Sequence relationships in the legume lectin fold and other jelly rolls

Distant sequence relationships in proteins containing the ßjelly-roll fold were investigated using sensitive sequence comparisonmethods, including PSI-BLAST and Hidden Markov Models. A relationshipwas identified between the rmlC-like and phosphomannose isomeraseSCOP (version 1.53) superfamilies, which were merged in themost recent SCOP release. No other distant sequence relationshipslinking jelly roll superfamilies were found.     

Hysteretic response of human erythrocyte pyruvate kinase to phosphoenolpyruvate. Potential role in regulation of 2,3-bisphosphoglycerate metabolism

Human erythrocyte pyruvate kinase (EC 2.7.1.40, ATP-pyruvate phosphotransferase) was found to display a time-dependent activation (lag phase) in the reaction progress curves. The extent of this lag phase depended upon the treatment of the enzyme prior to assay. Preincubation of the enzyme with adenine nucleotides amplified the lag, whereas prior treatment with phosphoenolpyruvate diminished it. The activation process was first order in enzyme with the pseudo first order rate constants being a hyperbolic function of phosphoenolpyruvate concentration. The data provide evidence for a phosphoenol-pyruvate-mediated conversion of the enzyme to a more active form. Studies with the irreversible sulfhydryl inhibitor, N-ethylmaleimide (MalNEt), provided additional evidence for different conformational states of the enzyme induced by its substrates and effectors. Adenine nucleotides were found to promote inactivation by MalNEt and phosphoenolpyruvate protected against MalNEt. The possible metabolic significance of this "hysteretic" pyruvate kinase is discussed in relation to the known role of this enzyme in 2,3-bisphosphoglycerate metabolism (Rose, I.A. (1971) Exp. Eye Res. 11, 264-272).     

AI-based algorithms for protein surface comparisons.

Many current methods for protein analysis depend on the detection of similarity in either the primary sequence, or the overall tertiary structure (the Calpha atoms of the protein backbone). These common sequences or structures may imply similar functional characteristics or active properties. Active sites and ligand binding sites usually occur on or near the surface of the protein; so similarly shaped surface regions could imply similar functions. We investigate various methods for describing the shape properties of protein surfaces and for comparing them. Our current work uses algorithms from computer vision to describe the protein surfaces, and methods from graph theory to compare the surface regions. Early results indicate that we can successfully match a family of related ligand binding sites, and find their similarly shaped surface regions. This method of surface analysis could be extended to help identify unknown surface regions for possible ligand binding or active sites.     

An investigation of multilevel service provision for voice over IP under catastrophic congestion

QoS has been the dominating issue faced in VoIP development today. In this article we investigate and empirically evaluate three DiffServ (Kilkki 1999, Blake et al. 1998) design strategies, WRED Dropper (Cisco Systems), PQ meter, and multiple differentiated meter (MDM), and study how multilevel communication services can be guaranteed for multiple VoIP classes. The novel aspect of our work is that we are trying to provide solutions with the use of features that are not currently available in real routers (Westhead, 2002). By taking advantage of network simulation techniques, a series of experiments have been designed and carried out under different network conditions by using the intersim simulation tool (Westhead, 2002). Our simulation results effectively reflect that: 1) all three designs can provide service differentiation for multiple VoIP classes; 2) the highest-priority VoIP class can always be protected under catastrophic congestion; and 3) each design has some pros and cons in terms of performance stability under varied traffic distribution and changed packet size mix. Based on this investigation, we conclude that MDM is comparatively better at providing even service distribution and staying robust against traffic distribution variation and packet size changes.     

Protein phosphorylation at a postreceptor site can block desensitization and induce potentiation of secretion in chromaffin cells

Desensitization or habituation to repeated or prolonged stimulation is a common property of secretory cells. Phosphorylation of receptors mediates some desensitization processes, but the relationship of phosphorylation to desensitization at postreceptor sites is not well understood. We have tested the effect of protein phosphorylation on desensitization in bovine chromaffin cells. To increase protein phosphorylation, we have used the protein phosphatase inhibitor okadaic acid at 12.5 nM, 100 microM 8-bromo-cyclic AMP to activate protein kinase A, and 10 nM phorbol 12,13-dibutyrate to activate protein kinase C. During repeated 6-s stimulation at 5-min intervals, catecholamine secretion from control cells decreases. Cells exposed to 8-bromo-cyclic AMP or okadaic acid alone show slightly decreased rates of desensitization. In cells pretreated with phorbol 12,13-dibutyrate, desensitization is blocked. Okadaic acid-treated cells stimulated in the presence of 8-bromo-cyclic AMP show potentiation of secretion with repeated stimulation. The protein kinase inhibitor 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine (H7) increases the desensitization rate. Because these phenomena are observed during secretion evoked with elevated K+ as well as by a nicotinic agonist, the effect of phosphorylation is at a postreceptor site. In contrast to desensitization to the repeated stimulations, desensitization to prolonged stimulation with high K+ is not altered by the above protocols in chromaffin cells.     

Transient Ionization Effects in Silicon Induced by 48 MeV Electron Pulses

Transient radiation effects induced in silicon irradiated in the temperature range 90 to 300°K by 0.007 to 4.5 microsecond pulses of 48 MeV electrons were studied using the transient response of resistivity and Hall effect voltages as the measuring probes. Results are given for one ohm-cm phosphorus-doped n-type silicon and 10 to 100 ohm-cm n-type and p-type samples. In the case of one ohmcm silicon the results clearly show the actual buildup of excess electrons produced by ionization during the time the electron pulse is irradiating the sample. Moreover, the shape of the pulse during buildup is independent of temperature as long as the electron beam pulse is kept constant. Dependence of the number of injected excess carriers on the ionization intensity (total integrated electron flux in the pulse) was found to be linear up to excess carrier concentrations of ~ 1017 cm-3. The lifetime is found to increase linearly with injection implying that the recombination may be dominated by one defect energy level. In p-type silicon the transient Hall and conductivity voltages decay in ~ 20-50 jsec. Relatively long saturation times (~ 10 to 100 microseconds) are observed in the transient Hall and conductivity voltage following an electron burst. The saturation time decreases with dose accumulation in p-type and also decreases as the irradiation temperature of the sample (both n- and p-type) is decreased. Very similar effects also are observed in n-type silicon samples.