Hydrophobic/hydrophobicity pocket

Heating Kemp s acid with appropriate aromatic diamines yields bis-imides with two convergently oriented carboxylic acid groups on the edges of a hydrophobic pocket. Dozens of interesting molecular complexes have been obtained from such compounds and can be traced in the Journal of the American Chemical Society under the authorship of J. Rebek, Jr., (1985 and later e.g. T. Tjivikua, 1990 B). 

The differences in sizes and locations of hydrophobic pockets or patches on proteins can be exploited in hydrophobic interaction chromatography (HIC) and reversed-pha.se chromatography (RPC) discrimination is based on interactions between the exposed hydro-... 

Figure 3.14 Sickle-cell hemoglobin molecules polymerize due to the hydrophobic patch introduced by the mutation Glu 6 to Val in the P chain. The diagram (a) illustrates how this hydrophobic patch (green interacts with a hydrophobic pocket (red) in a second hemoglobin molecule, whose hydrophobic patch interacts with the pocket in a third molecule, and so on. Electron micrographs of sickle-cell hemoglobin fibers are shown in cross-section in (b) and along the fibers in (c). [(b) and (c) from J.T. Finch et al., Proc. Natl. Acad. Set. USA 70 718-722, 1973.)...

This symmetry is important in bringing the two chlorophyll molecules of the "special pair" into close contact, giving them their unique function in initiating electron transfer. They are bound in a hydrophobic pocket close to the symmetry axis between the D and E transmembrane a helices of both... 

Figure 16.16 Schematic diagrams Illustrating the binding of an antiviral agent to human rhlnovirus strain 14. (a) The drug binds in a hydrophobic pocket of VPl below the floor of the canyon, (b) Schematic diagram of VPl Illustrating the pocket in the jelly roll barrel where the drug binds. (Adapted from T.J. Smith et al.. Science 233 1286-1293, 1986.)...

FIGURE 15.40 The polymerization of Hb S via the interactions between the hydrophobic Val side chains at position /36 and the hydrophobic pockets in the EF corners of /3-chains in neighboring Hb molecnles. The protruding block on Oxy S represents the Val hydrophobic protrusion. The complementary hydrophobic pocket in the EF corner of the /S-chains is represented by a sqnare-shaped indentation. (This indentation is probably present in Hb A also.) Only the /S9 Val protrusions and the /Si EF pockets are shown. (The /Si Val protrusions and the /S9 EF pockets are not involved, although they are present.)... 

A general phenomenon observed with chiral stationary phases having hydrophobic pockets is that a decrease of flow rate results in an increase in resolution. This change has significant impact mostly in reversed-phase mode (see Fig. 2-10). 

Fig. 7 The influenza virus A sialidase active site showing the five potential inhibitor binding subsites (with S5 containing the hydrophobic pocket formed by reorientation of the Glu276 side-chain), with oseltamivir carboxylate 18 placed in the active site...

The majority of NNRTIs share common conformational properties and structural features that allow them to fit into an asymmetric, hydrophobic pocket about 10 A away from the catalytic site of the HlV-1 RT, where they act as non-competitive inhibitors (Kohlstaedt et al. 1992). However, the NNRTIs select for mutant virus strains with several degrees of dmg resistance. 

Fig. 2. Stereo view of the active site off), gigas hydrogenase (reprinted with permission from (65) copyright 1997, American Chemical Society). LI and L2 are diatomic ligands that form hydrogen bonds with the protein- they are supposed to be the two CN s molecules. The third ligand L3 sits in a hydrophobic pocket and is assumed to be the CO. The designates the putative oxo bridging ligand.

Stereospecificity suggests that there are three geometrically distinct determinants of the structure which are important to agonist efficacy and potency, whereas previous models only utilized two features. A hydrophobic pocket may also be important 20) this could be supplied by the [4.2.1]nonene structure. Our intentions are to explore the domains of the agonist molecule to determine the specific determinants of agonist activity. 

Fig. 1.1 ATP bound to cAMP protein kinase and a schematic representation indicating the non-conserved regions (hydrophobic pocket and specificity surface) of the pocket utilised in the development of protein kinase inhibitors.

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