Hydrophobic interior

An agglomeration of molecules containing ionic heads and hydrophobic tails, which form into a structure with a hydrophobic interior and a hydrophilic exterior. 

The most common location for an a helix in a protein structure is along the outside of the protein, with one side of the helix facing the solution and the other side facing the hydrophobic interior of the protein. Therefore, with 3.6 residues per turn, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues. Although this trend can sometimes be seen in the amino acid sequence, it is not strong enough for reliable stmctural prediction by itself, because residues that face the solution can be hydrophobic and, furthermore, a helices can be either completely buried within the protein or completely exposed. Table 2.1 shows examples of the amino acid sequences of a totally buried, a partially buried, and a completely exposed a helix. 

In rhino viruses there are depressions, or "canyons," which are 25 A deep and 12 to 30 A wide and which encircle the protrusions (Figure 16.15b). One wall of the canyons is lined by residues from the base of VPl. The structure of VPl is such that the barrel is open at the base and permits access to the hydrophobic interior of the barrel, as in the up-and-down barrel structure of the retinol-binding protein described in Chapter 5. 

In globular protein structures, it is common for one face of an a-helix to be exposed to the water solvent, with the other face toward the hydrophobic interior of the protein. The outward face of such an amphiphilic helix consists mainly of polar and charged residues, whereas the inward face contains mostly nonpolar, hydrophobic residues. A good example of such a surface helix is that of residues 153 to 166 of flavodoxin from Anabaena (Figure 6.24). Note that the helical wheel presentation of this helix readily shows that one face contains four hydrophobic residues and that the other is almost entirely polar and charged. 

Dendrimers can be designed to have a hydrophobic interior and a hydrophilic periphery. This gives them properties that are similar to those of conventional surfactants, and they can solubilize hydrophobic substances such as pyridine in aqueous solution by including them as guest molecules. They are therefore effectively mimolecular micelles. 

Dendrimers can be fabricated so that they have a hydrophobic interior and a hydrophilic periphery. Indeed, organic dendrimers, with relatively non-polar... 

Dendrimer micelles of this type have been formulated as drug delivery vehicles. Dendrimers with a hydrophobic interior have been used to entrap a hydrophobic drug such as indomethacin. This is retained because of the hydrophilic periphery containing ethylene glycol functional groups, and is released slowly because of the collapsed configuration of the interior, through which molecular diffusion is obstructed. 

Many a helices have predominantly hydrophobic R groups on one side of the axis of the helix and predominantly hydrophilic ones on the other. These amphi-pathic helices are well adapted to the formation of interfaces between polar and nonpolar regions such as the hydrophobic interior of a protein and its aqueous envi-... 

Figure 4.5. Expansion of a micelle by inclusion of a hydrophobic guest into the hydrophobic interior of the micelles. The guest is hydrophobic, and thus does not like heing in water. The interior of the micelle is similarly water-repellent, and thus is a much more comfortahle environment for the guest. The incorporation of the guest into the centre of the micelle causes an expansion, which in turn leads to larger pores in the resultant material.

Additional evidence for conformational changes in the transporter has come from measurement of the intrinsic fluorescence of the protein tryptophan residues, of which there are six, in the presence of substrates and inhibitors of transport. The fluorescence emission spectrum of the transporter has a maximum at about 336 nm, indicating the presence of tryptophan residues in both non-polar environments (which would emit maximally at about 330 nm) and in polar environments (which would emit at 340-350 nm) [154], The extent of quenching by the hydrophilic quencher KI indicates that more than 75% of the fluorescence is not available for quenching, and so probably stems from tryptophan residues buried within the hydrophobic interior of the protein or lipid bilayer [155]. Fluorescence is quenched... 

Fluorescence spectroscopy offers several inherent advantages for the characterization of molecular interactions and reactions. First, it is 100-1000 times more sensitive than spectrophotometric techniques. Second, fluorescent compounds are extremely sensitive to their environment. Tryptophan residues that are buried in the hydrophobic interior of a... 

The DD site can be ensured by the chemical shift changes of the BPA signals. The chemical shift differences of the ring proton signals of BPA on the delivery from water to bilayer phases are —0.04 and —0.11 ppm for the ortho and meta sites, respectively. Negative values mean upfield shifts recall the HCS rule. It is concluded that both benzene rings of BPA are trapped in the bilayer from the water phase and the meta site penetrates more deeply into the hydrophobic interior. 

Either the transport mediators bind the transported substances into their interior in a manner preventing them from contact with the hydrophobic interior of the membrane or they modify the interior of the membrane so that it becomes accessible for the hydrophilic particles. 

Most hydrophilic, or water-soluble, substances are repelled by this hydrophobic interior and cannot simply diffuse through the membrane. Instead, these substances must cross the membrane using specialized transport mechanisms. Examples of lipid-insoluble substances that require such mechanisms include nutrient molecules, such as glucose and amino acids, and all species of ions (Na+, Ca++, H+, Cl, and HC03). Therefore, the plasma membrane plays a very important role in determining the composition of the intracellular fluid by selectively permitting substances to move in and out of the cell. 

There are two types of electron transport those involving flavoproteins and iron-sulfur proteins, and those requiring only flavoproteins. The X-ray crystal structure of the soluble cytochrome P450 from Pseudomonas putida grown on camphor (P-450-CAM) has been determined (Poulos et ah, 1985), as have several others. The haem group is deeply embedded in the hydrophobic interior of the protein, and the identity of the proximal haem iron ligand, based on earlier spectroscopic studies (Mason et ah, 1965) is confirmed as a specific cysteine residue. 

The membrane establishes in and out. The membrane is asymmetric because the inner and outer leaflets can have a different lipid composition and contain different proteins (Fig. 3-3). Proteins can be associated with either side of the membrane, or they can pass through the membrane using membrane-spanning segments. The functional part of the protein can be on the cytosolic side, the external side, or even in the membrane itself. A common structure for spanning a membrane is an a-helix (but there are examples of sheets spanning a membrane). It takes about 20 amino acid residues arranged in a helix to span to a 30 A hydrophobic interior of the bilayer. 

Hydrophobic solubilizates such as styrene (S) decrease the saponification rate of the EUP. Accordingly, the EUP-molecules in micelles containing S are more resistant against hydrolytic degradation than molecularly dissolved EUP-mole-cules. Obviously, the access of the base to the hydrophobic interior of these micelles and microemulsion droplets is more difficult. 

Stretches of a-helix are most often positioned on the protein s surface, with one face of the helix facing the hydrophobic interior and the other facing the surrounding aqueous medium. The amino acid sequence of these helices is such that hydrophobic amino acid residues are positioned on one... 

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