Home About us Contact
|
Home About us Contact | ||
|
|
||
Cooperative Manner (cooperative + manner)
Selected AbstractsDynamic zone topology routing protocol for MANETsEUROPEAN TRANSACTIONS ON TELECOMMUNICATIONS, Issue 4 2007Mehran Abolhasan The limited scalability of the proactive and reactive routing protocols have resulted in the introduction of new generation of routing in mobile ad hoc networks, called hybrid routing. These protocols aim to extend the scalability of such networks beyond several hundred to thousand of nodes by defining a virtual infrastructure in the network. However, many of the hybrid routing protocols proposed to date are designed to function using a common pre-programmed static zone map. Other hybrid protocols reduce flooding by grouping nodes into clusters, governed by a cluster-head, which may create performance bottlenecks or a single point of failures at each cluster-head node. We propose a new routing strategy in which zones are created dynamically, using a dynamic zone creation algorithm. Therefore, nodes are not restricted to a specific region. Additionally, nodes perform routing and data forwarding in a cooperative manner, which means that in the case failure, route recalculation is minimised. Routing overheads are also further reduced by introducing a number of GPS-based location tracking mechanisms, which reduces the route discovery area and the number of nodes queried to find the required destination. Copyright © 2006 AEIT [source] Physicochemical properties and distinct DNA binding capacity of the repressor of temperate Staphylococcus aureus phage ,11FEBS JOURNAL, Issue 7 2009Tridib Ganguly The repressor protein and cognate operator DNA of any temperate Staphylococcus aureus phage have not been investigated in depth, despite having the potential to enrich the molecular biology of the staphylococcal system. In the present study, using the extremely pure repressor of temperate Staphylococcus aureus phage ,11 (CI), we demonstrate that CI is composed of ,-helix and ,-sheet to a substantial extent at room temperature, possesses two domains, unfolds at temperatures above 39 °C and binds to two sites in the ,11 cI - cro intergenic region with variable affinity. The above CI binding sites harbor two homologous 15 bp inverted repeats (O1 and O2), which are spaced 18 bp apart. Several guanine bases located in and around O1 and O2 demonstrate interaction with CI, indicating that these 15 bp sites are used as operators for repressor binding. CI interacted with O1 and O2 in a cooperative manner and was found to bind to operator DNA as a homodimer. Interestingly, CI did not show appreciable binding to another homologous 15 bp site (O3) that was located in the same primary immunity region as O1 and O2. Taken together, these results suggest that ,11 CI and the ,11 CI,operator complex resemble significantly those of the lambdoid phages at the structural level. The mode of action of ,11 CI, however, may be distinct from that of the repressor proteins of , and related phages. [source] Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric formFEBS JOURNAL, Issue 10 2008Yuichi Koga The crystal structure of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-GK) in a dimeric form was determined at a resolution of 2.4 Å. This is the first crystal structure of a hyperthermophilic glycerol kinase. The overall structure of the Tk-GK dimer is very similar to that of the Escherichia coli glycerol kinase (Ec-GK) dimer. However, two dimers of Ec-GK can associate into a tetramer with a twofold axis, whereas those of Tk-GK cannot. This may be the reason why Tk-GK is not inhibited by fructose 1,6-bisphosphate, because the fructose 1,6-bisphosphate binding site is produced only when a tetrameric structure is formed. Differential scanning calorimetry analyses indicate that Tk-GK is a highly thermostable protein with a melting temperature (Tm) of 105.4 °C for the major transition. This value is higher than that of Ec-GK by 34.1 °C. Comparison of the crystal structures of Tk-GK and Ec-GK indicate that there is a marked difference in the number of ion pairs in the ,16 helix. Four ion pairs, termed IP1,IP4, are formed in this helix in the Tk-GK structure. To examine whether these ion pairs contribute to the stabilization of Tk-GK, four Tk-GK and four Ec-GK derivatives with reciprocal mutations at the IP1,IP4 sites were constructed. The determination of their stabilities indicates that the removal of each ion pair does not affect the stability of Tk-GK significantly, whereas the mutations designed to introduce one of these ion pairs stabilize or destabilize Ec-GK considerably. These results suggest that the ion pairs in the ,16 helix contribute to the stabilization of Tk-GK in a cooperative manner. [source] Design syntheses and mitochondrial complex I inhibitory activity of novel acetogenin mimicsFEBS JOURNAL, Issue 9 2000Kaoru Kuwabara Some natural acetogenins are the most potent inhibitors of mitochondrial complex I. These compounds are characterized by two functional units [i.e. hydroxylated tetrahydrofuran (THF) and ,,,-unsaturated ,-lactone ring moieties] separated by a long alkyl spacer. To elucidate which structural factors of acetogenins, including their active conformation, are crucial for the potent inhibitory activity we synthesized a novel bis-acetogenin and its analogues possessing two ,-lactone rings connected to bis-THF rings by flexible alkyl spacers. The inhibitory potency of the bis-acetogenin with bovine heart mitochondrial complex I was identical to that of bullatacin, one of the most potent natural acetogenins. This result indicated that one molecule of the bis-acetogenin does not work as two reactive inhibitors, suggesting that a ,-lactone and the THF ring moieties act in a cooperative manner on the enzyme. In support of this, either of the two ring moieties synthesized individually showed no or very weak inhibitory effects. Moreover, combined use of the two ring moieties at various molar ratios exhibited no synergistic enhancement of the inhibitory potency. These observations indicate that both functional units work efficiently only when they are directly linked by a flexible alkyl spacer. Therefore, some specific conformation of the spacer must be important for optimal positioning of the two units in the enzyme. Furthermore, the ,,,-unsaturated ,-lactone, the 4-OH group in the spacer region, the long alkyl tail attached to the THF unit and the stereochemistry surrounding the hydroxylated bis-THF rings were not crucial for the activity, although these are the most common structural features of natural acetogenins. The present study provided useful guiding principles not only for simplification of complicated acetogenin structure, but also for further wide structural modifications of these molecules. [source] Study of the subunit interactions in myosin phosphatase by surface plasmon resonanceFEBS JOURNAL, Issue 6 2000Attila Tóth The interactions of the catalytic subunit of type 1 protein phosphatase (PP1c) and the N-terminal half (residues 1,511) of myosin phosphatase target subunit 1 (MYPT1) were studied. Biotinylated MYPT1 derivatives were immobilized on streptavidin-biosensor chips, and binding parameters with PP1c were determined by surface plasmon resonance (SPR). The affinity of binding of PP1c was: MYPT11,296 > MYPT11,38 > MYPT123,38. No binding was detected with MYPT11,34, suggesting a critical role for residues 35,38, i.e. the PP1c binding motif. Binding of residues 1,22 was inferred from: a higher affinity binding to PP1c for MYPT11,38 compared to MYPT123,38, as deduced from SPR kinetic data and ligand competition assays; and an activation of the myosin light chain phosphatase activity of PP1c by MYPT11,38, but not by MYPT123,38. Residues 40,296 (ankyrin repeats) in MYPT11,296 inhibited the phosphorylase phosphatase activity of PP1c (IC50 = 0.2 nm), whereas MYPT11,38, MYPT123,38 or MYPT11,34 were without effect. MYPT140,511, which alone did not bind to PP1c, showed facilitated binding to the complexes of PP1c,MYPT11,38 and PP1c,MYPT123,38. The inhibitory effect of MYPT140,511 on the phosphorylase phosphatase activity of PP1c also was increased in the presence of MYPT11,38. The binding of MYPT1304,511 to complexes of PP1c and MYPT11,38, or MYPT11,296, was detected by SPR. These results suggest that within the N-terminal half of MYPT1 there are at least four binding sites for PP1c. The essential interaction is with the PP1c-binding motif and the other interactions are facilitated in an ordered and cooperative manner. [source] Self-Assembled PEO-Peptide Nanotapes as Ink for Plotting Nonwoven Silica Nanocomposites and Mesoporous Silica Fiber NetworksMACROMOLECULAR RAPID COMMUNICATIONS, Issue 4 2008Stefanie Kessel Abstract Macroscopic networks of oriented polymer-silica composite fibers can be accessed via a convenient 2D-plotting process. By using self-assembled PEO-peptide nanotapes as an ink to draw the composite fibers, the macroscopic form of the fiber networks, the line width, and both network orientation as well as network anisotropy can be defined. The plotting process relies on a biomimetic silicification route, which combines self-assembly and peptide-directed silicification in a cooperative manner. The local injection of PEO-peptide nanotapes into a thin layer of a dilute solution of pre-hydrolyzed TMOS leads to the rapid formation of the composite fibers, which exhibit several levels of hierarchical order. It was shown, that the rate of plotting is a parameter, enabling one to control the line width and the orientation of the nano- and sub-micrometer structure elements in the network. Moreover, the plotted composite fibers can be used as precursors for networks of oriented, mesoporous silica-fibers. After calcination procedures, nonwoven silica fabrics can be obtained with high surface areas and cylindrical pores aligned in plot direction. [source] Flame retarded polymer layered silicate nanocomposites: a review of commercial and open literature systems,POLYMERS FOR ADVANCED TECHNOLOGIES, Issue 4 2006Alexander B. Morgan Abstract This paper is a review of polymer nanocomposites used for flame retardancy applications, including commercial materials and open literature examples. Where possible, details on how the nanocomposite and flame retardant work together will be discussed. The key lesson from this review is that while the polymer nanocomposite can be considered to be flame retarded (or a flame retardant) by definition, these materials by themselves are unable to pass regulatory fire safety tests such as UL-94,V. Therefore, additional flame retardants are needed in combination with the polymer nanocomposite to pass these tests. In multiple examples, the nanocomposite works with other flame retardants in a synergistic or cooperative manner to lower the polymer flammability (heat release rate). Finally, a discussion on research needs and outlook for polymer nanocomposite flammability research is included. Copyright © 2006 John Wiley & Sons, Ltd. [source] Voltage-dependent and -independent titration of specific residues accounts for complex gating of a ClC chloride channel by extracellular protonsTHE JOURNAL OF PHYSIOLOGY, Issue 7 2009María Isabel Niemeyer The ClC transport protein family comprises both Cl, ion channel and H+/Cl, and H+/NO3, exchanger members. Structural studies on a bacterial ClC transporter reveal a pore obstructed at its external opening by a glutamate side-chain which acts as a gate for Cl, passage and in addition serves as a staging post for H+ exchange. This same conserved glutamate acts as a gate to regulate Cl, flow in ClC channels. The activity of ClC-2, a genuine Cl, channel, has a biphasic response to extracellular pH with activation by moderate acidification followed by abrupt channel closure at pH values lower than ,7. We have now investigated the molecular basis of this complex gating behaviour. First, we identify a sensor that couples extracellular acidification to complete closure of the channel. This is extracellularly-facing histidine 532 at the N-terminus of transmembrane helix Q whose neutralisation leads to channel closure in a cooperative manner. We go on to show that acidification-dependent activation of ClC-2 is voltage dependent and probably mediated by protonation of pore gate glutamate 207. Intracellular Cl, acts as a voltage-independent modulator, as though regulating the pKa of the protonatable residue. Our results suggest that voltage dependence of ClC-2 is given by hyperpolarisation-dependent penetration of protons from the extracellular side to neutralise the glutamate gate deep within the channel, which allows Cl, efflux. This is reminiscent of a partial exchanger cycle, suggesting that the ClC-2 channel evolved from its transporter counterparts. [source] Transcriptional activity of ecdysone receptor isoforms is regulated by modulation of receptor stability and interaction with Ab- and C-domains of the heterodimerization partner ultraspiracleARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 3 2009Heike Ruff Abstract The stability of ecdysone receptor (EcR) expressed in a heterologous system is regulated in an isoform-specific manner and modified by ligand and heterodimerization partner. Transcriptional activities of various receptor complexes with Usp and ligand as determined by reporter assays are the result of two effects: change in receptor concentration and altered transcriptional capability. Transcriptional activity of EcR-A is low when compared to EcR-B1 independent of the absence or presence of Ultraspiracle (Usp). Ligand increased the concentration of EcR-A, but had no effect on the transcriptional capability, in contrast to EcR-B1, which is not stabilized by hormone or Usp, but the transcriptional capability is enhanced by heterodimerization and ligand. Exchange of the AB-domain of Usp by the activation domain (AD) of Vp16 revealed that the N-terminus of Usp inhibited transcriptional activity only with EcR-B isoforms, whereas the hexapeptide in the AB-domain of wild type Usp adjacent to the C-domain of Usp harbours an activating function. Deletion of the C-domain of Usp did not affect the stability of the receptor complex, but reduced the transcriptional capability of heterodimers with all EcR-isoforms, indicating that the stability of the receptor, which is important for termination of the hormone signal transduction, is regulated in a cooperative manner by the AB-domains of EcR and Usp, and ligand. We show the active role of Usp in modulation of the transcriptional activity of the heterodimer in an isoform-specific manner by the inhibitory N-terminus, the activating hexapeptide in the AB-domain, and the C-domain of Usp. © 2009 Wiley Periodicals, Inc. [source] Kinetic, Thermodynamic, and Mechanistic Patterns for Free (Unbound) Cytochrome c at Au/SAM Junctions: Impact of Electronic Coupling, Hydrostatic Pressure, and Stabilizing/Denaturing AdditivesCHEMISTRY - A EUROPEAN JOURNAL, Issue 27 2006Dimitri E. Khoshtariya Prof. Dr. Abstract Combined kinetic (electrochemical) and thermodynamic (calorimetric) investigations were performed for an unbound (intact native-like) cytochrome c (CytC) freely diffusing to and from gold electrodes modified by hydroxyl-terminated self-assembled monolayer films (SAMs), under a unique broad range of experimental conditions. Our approach included: 1) fine-tuning of the charge-transfer (CT) distance by using the extended set of Au-deposited hydroxyl-terminated alkanethiol SAMs [-S-(CH2)n -OH] of variable thickness (n=2, 3, 4, 6, 11); 2) application of a high-pressure (up to 150,MPa) kinetic strategy toward the representative Au/SAM/CytC assemblies (n=3, 4, 6); 3) complementary electrochemical and microcalorimetric studies on the impact of some stabilizing and denaturing additives. We report for the first time a mechanistic changeover detected for "free" CytC by three independent kinetic methods, manifested through 1) the abrupt change in the dependence of the shape of the electron exchange standard rate constant (ko) versus the SAM thickness (resulting in a variation of estimated actual CT range within ca. 15 to 25 Å including ca. 11 Å of an "effective" heme-to-,-hydroxyl distance). The corresponding values of the electronic coupling matrix element vary within the range from ca. 3 to 0.02 cm,1; 2) the change in activation volume from +6.7 (n=3), to ,0 (n=4), and ,5.5 (n=6) cm3,mol,1 (disclosing at n=3 a direct pressure effect on the protein's internal viscosity); 3) a "full" Kramers-type viscosity dependence for ko at n=2 and 3 (demonstrating control of an intraglobular friction through the external dynamic properties), and its gradual transformation to the viscosity independent (nonadiabatic) regime at n=6 and 11. Multilateral cross-testing of "free" CytC in a native-like, glucose-stabilized and urea-destabilized (molten-globule-like) states revealed novel intrinsic links between local/global structural and functional characteristics. Importantly, our results on the high-pressure and solution-viscosity effects, together with matching literature data, strongly support the concept of "dynamic slaving", which implies that fluctuations involving "small" solution components control the proteins' intrinsic dynamics and function in a highly cooperative manner as far as CT processes under adiabatic conditions are concerned. [source] | |||||||||||||