Hydrophobic domains

It has been shown in Chapter 5, the fluorescence quenching of the DPA moiety by MV2 + is very efficient in an alkaline solution [60]. On the other hand, Delaire et al. [124] showed that the quenching in an acidic solution (pH 1.5-3.0) was less effective (kq = 2.5 x 109 M 1 s 1) i.e., it was slower than the diffusion-controlled limit. They interpreted this finding as due to the reduced accessibility of the quencher to the DPA group located in the hydrophobic domain of protonated PMA at acidic pH. An important observation is that, in a basic medium, laser excitation of the PMAvDPA-MV2 + system yielded no transient absorption. This implies that a rapid back ET occurs after very efficient fluorescence quenching. 

AChE-R (in purple) Naturally rare, stress-induced variant, which lacks a hydrophobic domain and is incapable of binding to ColQ or PRiMA. Therefore, it remains soluble, and its secreted form shows greater mobility than AChE-S. AChE-R can intra-cellularly interact through its C-terminal tail with the Protein Kinase C Receptor RACK1, a scaffold protein which modifies multiple cellular processes. 

After uptake, lipophilic pollutants tend to move into hydrophobic domains within animals or plants (membranes, lipoproteins, depot fat, etc.), unless they are biotransformed into more polar and water soluble with compounds having low Metabolism of lipophilic compounds proceeds in two stages ... 

Tropoelastin is the soluble precursor of elastin and consists of alternating hydrophobic and hydrophilic peptide domains. The most common amino acids in the hydrophobic domains are Gly, Val, Ala, and Pro, which are often present in repeats of tetra-, penta-, and hexapeptides, such as Gly-Gly-Val-Pro, Gly-Val-Gly-Val-Pro, Gly-Val-Pro-Gly-Val, and Gly-Val-Gly-Val-Ala-Pro, respectively [3, 4]. The hydrophilic domains are mainly composed of lysines interspersed by alanines. 

Miao M, Cirulis JT, Lee S et al (2005) Structural determinants of cross- linking and hydrophobic domains for self-assembly of elastin-like polypeptides. Biochemistry 44 14367-14375... 

Figure 8.7 Schematic diagram of the proposed structure of the noradrenaline neuronal transporter showing the 12 transmembrane, hydrophobic domains with the N- and C-termini projecting towards the cell cytoplasm. Binding domains for specific ligands are thought to be within regions indicated by the solid bars. (From Stanford 1999, reproduced with permission)...

Because the carotenoids favour hydrophobic domains they are generally localised in the membranes and lipoproteins of animal cells. In this location they can influence the oxidation of membrane lipids and prevent the passage of free radicals from one cellular compartment to another. Thus, DNA in the nucleus is protected from intracellularly generated ROS by (at least) the nuclear membrane and from extracellular ROS by a number of membranes. Should ROS reach the nucleus, base oxidation can occur. The base most susceptible to oxidation is guanine, although all other bases can also be affected. The cell has the ability to detect damaged bases, excise them. 

The discovery of this evolutionary activity has reeked havoc with the accepted PTS protein nomenclature. Instead of the time-honored E-I, E-II, E-III and HPr, we must resort to cumbersome phrases such as the E-III-like domain of E-IT etc. To alleviate the problem, Saier Jr and Reizer [3] have proposed a new nomenclature (Fig. 2) based on the original IIA/IIB nomenclature of Kundig and Roseman [4]. The old nomenclature is given above the bars representing the permeases in Fig. 2 and the new nomenclature below the bars. H and I still represent HPr and E-I, respectively, but IIA replaces E-IIl. IIC represents the hydrophobic domain of E-... 

Fig. 2. Schematic representation of various PTS enzymes and their domains (taken from [3]). The different domains are indicated as follows transmembrane hydrophobic domain IIC) the E-II domain...

There is one or more extended hydrophilic stretch in the hydrophobic domain which may be associated with carbohydrate binding. 

The second class, represented by E. coli 11°, consists of a hydrophobic domain of approximately 360 residues followed by hydrophilic domain of approximately 100 residues [10], Other representatives of this class are E. coli 11° [11], S. aureus 11 [12], E. coli [13,14] B. subtilis 11 [15] and 11 encoded by the plasmid pUR400 [16]. 

The third class, represented by E. coli consists again of a single hydrophobic domain of approximately 360 residues but with two covalently attached hydrophilic domains, equal, together, in size to the hydrophobic domain [17], The A domain is proposed to function as a covalently attached E-III. Other representatives of this class include B. subtilis II° [18,19], 5. mutans 11 [20], E. coli II [21,22] and [23,24],... 

The combination of hydrophilicity and hydrophobicity into a single pol5meric support can lead to interesting results. Amphiphilic materials, containing both hydrophilic and hydrophobic domains, appreciably swell in a range of solvents of quite different polarity (see for example the characterization of amphiphilic CFPs given in Ref. [82]). This concept has been elegantly applied by Uozumi and Nakao in both reduction [159] and oxidation reactions (see Section 5.2) [70] catalyzed by... 

III PEG MPD Steric exclusion Repulsion from charges To hydrophobic regions Good precipitants stabilizers of native structure at low temp., unfolded structure at high temp. stabilizers and solubilizers of hydrophobic domains in proteins... 

The vesicles made from lipid bilayers are analogous to polymersomes, which are vesicles formed from high molecular weight amphiphilic block copolymers [94—96], Unlike the micelles discussed earlier from the similar copolymer components, the presence of bilayer walls formed from the aggregation of hydrophobic domains provides new properties. They can be designed to respond, for example, by opening or by disassembly, to external stimuli such as pH, heat, light, and redox processes [97]. This makes them usable as scaffolds for cascade reactions, even those with combinations of enzymes [98, 99]. 

Dialkylanthracene-containing squaraine dyes 17 show intense absorption and emission in the NIR region (720-810 nm) [74]. They are compatible with aqueous environments and show substantial enhancement of quantum yields and fluorescence lifetimes in hydrophobic and micellar media, suggesting that these dyes can be potentially useful as fluorescent probes in biological applications, e.g., for imaging of hydrophobic domains such as cell membranes. 

This approach was followed by Yushmanov for the localization of papaverine in ionic micelles.42 Another interesting application was reported by Chien43 who measured 19F NMR relaxation times of trifluor-omethyl labelled atrazine induced by paramagnetic probes gadolinium ethylenediamine tetraacetic acid and 2,2,6,6-tertramethyl-piperidine-N-oxyl. The results showed that atrazine solubilized by humic micelles occupied a hydrophobic domain accessible only to neutral hydrophobic molecules. 

Hydrophobic domain (physical cross linking point)... 

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