Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation

The C-terminal Src kinase (Csk) phosphorylates and down-regulates Src family tyrosine kinases. The Csk-binding protein (Cbp) localizes Csk close to its substrates at the plasma membrane, and increases the specific activity of the kinase. To investigate this long-range catalytic effect, the phosphorylation of Src and the conformation of Csk were investigated in the presence of a high-affinity phosphopeptide derived from Cbp. This peptide binds tightly to the SH2 domain and enhances Src recognition (lowers K(m)) by increasing the apparent phosphoryl transfer rate in the Csk active site, a phenomenon detected in rapid quench flow experiments. Previous studies demonstrated that the regulation of Csk activity is linked to conformational changes in the enzyme that can be probed with hydrogen-deuterium exchange methods. We show that the Cbp peptide impacts deuterium incorporation into its binding partner (the SH2 domain), and into the SH2-kinase linker and several sequences in the kinase domain, including the glycine-rich loop in the active site. These findings, along with computational data from normal mode analyses, suggest that the SH2 domain moves in a cantilever fashion with respect to the small lobe of the kinase domain, ordering the active site for catalysis. The binding of a small Cbp-derived peptide to the SH2 domain of Csk modifies these motions, enhancing Src recognition.     

Mechanism of free radical nitric oxide-mediated Ras guanine nucleotide dissociation

Ras proteins cycle between GDP-bound and GTP-bound states to modulate a diverse array of cellular growth processes. In this study, we have elucidated a mechanism by which nitric oxide, in the presence of oxygen (NO/O2), regulates Ras activity. We show that treatment of Ras with NO/O2 causes conversion of Ras-bound GDP into a free 463.3 Da nucleotide-nitration product. Mass and UV/visible spectroscopic analyses suggest that this nitration product is 5-guanidino-4-nitroimidazole diphosphate (NIm-DP), a degradation product of 5-nitro-GDP. These results indicate that NO/O2 mediates Ras guanine nucleotide exchange (GNE) by conversion of Ras-bound GDP into an unstable 5-nitro-GDP. 5-Nitro-GDP can be produced by radical-based reaction of the GDP guanine base with nitrogen dioxide (*NO2). We also provide evidence that the Ras Phe28 side-chain plays a key role in the formation of a NO/O2-induced Ras 5-nitro-GDP product. We previously proposed a mechanism of NO/O2-mediated Ras GNE, in which *NO2, formed by the reaction of NO with O2, generates a Ras Cys118 thiyl radical (Ras-S118) intermediate. In the present study, we provide evidence for a radical-based mechanism of NO/O2-mediated Ras GNE. According to this mechanism, reaction of NO with O2 produces *NO2. *NO2 then reacts with Ras to produce Ras-S118, which withdraws an electron from the Ras-bound guanine nucleotide base to produce a guanine nucleotide diphosphate cation radical (G(+)-DP) via the Phe28 side-chain. G(+)-DP is subsequently converted to a neutral radical, and can react with another *NO2 to produce 5-nitro-GDP. This radical-based reaction process disrupts key binding interactions between Ras and the guanine base, resulting in release of GDP from Ras and its conversion to free 5-nitro-GDP. This mechanism is likely to be common to other NKCD motif-containing Ras superfamily GTPases, as NO/O2 also facilitates GNE on the redox-active Rap1A and Rab3A GTPases.     

Viability of invertebrate diapausing eggs exposed to saltwater: implications for Great Lakes’ ship ballast management

International shipping has been the dominant vector of nonindigenous species introductions to the Laurentian Great Lakes over the past century. Apparent ballast-mediated invasions have been recorded in recent years, despite the implementation of voluntary ballast water exchange regulations in 1989. Since unregulated no-ballast-on-board vessels currently dominate inbound traffic to the Great Lakes, it has been proposed that live or dormant organisms contained in residual ballast of these vessels may be partially responsible for recent invasions. Alternatively, euryhaline species may pose a significant invasion threat because they can potentially survive ballast exchange. In this study, we explored whether exposure to open-ocean water (32) reduced the viability of invertebrate diapausing eggs in ballast sediments. Sediments collected from three transoceanic ships and from three freshwater habitats were exposed to open-ocean seawater. Egg viability, assessed as the abundance of taxa hatched between exposed and unexposed sediments, was not affected by saltwater exposure in any experiment. Species richness of hatched diapausing eggs was reduced by saltwater exposure in only one of seven trials. Our results indicate that oligostenohaline zooplankton may pose an invasion risk because their diapausing eggs are largely resistant to exposure to open-ocean saltwater.     

Detection of a hidden folding intermediate in the focal adhesion target domain: Implications for its function and folding

The focal adhesion target (FAT) domain of focal adhesion kinase has a four-helix bundle structure. Based on a hydrogen exchange-constrained computer simulation study and some indirect experimental results, it has been suggested that a partially unfolded state of the FAT domain with the N-terminal helix unfolded plays an important role in its biological function. Here, using a native-state hydrogen exchange method, we directly detected an intermediate with the N-terminal helix unfolded in a mutant (Y925E) of the FAT domain. In addition, kinetic folding studies on the FAT domain suggest that this intermediate exists on the native side of the rate-limiting transition state for folding. These results provide more direct evidence of the existence of the proposed intermediate and help to understand the folding mechanism of small single domain proteins.     

Oxylipin analysis methods

Practical guidelines for monitoring and measuring compounds such as jasmonates, ketols, ketodi(tri)enes and hydroxy-fatty acids as well as detecting the presence of novel oxylipins are presented. Additionally, a protocol for the penetrant analysis of non-enzymatic lipid oxidation is described. Each of the methods, which employ gas chromatography/mass spectrometry, can be applied without specialist knowledge or recourse to the latest analytical instrumentation. Additional information on oxylipin quantification and novel protocols for preparing oxygen isotope-labelled internal standards are provided. Four developing areas of research are identified: (i) profiling of the unbound cellular pools of oxylipins; (ii) profiling of esterified oxylipins and/or monitoring of their release from parent lipids; (iii) monitoring of non-enzymatic lipid oxidation; (iv) analysis of unstable and reactive oxylipins. The methods and protocols presented herein are designed to give technical insights into the first three areas and to provide a platform from which to enter the fourth area.     

The "Kluge-Lüttge Kammer": a preliminary evaluation of an enclosed, Crassulacean acid metabolism (CAM) Mesocosm that allows separation of synchronized and desynchronized contributions of plants to whole system gas exchange

Crassulacean acid metabolism (CAM) is recognized as a photosynthetic adaptation of plants to arid habitats. This paper presents a proof-of-concept evaluation of partitioning net CO2 exchanges for soil and plants in an arid, exclusively CAM mesocosm, with soil depth and succulent plant biomass approximating that of natural Sonoran Desert ecosystems. We present the first evidence that an enclosed CAM-dominated soil and plant community exposed to a substantial day/night temperature difference (30/20 degrees C), exhibits a diel gas exchange pattern consisting of four consecutive phases with a distinct nocturnal CO2 uptake. These phases were modulated by plant assimilation and soil respiration processes. Day-time stomatal closure of the CAM cycle during phase III was used to eliminate aboveground photosynthetic assimilation and respiration and thereby to estimate belowground plant plus soil respiration. Rapid changes in temperature appeared to synchronize single plant gas exchange but individual plant gas exchange patterns were desynchronized at constant day/night temperatures (25 degrees C), masking the distinct mesocosm pattern. Overall, the mean carbon budget of this CAM model Sonoran Desert system was negative, releasing an average of 22.5 mmol CO2 m-2 d-1. The capacity for nocturnal CO2 assimilation in this exclusively CAM mesocosm was inadequate to recycle CO2 released by plant and soil respiration.     

Responses of Alnus glutinosa to anaerobic conditions--mechanisms and rate of oxygen flux into the roots

Upon exposure to waterlogged growing conditions two-year-old alder trees reduced total root mass. Roots were concentrated in the uppermost soil horizon, and only few coarse roots penetrated into deeper soil layers. Root porosity was only slightly affected and did not exceed 8 % in fine roots. Porosity of coarse roots was higher (27 %) but unaffected by growing conditions. The stem base area covered by lenticels increased strongly and so did the cross section diameter of the stem base. The latter showed a highly significant correlation with O (2) transport into the roots, measured by a Clark type oxygen electrode. Exposure of the lower 5 cm of the stem base, where lenticels were concentrated, to pure N (2) led to a cessation of O (2) transport, confirming that lenticels were the major site of air entry into the stem. In alder plants grown under waterlogged conditions, temperature had a pronounced effect on O (2) gas exchange of the root system. The temperature compensation point, i.e., the temperature where O (2) transport equals O (2) consumption by respiration, was 10.5 degrees C for the entire root system, when measured in a range of 0.15 - 0.20 mmol dissolved O (2) L (-1), which is typical for an open water surface equilibrated with air. O (2) net flow was inversely related to O (2) concentration in the rooting media, indicating that higher root and microbial respiration induced higher net fluxes of O (2) into the root system. With 0.04 mmol dissolved O (2) L (-1) nutrient solution, the temperature compensation point increased to 20 degrees C. Measurement of O (2) gradients in the rhizosphere of agar-embedded roots using O (2) microelectrodes showed a preference for O (2) release in the tip region of coarse roots. Increasing stem temperature over air temperature by 5 degrees C stimulated O (2) flux into the roots as suggested by the model of thermo-osmotic gas transport. However determination of stem and air temperature in a natural alder swamp in northern Germany revealed that within the experimental period of almost one year, temperature gradients required for thermo-osmotic gas transport were very seldom. From this it is concluded that under natural conditions in northern Germany, oxygen diffusion along the stem into the root system is driven by O (2) concentration gradients rather than by thermo-osmosis.     

Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments

Systems biology applies quantitative, mechanistic modelling to study genetic networks, signal transduction pathways and metabolic networks. Mathematical models of biochemical networks can look very different. An important reason is that the purpose and application of a model are essential for the selection of the best mathematical framework. Fundamental aspects of selecting an appropriate modelling framework and a strategy for model building are discussed. Concepts and methods from system and control theory provide a sound basis for the further development of improved and dedicated computational tools for systems biology. Identification of the network components and rate constants that are most critical to the output behaviour of the system is one of the major problems raised in systems biology. Current approaches and methods of parameter sensitivity analysis and parameter estimation are reviewed. It is shown how these methods can be applied in the design of model-based experiments which iteratively yield models that are decreasingly wrong and increasingly gain predictive power.     

Preparation and in vitro evaluation of polystyrene-coated diltiazem-resin complex by oil-in-water emulsion solvent evaporation method

The purpose of this study was to examine the suitability of polystyrene-coated (PS-coated) microcapsules of drug-resin complex for achieving prolonged release of diltiazem-HCl, a highly water-soluble drug, in simulated gastric and intestinal fluid. The drug was bound to Indion 254, a cation-exchange resin, and the resulting resinate was microencapsulated with PS using an oil-in-water emulsion-solvent evaporation method. The effect of various formulation parameters on the characteristics of the microcapsules was studied. Mean diameter and encapsulation efficiency of the microcapsules rose with an increase in the concentration of emulsion stabilizer and the coat/core ratio, while the same characteristics tended to decrease with an increase in the volume of the organic disperse phase. The desorption of drug from the uncoated resinate was quite rapid and independent of the pH of the dissolution media. On the other hand, the drug release from the microcapsules was prolonged for different periods of time depending on the formulation parameters and was also found to be independent of the pH of the dissolution media. Both the encapsulation efficiency and the retardation of drug release were found to be dependent on the uniformity of coating, which in turn was influenced by the formulation parameters. Kinetic studies revealed that the desorption of drug from the resinate obeyed the typical particle diffusion process, whereas the drug release from the microencapsulated resinate followed the diffusion-controlled model in accordance with the Higuchi equation. PS appeared to be a suitable polymer to provide prolonged release of diltiazem independent of the pH of the dissolution media.