N-acetylglucosaminyltransferase I
Authors: ZHU Shaoxian , HANNEMAN Andrew , REINHOLD Vernon N. , SPENCE Andrew M. , SCHACHTER Harry
Published: September 2004

We have previously reported, from the nematode worm Caenor-habditis elegans, three genes (gly-12, gly-13 and gly-14) encoding enzymically active UDP-N-acetyl-D-glucosamine:α-3-D-mannoside β1,2-N-acetylglucosaminyltransferase I (GnT I), an enzyme essential for hybrid, paucimannose and complex N-glycan synthesis. We now describe a worm with null mutations in all three GnT I genes, gly-14 (III);gly-12 gly-13 (X) (III and X refer to the chromosome number). The triple-knock-out (TKO) worms have a normal phenotype, although they do not express GnT I activity and do not synthesize 31 paucimannose, complex and fucosylated oligomannose N-glycans present in the wild-type worm. The TKO worm has increased amounts of non-fucosylated oligomannose N-glycan structures, a finding consistent with the site of GnT I action. Five fucosylated oligomannose N-glycan structures were observed in TKO, but not wild-type, worms, indicating the presence of unusual GnT I-independent fucosyltransferases. It is concluded that wild-type C. elegans makes a large number of GnT I-dependent N-glycans that are not essential for normal worm development under laboratory conditions. The TKO worm may be more susceptible to mutations in other genes, thereby providing an approach for the identification of genes that interact with GnT I.
Carbohydrate-binding modules: fine-tuning polysaccharide recognition
Authors: BORASTON Alisdair B. , BOLAM David N. , GILBERT Harry J. , DAVIES Gideon J.
Published: September 2004

The enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. Despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic CBMs (carbohydrate-binding modules). CBMs promote the association of the enzyme with the substrate. In view of the central role that CBMs play in the enzymic hydrolysis of plant structural and storage polysaccharides, the ligand specificity displayed by these protein modules and the mechanism by which they recognize their target carbohydrates have received considerable attention since their discovery almost 20 years ago. In the last few years, CBM research has harnessed structural, functional and bioinformatic approaches to elucidate the molecular determinants that drive CBM–carbohydrate recognition. The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands.
NAD+ surfaces again
Authors: ZIEGLER Mathias , NIERE Marc
Published: September 2004

NAD+ and its metabolites serve important functions in intracellular signalling. NAD+-mediated regulatory processes also take place on the cell surface, particularly of immune cells. In this issue of the Biochemical Journal, Gerth et al. have demonstrated a new mechanism of Ca2+ uptake into monocytes which is triggered by NAD+ or its degradation product, ADP-ribose. These observations point to a hitherto unknown Ca2+-influx mechanism and underscore the potential significance of NAD+ and ADP-ribose as signalling molecules on the extracellular side of the plasma membrane.
Syphilis bei HIV‐Koinfektion
Authors: Körber Andreas , Dissemond Joachim , Lehnen Michaela , Franckson Tom , Grabbe Stephan , Esser Stefan
Published: September 2004

In den letzten Jahren zeigt sich ein rapider Inzidenz‐Anstieg der Syphilis speziell in der Population homosexueller Männer. Aufgrund der erhöhten Suszeptibilität gegenüber einer HIV‐Infektion durch eine Syphilis‐Infektion, und dem wechselnden Sexualverhalten mit ansteigender Promiskuität und nachlassendem Kondomgebrauch, ist auch ein erneuter Anstieg der HIV‐Inzidenz in dieser Population zu beobachten. Der Verlauf der Syphilis zeigt bei HIV‐Koinfektion gehäuft klinisch atypische und foudroyante Verläufe. Stadienspezifisch finden sich bei der Manifestation der Syphilis bei HIV‐Koinfektion im Primärstadium vermehrt multiple Ulzerationen, im Sekundärstadium zahlreiche atypische kutane Variationen, sowie gehäuft eine rasche Progression ins Sekundär‐ oder Tertiärstadium. Aufgrund häufiger Serumabnormitäten und falsch positiver/negativer Testergebnisse ist auch die serologische Diagnostik erschwert. Eine erhöhte Affektion des ZNS durch die HIV‐Koinfektion wird aktuell kontrovers diskutiert und konnte in prospektiven Studien bislang nicht eindeutig belegt werden. Eine Liquordiagnostik aller HIV‐Koinfizierten mit Spätsyphilis oder unklarem Infektionszeitpunkt wird jedoch bereits heute von der WHO und CDC empfohlen. Die Therapie der Syphilis bei HIV‐Koinfektion ist mit Penicillin weltweit weitestgehend einheitlich. So wird die Frühsyphilis mit 2,4 Mio. IE Benzathin‐Penicillin ein bzw. zweimalig und die Spätsyphilis mit zwei bzw. dreimaliger Gabe von 2,4 Mio. IE Benzathin‐Penicillin jeweils i. m. therapiert. Bei klinischen oder serologischen Zeichen einer Neurosyphilis sollte mit 18 – 24 Mio. IE Penicillin über mindestens 14 Tage i.v. therapiert werden.
Interpolating moving least-squares methods for fitting potential energy surfaces: Applications to classical dynamics calculations
Authors: Guo Yin , Kawano Akio , Thompson Donald L. , Wagner Albert F. , Minkoff Michael
Published: September 2004

As a continuation of our efforts to develop efficient and accurate interpolating moving least-squares (IMLS) methods for generating potential energy surfaces, we carry out classical trajectories and compute kinetics properties on higher degree IMLS surfaces. In this study, we have investigated the choice of coordinate system, the range of points (i.e., the cutoff radius) used in fitting, and strategies for selections of data points and basis elements. We illustrate and test the method by applying it to hydrogen peroxide (HOOH). In particular, reaction rates for the O-O bond breaking in HOOH are calculated on fitted surfaces using the classical trajectory approach to test the accuracy of the IMLS method for providing potentials for dynamics calculations.
A perturbative analysis of modulated amplitude waves in Bose–Einstein condensates
Authors: Porter Mason A. , Cvitanović Predrag
Published: September 2004

We apply Lindstedt’s method and multiple scale perturbation theory to analyze spatio-temporal structures in nonlinear Schrödinger equations and thereby study the dynamics of quasi-one-dimensional Bose–Einstein condensates with mean-field interactions. We determine the dependence of the amplitude of modulated amplitude waves on their wave number. We also explore the band structure of Bose–Einstein condensates in detail using Hamiltonian perturbation theory and supporting numerical simulations.
Effect of time-dependent basis functions and their superposition error on atom-centered density matrix propagation (ADMP): Connections to wavelet theory of multiresolution analysis
Authors: Iyengar Srinivasan S. , Frisch Michael J.
Published: September 2004

We present a rigorous analysis of the primitive Gaussian basis sets used in the electronic structure theory. This leads to fundamental connections between Gaussian basis functions and the wavelet theory of multiresolution analysis. We also obtain a general description of basis set superposition error which holds for all localized, orthogonal or nonorthogonal, basis functions. The standard counterpoise correction of quantum chemistry is seen to arise as a special case of this treatment. Computational study of the weakly bound water dimer illustrates that basis set superposition error is much less for basis functions beyond the 6-31+G* level of Gaussians when structure, energetics, frequencies, and radial distribution functions are to be calculated. This result will be invaluable in the use of atom-centered Gaussian functions for ab initio molecular dynamics studies using Born-Oppenheimer and atom-centered density matrix propagation.
On the vertical excitation energy of cyclopentadiene
Authors: Bomble Yannick J. , Sattelmeyer Kurt W. , Stanton John F. , Gauss Jürgen
Published: September 2004

The vertical excitation energy for the lowest valence π→π* transition of cyclopentadiene is investigated. Using a combination of high-level theoretical methods and spectroscopic simulations, the vertical separation at the ground state geometry is estimated to be 5.43±0.05 eV. This value is intermediate between those calculated with coupled-cluster and multireference perturbation theory methods and is about 0.13 eV higher than the observed maximum in the absorption profile.
Electric field induced switching of poly(ethylene glycol) terminated self-assembled monolayers: A parallel molecular dynamics simulation
Authors: Vemparala Satyavani , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: September 2004

Effects of electric field on the structure of poly(ethylene glycol) (PEG) terminated alkanethiol self-assembled monolayer (SAM) on gold have been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied antiparallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside. The parallel field affects the overall tilt structure of SAMs more adversely than the antiparallel field.
Dielectric and vibrational properties of amino acids
Authors: Tulip P. R. , Clark S. J.
Published: September 2004

We calculate polarizability tensors and normal mode frequencies for the amino acids alanine, leucine, isoleucine, and valine using density functional perturbation theory implemented within the plane wave pseudopotential framework. It is found that the behavior of the electron density under external fields depends to a large extent on the geometrical structure of the molecule in question, rather than simply on the constituent functional groups. The normal modes are able to help distinguish between the different types of intramolecular hydrogen bonding present, and help to explain why leucine is found in the zwitterionic form for the gaseous phase. Calculated IR spectra show a marked difference between those obtained for zwitterionic and nonzwitterionic molecules. These differences can be attributed to the different chemical and hydrogen bonds present. Effective dynamical charges are calculated, and compared to atomic charges obtained from Mulliken population analysis. It is found that disagreement exists, largely due to the differing origins of these quantities.
A note on geometry relaxation of molecular positron complexes
Authors: Mohallem José R. , Gonçalves Cristina P.
Published: September 2004

A molecular model for positron complexes is used to show that the geometry relaxation of the parent molecule plays an important role in the determination of the positron affinity. An application is presented to the [urea;e+] complex.
Simplified diagrammatic expansion for effective operators
Authors: Duan Chang-Kui , Gong Yun-Gui , Dong Hui-Ning , Reid Michael F.
Published: September 2004

For a quantum many-body problem, effective Hamiltonians that give exact eigenvalues in reduced model space usually have different expressions, diagrams, and evaluation rules from effective transition operators that give exact transition matrix elements between effective eigenvectors in reduced model space. By modifying these diagrams slightly and considering the linked diagrams for all the terms of the same order, we find that the evaluation rules can be made the same for both effective Hamiltonian and effective transition operator diagrams, and in many cases it is possible to combine many diagrams into one modified diagram. We give the rules to evaluate these modified diagrams and show their validity.
Conservation of connectivity of model-space effective interactions under a class of similarity transformation
Authors: Duan Chang-Kui , Gong Yungui , Dong Hui-Ning , Reid Michael F.
Published: September 2004

Effective interaction operators usually act on a restricted model space and give the same energies (for Hamiltonian) and matrix elements (for transition operators, etc.) as those of the original operators between the corresponding true eigenstates. Various types of effective operators are possible. Those well defined effective operators have been shown to be related to each other by similarity transformation. Some of the effective operators have been shown to have connected-diagram expansions. It is shown in this paper that under a class of very general similarity transformations, the connectivity is conserved. The similarity transformation between Hermitian and non-Hermitian Rayleigh-Schrödinger perturbative effective operators is one of such transformations and hence the connectivity can be deducted from each other.
Phase behavior of polarizable spherocylinders in external fields
Authors: Rotunno Melissa , Bellini Tommaso , Lansac Yves , Glaser Matthew A.
Published: September 2004

Applied electric fields are known to induce significant changes in the properties of systems of polarizable molecules or particles. For rod-shaped molecules, the field-induced behavior can be rather surprising, as in the case of the negative electric birefringence of concentrated solutions of rodlike polyelectrolytes. We have investigated the interplay of shape anisotropy and field-induced anisotropy in molecular dynamics simulations of systems of polarizable soft spherocylinders in an electric field, in the limit of infinitely anisotropic polarizability, taking full account of mutual induction effects. We find a novel crystalline structure (K2) in the high-field limit, whose formation is driven by interactions between induced dipoles. For high pressures, the phase diagram exhibits a polar nematic phase between the hexagonal close-packed crystal phase and the K2 phase. We also compare this system with an analogous system of spherocylinders with permanent electric dipoles and find that qualitatively similar behavior is obtained in the limit of strong coupling of the permanent dipoles to the external field.
On the nucleation mechanism of the β-δ phase transition in the energetic nitramine octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine
Authors: Smilowitz L. , Henson B. F. , Greenfield M. , Sas A. , Asay B. W. , Dickson P. M.
Published: September 2004

In our previous work on the mechanism for the β-δ solid-solid phase transition in octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), we used an empirical mechanism for the nucleation step and hypothesized a defect mechanism that was greatly affected by the presence of a nitroplasticizer/estane binder in the HMX formulation. Since then, we have acquired further evidence for this and have separated out the components of the binder to confirm that it is the nitroplasticizer that controls the nucleation energy in HMX formulations containing a nitroplasticizer/estane binder. While the exact distribution of nucleation energies as a function of synthesis route/defect type has not been worked out, it is likely that the solubility of the HMX in the nitroplasticizer is responsible for lowering the nucleation energy at the crystal surface, and therefore determines the nucleation rate for the formulation.
Mobility-induced instability and pattern formation in a reaction-diffusion system
Authors: Riaz Syed Shahed , Kar Sandip , Ray Deb Shankar
Published: September 2004

Ions undergoing a reaction-diffusion process are susceptible to electric field. We show that a constant external field may induce a kind of instability on the state stabilized by diffusion in a reaction-diffusion system giving rise to formation of pattern even when the diffusion coefficients of the reactants are equal. The origin of the pattern is due to the difference in mobilities of the two species and is thus markedly different from that of deformed Turing pattern in presence of the field. While this differential flow instability had been shown earlier to result in traveling waves, we realize in the context of stationary pattern formation in a typical reaction-diffusion-advective system. Our analysis is based on a numerical simulation of a generic model on a two-dimensional domain.
Lanthanide transport in stabilized zirconias: Interrelation between ionic radius and diffusion coefficient
Authors: Kilo Martin , Taylor Marcela A. , Argirusis Christos , Borchardt Günter , Weber Sylvain , Scherrer Hubert , Jackson Robert A.
Published: September 2004

The diffusion of all stable lanthanides was measured both in calcia stabilized zirconia (CSZ) and in yttria stabilized zirconia (YSZ) in the temperature range between 1286 and 1600 °C. The lanthanide diffusion coefficients obtained increase with increasing ionic radius. The experimental activation enthalpy of diffusion is near 6 eV for CSZ and between 4 and 5 eV for YSZ and is not strongly affected by the type of lanthanide. The results were correlated with defect energy calculations of the lanthanide diffusion enthalpy using the Mott-Littleton approach. An association enthalpy of cation vacancies with oxygen vacancies of about 1 eV (96 kJ/mol) was deduced in the case of CSZ, while there is no association in the case of YSZ. Furthermore, the change in diffusion coefficients can be correlated to the interaction parameter for the interaction between the lanthanide oxide with zirconia: The higher the interaction parameter, the higher the lanthanide diffusion coefficient.
Rotational stability of plasma blobs
Authors: D’Ippolito D. A. , Myra J. R. , Russell D. A. , Yu G. Q.
Published: September 2004

The stability of plasma blobs which have both density and temperature higher than the surrounding plasma, and can transport heat as well as particles, is considered. It is shown that the internal blob temperature profile Te(r) can drive azimuthal rotation or spin vθ(r) about the blob axis, which produces a robust m=2 rotational instability in the interchange limit (k∥=0). The theory includes the effects of the centrifugal and Coriolis forces, the sheared velocity vθ(r), and the axial sheath boundary condition. Estimates show that finite-Larmor-radius stabilization is ineffective, but the sheath conductivity can be strongly stabilizing. The blob rotational instability has only a small direct impact on the particle and energy transport, but it serves as a useful diagnostic for the underlying blob spin, which is an important variable in determining the blob’s radial velocity. A separate branch of temperature-gradient-driven sheath instabilities, predicted in the eikonal limit, is not observed for low mode numbers.
Electron spin relaxation due to reorientation of a permanent zero field splitting tensor
Authors: Schaefle Nathaniel , Sharp Robert
Published: September 2004

Electron spin relaxation of transition metal ions with spin S⩾1 results primarily from thermal modulation of the zero field splitting (zfs) tensor. This occurs both by distortion of the zfs tensor due to intermolecular collisions and, for complexes with less than cubic symmetry, by reorientational modulation of the permanent zfs tensor. The reorientational mechanism is much less well characterized in previous work than the distortional mechanism although it is an important determinant of nuclear magnetic resonance (NMR) paramagnetic relaxation enhancement phenomena (i.e., the enhancement of NMR relaxation rates produced by paramagnetic ions in solution or NMR-PRE). The classical density matrix theory of spin relaxation does not provide an appropriate description of the reorientational mechanism at low Zeeman field strengths because the zero-order spin wave functions are stochastic functions of time. Using spin dynamics simulation techniques, the time correlation functions of the spin operators have been computed and used to determine decay times for the reorientational relaxation mechanism for S=1. In the zfs limit of laboratory field strengths (HZeem≪Hzfs∘), when the zfs tensor is cylindrical, the spin decay is exponential, the spin relaxation time, τS∘≈0.53τR(1), where τR(1) is the reorientational correlation time of a molecule-fixed vector. The value of τS∘ is independent of the magnitude of the cylindrical zfs parameter (D), but it depends strongly on low symmetry zfs terms (the E/D ratio). Other spin dynamics (SD) simulations examined spin decay in the intermediate regime of field strengths where HZeem≈Hzfs∘, and in the vicinity of the Zeeman limit. The results demonstrate that the reorientational electron spin relaxation mechanism is often significant when Hzfs∘⩾HZeem, and that its neglect can lead to serious errors in the interpretation of NMR-PRE data.
Control of drop rebound with solid target motion
Authors: Lee Heon Ju , Kim Ho-Young
Published: September 2004

Drops with a high surface tension and a low viscosity, such as water and molten metal drops, exhibit a vigorous recoiling and a long-lasting oscillation upon impacting with nonwetting solid surfaces. Here we report a scheme of controlling drop rebound using target movement, without resorting to chemical modification of either drop liquid or solid surface. Our experimental study reveals that drop rebound is promoted when the target moves upward at the moment of impact. On the other hand, an effective suppression of drop rebound is achieved by moving the target downward upon drop impact. It is shown that these modifications in drop rebound behavior are not due to the drop impact speed change. Furthermore, a properly timed reversal of the target’s moving direction is shown to control drop rebound more effectively than the monotonous target motions.
Reaction-path switching induced by spatial-distribution change of reactants: CO oxidation on Pt(111)
Authors: Nakai I. , Kondoh H. , Amemiya K. , Nagasaka M. , Nambu A. , Shimada T. , Ohta T.
Published: September 2004

We studied the mechanism of CO oxidation on O-covered Pt(111) surfaces during CO exposure by means of time-resolved near edge x-ray absorption fine structure spectroscopy. Two distinct reaction processes were found to occur sequentially; isolated O atoms and island-periphery O atoms contribute to each process. Combination of in situ monitoring of the reaction kinetics and Monte Carlo simulations revealed that CO coadsorption plays a role of inducing the dynamic change in spatial distribution of O atoms, which switches over the two reaction paths.
Small Molecules that Mimic Components of Bioactive Protein Surfaces
Authors: Fairlie David P.
Published: September 2004

Small molecules designed to mimic specific structural components of a protein (peptide strands, sheets, turns, helices, or amino acids) can be expected to display agonist or antagonist biological responses by virtue of interacting with the same receptors that recognize the protein. Here we describe some minimalist approaches to structural mimetics of amino acids and of strand, turn, or helix segments of proteins. The designed molecules show potent and selective inhibition of protease, transferase, and phospholipase enzymes, or antagonism of G-protein coupled or transcriptional receptors, and have potent anti-tumour, anti-inflammatory, or antiviral activity.
Systematics of the Californian euctenizine spider genus Apomastus (Araneae : Mygalomorphae : Cyrtaucheniidae): the relationship between molecular and morphological taxonomy
Authors: Bond Jason E.
Published: September 2004

The genus Apomastus Bond & Opell is a relatively small group of mygalomorph spiders with a limited geographic distribution. Restricted to the Los Angeles Basin, San Juan Mountains, and San Joaquin Hills, Apomastus occupies a fragile habitat rapidly succumbing to urban encroachment. Although originally described as monotypic, the genus was hypothesised to contain at least one additional species. However, females of the two reputed species are morphologically indistinguishable and the authors were unable confidently to assign specific status to populations for which they lacked male specimens. Using an approach that combines geographic, morphological and molecular data, all known populations are assigned to one of two hypothesised species. Mitochondrial DNA cytochrome c oxidase I sequences are used to infer population phylogeny, providing the evolutionary framework necessary to resolve population and species identity issues. Conflicts between the parsimony and Bayesian analyses raise questions about species delineation, species paraphyly, and the application of molecular taxonomy to these taxa. Issues relevant to the conservation of Apomastus species are discussed in light of the substantive intraspecific species divergence observed in the mtDNA data. The type species, Apomastus schlingeri Bond & Opell, is redescribed and a second species, Apomastus kristenae, sp. nov., is described.
Reduction of nitrite to nitric oxide during ischemia protects against myocardial ischemia–reperfusion damage
Authors: Webb Andrew , Bond Richard , McLean Peter , Uppal Rakesh , Benjamin Nigel , Ahluwalia Amrita
Published: September 2004

Nitric oxide (NO
•
) is thought to protect against the damaging effects of myocardial ischemia–reperfusion injury, whereas xanthine oxidoreductase (XOR) normally causes damage through the generation of reactive oxygen species. In the heart, inorganic nitrite

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has the potential to act as an endogenous store of NO
•
, liberated specifically during ischemia. Using a detection method that we developed, we report that under ischemic conditions both rat and human homogenized myocardium and the isolated perfused rat heart (Langendorff preparation) generate NO
•
from

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in a reaction that depends on XOR activity. Functional studies of rat hearts in the Langendorff apparatus showed that nitrite (10 and 100 μM) reduced infarct size from 47.3 ± 2.8% (mean percent of control ± SEM) to 17.9 ± 4.2% and 17.4 ± 1.0%, respectively (
P
< 0.001), and was associated with comparable improvements in recovery of left ventricular function. This protective effect was completely blocked by the NO
•
scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazole-1-oxyl 3-oxide (carboxy-PTIO). In summary, the generation of NO
•
from

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, by XOR, protects the myocardium from ischemia–reperfusion injury. Hence, if XOR is presented with

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as an alternative substrate, the resultant effects of its activity may be protective, by means of its production of NO
•
, rather than damaging.
Dynamic alterations of membrane tethers stabilize leukocyte rolling on P-selectin
Authors: Ramachandran Vishwanath , Williams Marcie , Yago Tadayuki , Schmidtke David W. , McEver Rodger P.
Published: September 2004

Leukocytes rolling on selectins extrude thin membrane tethers that might stabilize rolling velocities despite marked alterations in wall shear stress. To test this hypothesis, we used differential interference contrast videomicroscopy to visualize formation and breakage of membrane tethers as neutrophils rolled on P-selectin under flow. Neutrophils rapidly increased tether number as wall shear stress rose and decreased tether number as wall shear stress declined. Membrane tethers invariably accompanied slower, more uniform rolling steps that translated into lower mean rolling velocities and variances in velocity. Unexpectedly, neutrophils, but not fixed cells or microspheres bearing selectin ligands, rolled progressively more slowly and uniformly over time. Scanning electron microscopy revealed that neutrophils developed larger, more complex tether structures as they rolled for longer periods. These data provide evidence that neutrophils stabilize selectin-mediated rolling by rapidly adjusting tether number in response to changes in wall shear stress. Gradual remodeling of tether architecture may further reduce rolling velocities, facilitating integrin-dependent deceleration and arrest on inflamed vascular surfaces.
Olfactory receptor surface expression is driven by association with the β2-adrenergic receptor
Authors: Hague Chris , Uberti Michelle A. , Chen Zhongjian , Bush Cristina F. , Jones Seth V. , Ressler Kerry J. , Hall Randy A. , Minneman Kenneth P.
Published: September 2004

Olfactory receptors (ORs) comprise more than half of the large class I G protein-coupled receptor (GPCR) superfamily. Although cloned over a decade ago, little is known about their properties because wild-type ORs do not efficiently reach the cell surface following heterologous expression. Receptor–receptor interactions strongly influence surface trafficking of other GPCRs, and we examined whether a similar mechanism might be involved in OR surface expression. Olfactory neurons are known to express β-adrenergic receptors (ARs), and we found that coexpression with β2-ARs, but not any other AR subtypes, dramatically increased mouse 71 (M71) OR surface expression in human embryonic kidney 293 cells. A persistent physical interaction between M71 ORs and β2-ARs was shown by coimmunoprecipitation and by cointernalization of the two receptors in response to their specific ligands. Also, coexpression of wild-type M71 ORs with β2-ARs resulted in cAMP responses to the M71 ligand acetophenone. Finally,in situhybridization studies showed extensive colocalization of M71 OR and β2-AR expression in mouse olfactory epithelium. These data demonstrate the successful heterologous surface expression of a functional wild-type OR and reveal that persistent physical association with other GPCRs can control OR surface expression.
Role of KaiC phosphorylation in the circadian clock system of
Synechococcus elongatus
PCC 7942
Authors: Nishiwaki Taeko , Satomi Yoshinori , Nakajima Masato , Lee Cheolju , Kiyohara Reiko , Kageyama Hakuto , Kitayama Yohko , Temamoto Mioko , Yamaguchi Akihiro , Hijikata Atsushi , Go Mitiko , Iwasaki Hideo , Takao Toshifumi , Kondo Takao
Published: September 2004

In the cyanobacterium
Synechococcus elongatus
PCC 7942, KaiA, KaiB, and KaiC are essential proteins for the generation of a circadian rhythm. KaiC is proposed as a negative regulator of the circadian expression of all genes in the genome, and its phosphorylation is regulated positively by KaiA and negatively by KaiB and shows a circadian rhythm
in vivo
. To study the functions of KaiC phosphorylation in the circadian clock system, we identified two autophosphorylation sites, Ser-431 and Thr-432, by using mass spectrometry (MS). We generated
Synechococcus
mutants in which these residues were substituted for alanine by using site-directed mutagenesis. Phosphorylation of KaiC was reduced in the single mutants and was completely abolished in the double mutant, indicating that KaiC is also phosphorylated at these sites
in vivo
. These mutants lost circadian rhythm, indicating that phosphorylation at each of the two sites is essential for the control of the circadian oscillation. Although the nonphosphorylatable mutant KaiC was able to form a hexamer
in vitro
, it failed to form a clock protein complex with KaiA, KaiB, and SasA in the
Synechococcus
cells. When nonphosphorylatable KaiC was overexpressed, the
kaiBC
promoter activity was only transiently repressed. These results suggest that KaiC phosphorylation regulates its transcriptional repression activity by controlling its binding affinity for other clock proteins.
Fast folding of a helical protein initiated by the collision of unstructured chains
Authors: Meisner W. Kevin , Sosnick Tobin R.
Published: September 2004

To examine whether helix formation necessarily precedes chain collision, we have measured the folding of a fully helical coiled coil that has been specially engineered to have negligible intrinsic helical propensity but high overall stability. The folding rate approaches the diffusion-limited value and is much faster than possible if folding is contingent on precollision helix formation. Therefore, the collision of two unstructured chains is the initial step of the dominant kinetic pathway, whereas helicity exerts its influence only at a later step. Folding from an unstructured encounter complex may be efficient and robust, which has implications for any biological process that couples folding to binding.
A mucosally targeted subunit vaccine candidate eliciting HIV-1 transcytosis-blocking Abs
Authors: Matoba Nobuyuki , Magérus Aude , Geyer Brian C. , Zhang Yunfang , Muralidharan Mrinalini , Alfsen Annette , Arntzen Charles J. , Bomsel Morgane , Mor Tsafrir S.
Published: September 2004

A vaccine that would engage the mucosal immune system against a broad range of HIV-1 subtypes and prevent epithelial transmission is highly desirable. Here we report fusing the mucosal targeting B subunit of cholera toxin to the conserved galactosylceramide-binding domain (including the ELDKWA-neutralizing epitope) of the HIV-1 gp41 envelope protein, which mediates the transcytosis of HIV-1 across the mucosal epithelia. Chimeric protein expressed in bacteria or plants assembled into oligomers that were capable of binding galactosyl-ceramide and GM1gangliosides. Mucosal (intranasal) administration in mice of the purified chimeric protein followed by an i.p. boost resulted in transcytosis-neutralizing serum IgG and mucosal IgA responses and induced immunological memory. Plant production of mucosally targeted immunogens could be particularly useful for immunization programs in developing countries, where desirable product traits include low cost of manufacture, heat stability, and needle-free delivery.