Funnel structures

Fig. 16.13. Pore structure of the acetylcholine receptor, based on electron microscopy studies. a) Electron density map of the acetylcholine receptor of the postsynaptic membrane of the electric organ of the ray Torpedo californicus, based on electron microscopy studies. The receptor has a long funnel-like structure in the extracellular region, which narrows at the center of the pore. A smaller funnel structure is observed in the cytoplasmic region of the receptor. Another protein is situated on the cytoplasmic side. The long arrow indicates the direction of ion passage and the small arrow shows the postulated binding site for acetylcholine, b) Schematic representation of the acetylcholine receptor with the M2 hehx as the central block in the ion channel. According to Unwin, (1993).

The sticker liquid, which is in the tank shown below the forward edge of the wing, is metered into a mixing chamber located immediately below the funnel-like structure located behind the tank. A wind-driven propeller mixes the sticker and the flake, which originates in the funnel structure, and forces the mixture out of the chamber via a screw-type arrangement toward a terminus equipped with a blade-like arrangement that rotates rapidly in flight. With the aid of the slip stream, the blade dispenses the flakes as individual particles. 

Initial lymphatics in skeletal muscle have intraluminal valves that consist of bileaflets and a funnel structure [Mazzoni et al., 1987]. The leaflets are flexible structures and are opened and closed by a viscous pressure drop along the valve funnel. In closed position, these leaflets can support considerable pressures [Eisenhoffer et al., 1995 Ikomi et aL, 1997]. This arrangement preserves normal valve function even in initial lymphatics with irregularly shaped lumen cross sections. 

The approach calls for the specific funnel structure of the more realistic multidimensional V( )-hypersurface, which might provide the basis for fast conformational transitions. Actually, existence of the local funnel-like regions in V(fe)-hypersurface is assumed, with the following main idea The funnel-like shape restricts the set of the allowed trajectories (pathways) for the conformational change. The different trajectories should be stochastically taken by the different (single) molecules in the ensemble of molecules from the set of the possible trajectories in the restricted f-space. 

The CANDU bundle verifier for stacks (CBVS) moves vertically along the space between columns of trays (10 cm gap) of spent fuel and uses a CdZnTe detector for bundle identification (Ahmed et al. 2001). It employs thick lead shielding to protect the electronics and detector. The CBVS is unable to verify the spent fuel at the bottom layer of a stack due to limited accessibility of a large-size detector part through the funnel structure. During inspection, the tray must be moved. In addition, the large size of the scanning part is both heavy and difficult to handle. 

Bryngelson J D, J N Onuchic, N D Socci and P G Wolynes 1995. Funnels, Pathways, and the Energy Landscape of Protein Folding A Synthesis. Proteins Structure, Function and Genetics 21 167-195. 

Until Jenike developed the rationale for storage-vessel design, a common criterion was to measure the angle of repose, use this value as the hopper angle, and then fit the bin to whatever space was available. Too often, bins were designed from an architectural or structural-engineering viewpoint rather than from the role they were to play in a process. Economy of space is certainly one vahd criterion in bin design, but others must be considered equally as well. Table 21-14 compares the principal characteristics of mass-flow and funnel-flow bins. 

PE Leopold, M Montal, JN Onuchic. Protein folding funnels A kinetic approach to the sequence-structure relationship. Pi oc Natl Acad Sci USA 89 8721-8725, 1992. 

The general shapes of the active sites are quite different, however. Open I a/p structures cannot form funnel-shaped active sites like the barrel struc-Itures. Instead, they form crevices at the edge of the p sheet. Such crevices loccur when there are two adjacent connections that are on opposite sides of Ithe P sheet. One of the loop regions in these two connections goes out from... 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Figure 5.9 The six four-stranded motifs in a single subunit of neuraminidase form the six blades of a propeller-like structure. A schematic diagram of the subunit structure shows the propeller viewed from its side (a). An idealized propeller structure viewed from the side to highlight the position of the active site is shown in (b). The loop regions that connect the motifs (red in b) in combination with the loops that connect strands 2 and 3 within the motifs (green in b) form a wide funnel-shaped active site pocket, [(a) Adapted from P. Colman et ah, Nature 326 358-363, 1987.]...

Dill, K. A., and Chan, H. S., 1997. From Levinthal to pathways to funnels. Nature Structural Biology 4 10—19. 

A 300 ml three-neck flask equipped with condenser, stirrer, dropping funnel, dry nitrogen inlet tube, and containing 5.5 g (0.145 mol) lithium aluminum hydride LAH suspension in 100 ml anhydrous diethyl ether, was placed in an ice bath. Over a period of 25 min 30 ml (0.123 mol) 1 was added dropwise into the stirred suspension. The mixture was stirred for an additional hour at 0 °C, then poured over a mixture of 50 ml ether, 100 g crushed ice, and 50 ml ice water with stirring. When necessary more crushed ice was added to cool the mixture. The layers were separated, and the organic layer was concentrated first by distillation over calcium hydride, then by vacuum distillation over calcium hydride. The yield of 4 was 22.5 g (86%). Bp. 78-9 °C, 0.4 mm. The product was stored in a freezer. The structure of 4 was confirmed by its H NMR spectrum as shown in Fig. 4. 

In order, for the two liquids to separate into two phases, they must be very weakly soluble in each other. When exposed to each other by mixing or shaking in a separatory funnel, they may not interpenetrate each other s realm to any extent. At the molecular level, we infer that the two species of molecules have no significant affinity for each other, rather they are predominantly attracted to other molecules with the same structure. To model this aversion, the joining and breaking rules must encode this behavior. The cells of liquids X and Y must respond to rules typified by those shown in the parameter setup tables below. With these rules we anticipate that liquid X will favor associating with other X molecules, while molecule Y will be found predominantly among other Y molecules. 

Phosphorus acid (260 mg, 3.17 mol) was placed into a 250-ml, threenecked, round-bottomed flask suspended in an oil bath. The flask was equipped with a three-way adapter, carrying a pressure-equalizing addition funnel, a reflux condenser with a drying tube, a mechanical stirrer, and a thermometer. Acetonitrile (33 g, 0.80 mol) was introduced to the reaction flask dropwise over a 2-h period while the phosphorous acid was agitated and maintained at a temperature of 138 to 142°C. After completion of the addition, the reaction mixture was maintained at that temperature for an additional 12 h. Methanol was then added to precipitate the pure l-aminoethane-l,l-diphos-phonic acid (13.9 g, 85%), which exhibited spectral and analytical data in accord with the proposed structure. 

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