Hydrophobic environments

Approximately a minimum of 1 to 5,000 is required before complexation is no longer dependent on molecular weight for small anions such as KI and l-ariiLinonaphthaLine-8-sulfonate (ANS) (86,87). The latter anion is a fluorescent probe that, when bound in hydrophobic environments, will display increased fluorescence and, as expected, shows this effect in the presence of aqueous PVP. PVP, when complexed with Hl, shrinks in si2e as it loses hydrodynamic volume, possibly because of interchain complexation. ANS, on the other hand, causes the polymer to swell by charge repulsion because it behaves like a typical polyelectrolyte (88). 

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

Alpha helices are sufficiently versatile to produce many very different classes of structures. In membrane-bound proteins, the regions inside the membranes are frequently a helices whose surfaces are covered by hydrophobic side chains suitable for the hydrophobic environment inside the membranes. Membrane-bound proteins are described in Chapter 12. Alpha helices are also frequently used to produce structural and motile proteins with various different properties and functions. These can be typical fibrous proteins such as keratin, which is present in skin, hair, and feathers, or parts of the cellular machinery such as fibrinogen or the muscle proteins myosin and dystrophin. These a-helical proteins will be discussed in Chapter 14. 

The thioredoxin domain (see Figure 2.7) has a central (3 sheet surrounded by a helices. The active part of the molecule is a Pa(3 unit comprising p strands 2 and 3 joined by a helix 2. The redox-active disulfide bridge is at the amino end of this a helix and is formed by a Cys-X-X-Cys motif where X is any residue in DsbA, in thioredoxin, and in other members of this family of redox-active proteins. The a-helical domain of DsbA is positioned so that this disulfide bridge is at the center of a relatively extensive hydrophobic protein surface. Since disulfide bonds in proteins are usually buried in a hydrophobic environment, this hydrophobic surface in DsbA could provide an interaction area for exposed hydrophobic patches on partially folded protein substrates. 

A selection of amino acids (acid A, acid B,...) terminated at both ends by amide functionality, i.e., MeNHCO-CHR-NHCOMe, are provided. These are given in the ionization states found at neutral pH. For each, first identify the amino acid, and then the ionization state (neutral, protonated or deprotonated). Next compare electrostatic potential maps among the different amino acids. Which amino acids would prefer hydrophobic environments Hydrophilic environments Explain your reasoning. 

Electrostatic potential map for acid B shows positively and negatively-charged regions (in red and blue, respectively) and neutral regions (in green). The former would prefer hydrophilic environments while the latter would prefer hydrophobic environments. 

The product coelenteramide is not noticeably fluorescent in aqueous solutions, but is highly fluorescent in organic solvents and also when the compound is in the hydrophobic environment of a protein. When coelenterazine is luminesced in the presence of Oplophorus luciferase, the solution after luminescence (the spent solution) is not fluorescent, presumably due to the dissociation of coelenteramide from the luciferase that provided a hydrophobic environment at the time of light emission. An analogous situation exists in the bioluminescence system of Renilla (Hori et al., 1973). 

Although aequorin is non-fluorescent, the spent solution after luminescence is brightly fluorescent in blue due to the presence of coelenteramide. Although pure coelenteramide is poorly fluorescent in aqueous solutions, it becomes strongly fluorescent in a hydrophobic environment. In the presence of Ca2+, coelenteramide... 

Based on a series of studies of the effect of organic solvent on the reaction of Ca-ATPase with Pj and ATP synthesis, De Meis et al. proposed that a different solvent structure in the phosphate microenvironment in Ej and E2 forms the basis for existence of high- and low-energy forms of the aspartyl phosphate [93]. Acyl phosphates have relatively low free energy of hydrolysis when the activity of water is reduced, due to the change of solvation energy. The covalently bound phosphate may also reside in a hydrophobic environment in E2P of Na,K-ATPase since increased partition of Pj into the site is observed in presence of organic solvent [6] in the same manner as in Ca-ATPase. 

Recently Rabon et al. [100] reported on a new conformational probe of H,K-ATPase. This fluorescent quinoline derivative MDPQ was shown to be a reversible luminal K -site inhibitor of both K -ATPase and K -pNPPase activity. High-affinity MgATP binding induced a conformational change with fluorophore movement into a more hydrophobic environment. 

NCD-4 is a nonfluorescent carbodiimide derivative that forms a fluorescent adduct with the Ca -ATPase, accompanied by inhibition of ATPase activity and phos-phoenzyme formation [376-378]. Ca protected the enzyme against the inhibition by NCD-4 and reduced the extent of labeling, suggesting that the reaction may involve the Ca " " binding site. The stoichiometry of the Ca -protected labeling was i 2mole/mol ATPase. The fluorescence emission of the modified Ca -ATPase is consistent with the formation of a protein bound A-acylurea adduct in a relatively hydrophobic environment. After tryptic proteolysis of the NCD-4 labeled ATPase the fluorescence was associated with the A2 band of 24 kDa [376,379]. 

The synthetic alkaloid coralyne (Scheme 1) on the other hand is a planar molecule and is not readily soluble in aqueous buffers. It is highly soluble in ethanol and methanol. Coralyne is characterized by strong absorption maxima at 219, 300, 311, 326 and 424 nm with characteristic humps at 231, 360 and 405 nm in 30% (v/v) ethanol. It is highly fluorescent and gives an emission spectrum with a maximum at 460 nm when excitation was done either at 310 or 424 nm. It was observed that both absorbance and the fluorescence pattern of coralyne remained unaltered in buffer of various pH values ranging from 1.0 to 13.0 and also with salt concentration ranging from 4.0 to 500 mM. This implied that hydrophobic environment favoured the increment of their fluorescence properties [144]. 

As stated earlier, the primary site of association of [ H]MDA with brain synaptosomes is with membrane components, not with the intrasynaptic space. While the phenolic ends of these compounds may enable them to interact with hydrophobic environments of brain membrane components, their polar side chains may inhibit the ability of these compounds to move freely across the membranes, thus inhibiting internalization. The pKa of... 

Several enzymes like lipases, esterases, and dehydrogenases have been active in hydrophobic environments. Thermodynamic water activity is a good predictor of the optimal hydration conditions for catalytic activity [51]. Enzyme preparation can be equilibrated at a specific water activity before the reaction [52]. When water concentration is very low, enzyme is suspended in the solid state in the water-immiscible organic solvent [46]. Enzymes are easily recovered after the reaction by the method of filtration. 

The reaction mechanism for the heterogeneous and homogeneous acid-catalysed esterification were reported to be similar (17). However, there is a major difference concerning the snrface hydrophobicity. Reaction pockets are created inside a hydrophobic environment, where the fatty acid molecules can be absorbed and react further. Water molecules are unlikely to be absorbed on sites enclosed in hydrophobic areas. 

The DBSA-system is also applicable for the dithioacetalization of aldehdyes and ketones with 1,2-ethanedithiol to give the corresponding dithioacetals (Scheme 5.4, d). Increasing the reaction temperature decreases the yield of the products. Interestingly, increases in the concentration of the surfactant also decrease the yield of products formed, while shortening the alkyl chain of the surfactant abolishes its catalytic activity. Optical microscopy shows the formation of micelles, which are proposed to form hydrophobic environments and decrease the effective concentration of water and facilitate the dehydrative condensation reactions. 

Positive ROA bands in the range 1297-1312 cm-1 are also characteristic of a-helix. These are observed at 1300 cm-1 in human serum albumin (Fig. 4) and at 1297 cm-1 in a-helical poly-L-lysine (Fig. 3). These additional bands appear to be associated with a-helix in a more hydrophobic environment (Barron etal., 2000). The striking absence of a positive ROA band in the range 1297-1312 cm-1 in a-helical poly-L-glutamic acid would then suggest that only the hydrated form of a-helix is present, possibly due to the shorter side chains relative to poly-L-lysine,... 

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