Hydrophobic channel

Both methods suggest that the chemical structure of A A (cis double bonds connected by two single bonds) allows the fatty acid to access the cyclooxygenase active site of PGHS-1 through a narrow hydrophobic channel and to bind in a shape favorable for the cyclooxygenation reaction. 

The binding site is located at the tip of the subunit within the jelly roll structure (Figure 5.23). The sialic acid moiety of the hemagglutinin inhibitors binds in the center of a broad pocket on the surface of the barrel (Figure 5.24). In addition to this groove there is a hydrophobic channel that can accomodate large hydrophobic substituents at the C2 position of sialic acid (Figures 5.22 and 5.24). 

Figure 5.24 Space-filling model (green) of the sialic acid binding domain of hemagglutinin with a bound inhibitor (red) Illustrating the different binding grooves. The sialic acid moiety of the Inhibitor binds in the central groove. A large hydrophobic substituent, Ri, at the Cz position of sialic acid binds in a hydrophobic channel that runs from the central groove to the bottom of the domain. (Adapted from S.J. Watowich et al.. Structure 2 719-731, 1994.)...

A crystallographic analysis of xenon binding to [NiFe] hydrogenase, together with a molecular dynamic simulation study of xenon and dihydrogen diffusion in the enzyme interior, suggests the existence of hydrophobic channels connecting the molecular surface with the active site 184). 

The GDE for hydrochloric acid electrolysis is characterised by micro-scale hydraulic problems connected with the competition between the gas phase (oxygen), which has to diffuse towards the catalyst, and the liquid phase (water), which must be released. This competition is managed basically by a flow-through structure provided with hydrophobic channels of relatively large diameter. These are formed from PTFE (the binder of the structure) and catalyst particles and account for regulating the gas phase. Hydrophilic channels with smaller diameters (one order of magnitude smaller), which are located in the micro-porous carbon particles of the catalyst support (e.g. Vulcan XC-72), act as water absorbers. A consequence of the electrolysis process is that the catalyst itself is partially covered by liquid. This reduces its effectiveness and accounts for extra voltage. 

Fig. 4 Hydrophobic channels of y3-Cu(03PCH3) the methyl groups point toward the center of the channels (after [21])...

The large number of newly developed COX-2 inhibitors demonstrates how promising this field of anti-inflammatory agents is expected to be. More than 1000 COX-2 inhibitors have been described over the past few years (Prous database, March 2002). The chemical structures of COX-2 inhibitors are heterogenic. Contrary to the classical NSAIDs, this new class of enzyme inhibitors lacks a carboxylic acid group, thus effecting COX-2 affinity by a different orientation within the enzyme without formation of a salt bridge in the hydrophobic channel of the enzyme. 

The entire iron-porphyrin-protein complex is called a cytochrome and such proteins are important electron-transfer components of cells. Generally, access to the macromolecular region in which the oxidation reactions occur is via a hydrophobic channel through the protein (Mueller et al., 1995). As a result, organic substrates are transferred from aqueous solution into the enzyme s active site primarily due to their hydrophobicity and are limited by their size. This important feature seems very appropriate hydrophobic molecules are selected to associate with this enzyme, and these are precisely the ones that are most difficult for organisms to avoid accumulating from a surrounding aquatic environment. 

COX-1 and COX-2 have virtually identical tertiary and quaternary structures, but they differ subtly in a long, thin hydrophobic channel extending from the membrane interior to the lumenal surface. The channel includes both catalytic sites and is presumed to be the binding site for the hydrophobic substrate, arachidonate. Both COX-1 and COX-2 have been crystallized in the presence of several different bound NSAID compounds, defining the NSAID-binding site (Fig. 1). The bound drugs block the hydrophobic channel and prevent arachidonate entry The subtle differences between the channels of COX-1 and COX-2 have guided... 

FIGURE 1 Structures of COX-1 and COX-2, (a) COX-1 with an NSAID inhibitor (flurbiprofen, orange) bound (PDB ID 3PGH). The enzyme consists of two identical monomers (gray and blue) each with three domains a membrane anchor consisting of four amphipathic helices a second domain that somewhat resembles a domain of the epidermal growth factor and the catalytic domain, which contains the cyclooxygenase and peroxidase activities, as well as the hydrophobic channel in which the substrate (arachidonate) binds. The heme that is part of the peroxidase active sites is shown in red ... 

Figure 42 The structure of apoferritin. N = N-terminus protein helices E form hydrophobic channels (reproduced with permission from Adv. Inorg. Biochem., 1984, 5, 39, Elsevier, Amsterdam)...

With larger guest molecules that do not fit the cavity, all three principal cyclodextrins are capable of forming channel structures in which the cyclodextrin cavities line up in order to produce an extended hydrophobic channel into which guests can be threaded in a similar way to urea clathrates... 

Besides PMMA, compression molding was also used to fabricate microstructures on PC chips (1 mm thick). High temperature (188°C) and pressure (11 metric ton pressure applied by a hydraulic press) were used. Before bonding, the hydrophobic channel surface was treated with UV irradiation (220 nm) to increase surface charge, which would assist aqueous solution transport. The molded chip was thermally bonded to another PC wafer. During use, the bonded chip did not yield to a liquid pressure up to 150 psi (134°C, 4 metric ton, 10 min) [938],... 

On the other hand, if a hydrophobic channel, the oxidized PDMS chip can be placed at 90°C in order to recover the hydrophobicity of the channels [260]. 

A two-phase air-liquid flow was developed on a PDMS chip (see also Chapter 3, section 3.1.2). It was found that the focused two-phase flow was stable in hydrophobic channels (down to 6 mL/h) see Figure 8.38. Below this flow rate, the sample column no longer maintained its integrity and broke up. This method was used to provide aerodynamic focusing of myoblast cells (C2Ci2) for the flow cytometry study. The cells, which were labeled with Syto 9, was focused and counted in the chip at a rate of 100 cells/s [382]. 

The a-helical regions of the moth CSP1, CSP2 and CSP3 proteins differ in amino acid sequence. The a-helix (al)in the N-terminal region anchors a narrow hydrophobic channel and includes residues 5 (or 12)—18 al is conserved in all... 

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