bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acidity predictions in an electron propagator approach
Authors: Agacino Esther , Gaitán Ricardo , Menconi Italo 
Published: February 2006

AbstractAn alternative way to calculate vertical ionization potentials (VIP) and vertical electron affinity (VEA) is the application of Koopman's theorem, using the electron propagator theory. In the present work, the results of the application of this theorem using the electron propagator formalism have been compared with the experiment in order to validate different basis set. Using the basis set with the best performance, the acidity tendencies in some substituted acetic acid molecules have been analyzed by correlating the proton affinity (PA) with molecular electronegativity (χ) and hardness (η); these last indexes were obtained from the calculated VIP and VEA considering the finite difference approximation. The above correlations were compared with equivalent correlations using the energy of the frontier Hartree–Fock orbitals and the corresponding Kohn–Sham orbitals, which were calculated with the B3LYP‐DFT procedure. The results indicate that the electron propagator theory could be an interesting alternative to evaluate reactivity indexes, since this theory gives reliable values of VIP and VEA. It was also found that (i) the VIP values are very close to experiment, with only a 0.38% of error; (ii) acceptable results are inferred for VEA; (iii) a triple zeta quality function works quite well in these calculations, and particularly the 6‐311G(d,p) basis set is the best, as it had been reported; and (iv) using the depronation energy (DPE), good results were obtained in the correlations δDPE‐VEA and δDPE‐χ. The results tested that P3 approximation in the electron propagator approach can be a new and interesting alternative in predicting VIP, VEA, and some reactivity indexes, such as χ and η, at least for the compounds studied. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Molecular design of a π‐conjugated single‐chain electronically conductive polymer
Authors: Imamura Akira , Aoki Yuriko 
Published: February 2006

AbstractThis study demonstrates that single‐chain π‐conjugated systems can be made electrically conductive by modifying the molecular structures of both ends of the oligomers making up a polymer. That is, the highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gaps of a fairly long polyyne‐type oligomer with appropriately modified molecular structures at both ends are found to be on the order of thermal energy by calculations using density functional theory (DFT) with B3LYP functionals. This result applies to molecular structures with characteristic bond alternations. The peculiar bond alternations are caused by competition between two effects of the bond alternations of the two mutually perpendicular π‐conjugated systems, which partially cancel each other out. It is probable that we can design one‐dimensional polymers with HOMO–LUMO gaps small enough to be conductive by combining the above‐mentioned oligomers with each other as monomer units in the polymer. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Comment on “Relative Energies, Stereoelectronic Interactions, and Conformational Interconversion in Silacycloalkanes”
Authors: Arnason Ingvar , Kvaran Ágúst , Bodi Andras 
Published: February 2006

AbstractRelative energies for local minima and transition states on the potential energy surface (PES) of silacylohexane have been calculated at the B3LYP/6‐311+G(d,p) level of theory. STQN(path), and intrinsic reaction path (IRC) calculations were used to calculate the lowest‐energy pathway for the chair‐to‐chair interconversion. Both methods gave identical results. An earlier description of the PES of silacyclohexane, derived with the MM3 force field, was confirmed. A different path for the ring inversion of silacyclohexane, proposed in a recent work, is shown to be incorrect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Theoretical studies of the geometries of H2GeNaF and its insertion reaction with RH (RF, OH, NH2, CH3)
Authors: Tan Xiaojun , Li Ping , Yang Xiuli , Wang Dangsheng 
Published: February 2006

AbstractThe geometries and insertion reactions of germylene H2GeNaF with RH (RF, OH, NH2, CH3) have been investigated at the B3LYP/6‐311+G level of theory. The potential barriers of the four reactions are ∼52, 120, 184, and 257 kJ/mol, including the ZPVE corrections, respectively. Here, all the mechanisms of the four reactions are identical to each other; i.e., an intermediate has been located during the insertion reaction. The intermediate could dissociate into substituted germylane and NaF with the barrier corresponding to the dissociation energy. Correspondingly, the reaction energies for the four reactions are −43, −4, 21, and 51 kJ/mol, respectively. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
A framework to monitor environment‐induced major genes for developmental trajectories: implication for a prenatal cocaine exposure study
Authors: Hou Wei , Garvan Cynthia W. , Littell Ramon C. , Behnke Marylou , Eyler Fonda Davis , Wu Rongling 
Published: February 2006

AbstractWhether there are specific genes involved in response to different environmental agents and how such genes regulate developmental trajectories during lifetime are of fundamental importance in health, clinical and pharmaceutical research. In this article, we present a novel statistical model for monitoring environment‐induced genes of major effects on longitudinal outcomes of a trait. This model is derived within the maximum likelihood framework, incorporated by mathematical aspects of growth and developmental processes. A typical structural model is implemented to approximate time‐dependent covariance matrices for the longitudinal trait. This model allows for a number of biologically meaningful hypothesis tests regarding the effects of major genes on overall growth trajectories or particular stages of development. It can be used to test whether and how major genetic effects are expressed differently under altered environmental agents. In a well‐designed case–control study, our model has been employed to detect cocaine‐dependent genes that affect growth trajectories for head circumference during childhood. The detected gene triggers significant effects on growth curves in both cocaine‐exposed (case) and unexposed groups (control), but with different extents. Significant genotype–environment interactions due to this so‐called environment‐sensitive gene are promising for further studies toward its genomic mapping using polymorphic molecular markers. Copyright © 2006 John Wiley & Sons, Ltd.
Regulation of FAK Ser-722 phosphorylation and kinase activity by GSK3 and PP1 during cell spreading and migration
Authors: Bianchi Mariarita , De Lucchini Stefania , Marin Oriano , Turner David L. , Hanks Steven K. , Villa-Moruzzi Emma 
Published: February 2006

In addition to tyrosine sites, FAK (focal adhesion kinase) is phosphorylated on multiple serine residues. In the present study, the regulation of two of these sites, Ser-722 (S1) and Ser-911 (S4), was investigated. Phosphorylation of S1 (but not S4) decreased in resuspended cells, and recovered during spreading on fibronectin, indicating adhesion-dependent regulation. GSK3 (glycogen synthase kinase 3) inhibitors decreased S1 phosphorylation, and siRNA (short interfering RNA) silencing indicated further the involvement of GSK3β. Furthermore, GSK3β was found to become activated during cell spreading on fibronectin, and to physically associate with FAK. S1 phosphorylation was observed to decrease in wounded cell monolayers, while GSK3β underwent inactivation and later was observed to increase to the original level within 24 h. Direct phosphorylation of S1, requiring pre-phosphorylation of Ser-726 in the +4 position, was demonstrated using purified GSK3 and a synthetic peptide containing FAK residues 714–730. An inhibitory role for S1 phosphorylation in FAK signalling was indicated by findings that both alanine substitution for S1 and dephosphorylation of S1 by PP1 (serine/threonine protein phosphatase type-1) resulted in an increase in FAK kinase activity; likewise, this role was also shown by cell treatment with the GSK3 inhibitor LiCl. The inhibitory role was confirmed by the finding that cells expressing FAK with alanine substitution for S1 displayed improved cell spreading and faster migration in wound-healing and trans-well assays. Finally, the finding that S1 phosphorylation increased in cells treated with the PP1 inhibitor okadaic acid indicated targeting of this site by PP1. These results indicate an additional mechanism for regulation of FAK activity during cell spreading and migration, involving Ser-722 phosphorylation modulated through the competing actions of GSK3β and PP1.
A novel α-glucosidase from the acidophilic archaeonFerroplasma acidiphilumstrain Y with high transglycosylation activity and an unusual catalytic nucleophile
Authors: Ferrer Manuel , Golyshina Olga V. , Plou Francisco J. , Timmis Kenneth N. , Golyshin Peter N. 
Published: February 2006

Ferroplasma acidiphilum strain Y (DSM 12658), a ferrous iron-oxidizing, acidophilic and mesophilic archaeon, was found to produce a membrane-bound α-glucosidase (αGluFa) showing no significant similarity to any of the known glycoside hydrolases classified in different families and having an unusual catalytic site consisting of a threonine and a histidine residue. The highest α-glucosidase activity was found at low pH, 2.4–3.5, and the substrate preference order was: sucrose&gt;maltose&gt;maltotriose ≫maltotetraose≫malto-oligosaccharides from maltopentaose to maltoheptaose⋙soluble starch (kcat/Km was 293.0, 197.0, 18.8, 0.3 and 0.02 s−1·mM−1 respectively). The enzyme was able to transfer glucosyl groups from maltose as donor, to produce exclusively maltotriose (up to 300 g/l). Chemical modification and electrospray ionization MS analysis of 5-fluoro-α-D-glucopyranosyl-enzyme derivatives, coupled with site-directed mutagenesis, strongly suggested that the putative catalytic nucleophile in this enzyme is Thr212. Iron was found to be essential for enzyme activity and integrity, and His390 was shown to be essential for iron binding. These results suggest that the metalloenzyme αGluFa is a new member of the glycosyl hydrolase family that uses a novel mechanism for sugar glycosylation and/or transglycosylation.
H-NS is a part of a thermally controlled mechanism for bacterial gene regulation
Authors: Ono Shusuke , Goldberg Martin D. , Olsson Tjelvar , Esposito Diego , Hinton Jay C. D. , Ladbury John E. 
Published: February 2006

Temperature is a primary environmental stress to which micro-organisms must be able to adapt and respond rapidly. Whereas some bacteria are restricted to specific niches and have limited abilities to survive changes in their environment, others, such as members of the Enterobacteriaceae, can withstand wide fluctuations in temperature. In addition to regulating cellular physiology, pathogenic bacteria use temperature as a cue for activating virulence gene expression. This work confirms that the nucleoid-associated protein H-NS (histone-like nucleoid structuring protein) is an essential component in thermoregulation of Salmonella. On increasing the temperature from 25 to 37 °C, more than 200 genes from Salmonella enterica serovar Typhimurium showed H-NS-dependent up-regulation. The thermal activation of gene expression is extremely rapid and change in temperature affects the DNA-binding properties of H-NS. The reduction in gene repression brought about by the increase in temperature is concomitant with a conformational change in the protein, resulting in the decrease in size of high-order oligomers and the appearance of increasing concentrations of discrete dimers of H-NS. The present study addresses one of the key complex mechanisms by which H-NS regulates gene expression.
Zn2+-induced reversible dissociation of subunit Rpn10/p54 of theDrosophila26 S proteasome
Authors: Kiss Petra , Szabó Áron , Hunyadi-Gulyás Éva , Medzihradszky Katalin F. , Lipinszki Zoltán , Pál Margit , Udvardy Andor 
Published: February 2006

In the presence of Zn2+, the Drosophila 26 S proteasome disassembles into RP (regulatory particle) and CP (catalytic particle), this process being accompanied by the dissociation of subunit Rpn10/p54, the ubiquitin receptor subunit of the proteasome. The dissociation of Rpn10/p54 induces extensive rearrangements within the lid subcomplex of the RP, while the structure of the ATPase ring of the base subcomplex seems to be maintained. As a consequence of the dissociation of the RP, the peptidase activity of the 26 S proteasome is lost. The Zn2+-induced structural and functional changes are fully reversible; removal of Zn2+ is followed by reassociation of subunit Rpn10/p54 to the RP, reassembly of the 26 S proteasome and resumption of the peptidase activity. After the Zn2+-induced dissociation, Rpn10/p54 interacts with a set of non-proteasomal proteins. Hsp82 (heat-shock protein 82) has been identified by MS as the main Rpn10/p54-interacting protein, suggesting its role in the reassembly of the 26 S proteasome after Zn2+ removal. The physiological relevance of another Rpn10/p54-interacting protein, the Smt3 SUMO (small ubiquitin-related modifier-1)-activating enzyme, detected by chemical cross-linking, has been confirmed by yeast two-hybrid analysis. Besides the Smt3 SUMO-activating enzyme, the Ubc9 SUMO-conjugating enzyme also exhibited in vivo interaction with the 5′-half of Rpn10/p54 in yeast cells. The mechanism of 26 S proteasome disassembly after ATP depletion is clearly different from that induced by Zn2+. Rpn10/p54 is permanently RP-bound during the ATP-dependent assembly–disassembly cycle, but during the Zn2+ cycle it reversibly shuttles between the RP-bound and free states.
A direct, continuous, sensitive assay for protein disulphide-isomerase based on fluorescence self-quenching
Authors: Raturi Arun , Vacratsis Panayiotis O. , Seslija Dana , Lee Lana , Mutus Bulent 
Published: February 2006

PDI (protein disulphide-isomerase) activity is generally monitored by insulin turbidity assay or scrambled RNase assay, both of which are performed by UV–visible spectroscopy. In this paper, we present a sensitive fluorimetric assay for continuous determination of disulphide reduction activity of PDI. This assay utilizes the pseudo-substrate diabz-GSSG [where diabz stands for di-(o-aminobenzoyl)], which is formed by the reaction of isatoic anhydride with the two free N-terminal amino groups of GSSG. The proximity of two benzoyl groups leads to quenching of the diabz-GSSG fluorescence by approx. 50% in comparison with its non-disulphide-linked form, abz-GSH (where abz stands for o-aminobenzoyl). Therefore the PDI-dependent disulphide reduction can be monitored by the increase in fluorescence accompanying the loss of proximity-quenching upon conversion of diabz-GSSG into abz-GSH. The apparent Km of PDI for diabz-GSSG was estimated to be approx. 15 μM. Unlike the insulin turbidity assay and scrambled RNase assay, the diabz-GSSG-based assay was shown to be effective in determining a single turnover of enzyme in the absence of reducing agents with no appreciable blank rates. The assay is simple to perform and very sensitive, with an estimated detection limit of approx. 2.5 nM PDI, enabling its use for the determination of platelet surface PDI activity in crude sample preparations.
Tumour necrosis factor α induces co-ordinated activation of rat GSH synthetic enzymes via nuclear factor κB and activator protein-1
Authors: Yang Heping , Magilnick Nathaniel , Ou Xiaopeng , Lu Shelly C. 
Published: February 2006

GSH synthesis occurs via two enzymatic steps catalysed by GCL [glutamate–cysteine ligase, made up of GCLC (GCL catalytic subunit), and GCLM (GCL modifier subunit)] and GSS (GSH synthetase). Co-ordinated up-regulation of GCL and GSS further enhances GSH synthetic capacity. The present study examined whether TNFα (tumour necrosis factor α) influences the expression of rat GSH synthetic enzymes. To facilitate transcriptional studies of the rat GCLM, we cloned its 1.8 kb 5′-flanking region. TNFα induces the expression and recombinant promoter activities of GCLC, GCLM and GSS in H4IIE cells. TNFα induces NF-κB (nuclear factor κB) and AP-1 (activator protein 1) nuclear-binding activities. Blocking AP-1 with dominant negative c-Jun or NF-κB with IκBSR (IκB super-repressor, where IκB stands for inhibitory κB) lowered basal expression and inhibited the TNFα-mediated increase in mRNA levels of all three genes. While all three genes have multiple AP-1-binding sites, only GCLC has a NF-κB-binding site. Overexpression with p50 or p65 increased c-Jun mRNA levels, c-Jun-dependent promoter activity and the promoter activity of GCLM and GSS. Blocking NF-κB also lowered basal c-Jun expression and blunted the TNFα-mediated increase in c-Jun mRNA levels. TNFα treatment resulted in increased c-Jun and Nrf2 (nuclear factor erythroid 2-related factor 2) nuclear binding to the antioxidant response element of the rat GCLM and if this was prevented, TNFα no longer induced the GCLM promoter activity. In conclusion, both c-Jun and NF-κB are required for basal and TNFα-mediated induction of GSH synthetic enzymes in H4IIE cells. While NF-κB may exert a direct effect on the GCLC promoter, it induces the GCLM and GSS promoters indirectly via c-Jun.
UDP-glucose dehydrogenases of maize: a role in cell wall pentose biosynthesis
Authors: Kärkönen Anna , Murigneux Alain , Martinant Jean-Pierre , Pepey Elodie , Tatout Christophe , Dudley Bernard J. , Fry Stephen C. 
Published: February 2006

UDPGDH (UDP-D-glucose dehydrogenase) oxidizes UDP-Glc (UDP-D-glucose) to UDP-GlcA (UDP-D-glucuronate), the precursor of UDP-D-xylose and UDP-L-arabinose, major cell wall polysaccharide precursors. Maize (Zea mays L.) has at least two putative UDPGDH genes (A and B), according to sequence similarity to a soya bean UDPGDH gene. The predicted maize amino acid sequences have 95% similarity to that of soya bean. Maize mutants with a Mu-element insertion in UDPGDH-A or UDPGDH-B were isolated (udpgdh-A1 and udpgdh-B1 respectively) and studied for changes in wall polysaccharide biosynthesis. The udpgdh-A1 and udpgdh-B1 homozygotes showed no visible phenotype but exhibited 90 and 60–70% less UDPGDH activity respectively than wild-types in a radiochemical assay with 30 μM UDP-glucose. Ethanol dehydrogenase (ADH) activity varied independently of UDPGDH activity, supporting the hypothesis that ADH and UDPGDH activities are due to different enzymes in maize. When extracts from wild-types and udpgdh-A1 homozygotes were assayed with increasing concentrations of UDP-Glc, at least two isoforms of UDPGDH were detected, having Km values of approx. 380 and 950 μM for UDP-Glc. Leaf and stem non-cellulosic polysaccharides had lower Ara/Gal and Xyl/Gal ratios in udpgdh-A1 homozygotes than in wild-types, whereas udpgdh-B1 homozygotes exhibited more variability among individual plants, suggesting that UDPGDH-A activity has a more important role than UDPGDH-B in UDP-GlcA synthesis. The fact that mutation of a UDPGDH gene interferes with polysaccharide synthesis suggests a greater importance for the sugar nucleotide oxidation pathway than for the myo-inositol pathway in UDP-GlcA biosynthesis during post-germinative growth of maize.
Phenotypic analysis of trypanothione synthetase knockdown in the African trypanosome
Authors: Ariyanayagam Mark R. , Oza Sandra L. , Guther Maria Lucia S. , Fairlamb Alan H. 
Published: February 2006

Trypanothione plays a pivotal role in defence against chemical and oxidant stress, thiol redox homoeostasis, ribonucleotide metabolism and drug resistance in parasitic kinetoplastids. In Trypanosoma brucei, trypanothione is synthesized from glutathione and spermidine by a single enzyme, TryS (trypanothione synthetase), with glutathionylspermidine as an intermediate. To examine the physiological roles of trypanothione, tetracycline-inducible RNA interference was used to reduce expression of TRYS. Following induction, TryS protein was reduced &gt;10-fold and growth rate was reduced 2-fold, with concurrent 5–10-fold decreases in glutathionylspermidine and trypanothione and an up to 14-fold increase in free glutathione content. Polyamine levels were not significantly different from non-induced controls, and neither was the intracellular thiol redox potential, indicating that these factors are not responsible for the growth defect. Compensatory changes in other pathway enzymes were associated with prolonged suppression of TryS: an increase in trypanothione reductase and γ-glutamylcysteine synthetase, and a transient decrease in ornithine decarboxylase. Depleted trypanothione levels were associated with increases in sensitivity to arsenical, antimonial and nitro drugs, implicating trypanothione metabolism in their mode of action. Escape mutants arose after 2 weeks of induction, with all parameters, including growth, returning to normal. Selective inhibitors of TryS are required to fully validate this novel drug target.
High-affinity interaction of the N-terminal myristoylation motif of the neuronal calcium sensor protein hippocalcin with phosphatidylinositol 4,5-bisphosphate
Authors: O'Callaghan Dermott W. , Haynes Lee P. , Burgoyne Robert D. 
Published: February 2006

Many proteins are associated with intracellular membranes due to their N-terminal myristoylation. Not all myristoylated proteins have the same localization within cells, indicating that other factors must determine their membrane targeting. The NCS (neuronal calcium sensor) proteins are a family of Ca2+-binding proteins with diverse functions. Most members of the family are N-terminally myristoylated and are either constitutively membrane-bound or have a Ca2+/myristoyl switch that allows their reversible membrane association in response to Ca2+ signals. In the case of hippocalcin and NCS-1, or alternatively KChIP1 (K+ channel-interacting protein 1), their N-terminal myristoylation motifs are sufficient for targeting to distinct organelles. We have shown that an N-terminal myristoylated hippocalcin peptide is able to specifically reproduce the membrane targeting of hippocalcin/NCS-1 when introduced into permeabilized cells. The peptide binds to liposomes containing phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] with high affinity (Kd 50 nM). Full-length hippocalcin also bound preferentially to liposomes supplemented with PtdIns(4,5)P2. Co-expression of hippocalcin-(1–14)–ECFP (enhanced cyan fluorescent protein) or NCS-1–ECFP partially displaced the expressed PH (pleckstrin homology) domain of phospholipase δ1 from the plasma membrane in live cells, indicating that they have a higher affinity for PtdIns(4,5)P2 than does this PH domain. The Golgi localization of the PH domain of FAPP1 (four-phosphate-adaptor protein 1), which binds to phosphatidylinositol 4-phosphate, was unaffected. The localization of NCS-1 and hippocalcin is likely to be determined, therefore, by their interaction with PtdIns(4,5)P2.