Nonpolar patches

Structural information about the oxygenases provided limited insight into the mechanism (Schmidt et al. 2006). The crystallized enzyme from Synechocystis sp. PCC6803 is membrane associated and the interaction with the membrane is believed to be mediated by a nonpolar patch on the surface of the enzyme. This hydrophobic patch is thought to provide the necessary access of the protein to the membrane-bound carotenoids. Following withdrawal from the membrane, the substrate moves through the hydrophobic tunnel toward the metal center. The substrate orients the... 

Fig. 14.1 Scheme and plots illustrating the dependence of nanoscale-confinement parameters T and/on the radius 6 of the osculating sphere at the protein-water interface. First-order contacts with a polar or nonpolar patch on the protein surface are treated individually. Values were determined at equilibrium obtained by integrating Newton s equations of motion in an NPT ensemble with box size 103 nm3, starting with the PDB structure embedded in a pre-equilibrated cell of water molecules. The box size was calibrated so that the solvation shell extended at least 10 A from the protein surface at all times. Simulations were performed as described in Chap. 4... 

To summarize, three conclusions transpire from the nanoscale thermodynamics results (a) The interfacial tension between protein and water is patchy and the result of both nanoscale confinement of interfacial water and local redshifts in dielectric relaxation (b) the poor hydration of polar groups (a curvature-dependent phenomenon) generates interfacial tension, a property previously attributed only to hydrophobic patches and (c) because of its higher occurrence at protein-water interfaces, the poorly hydrated dehydrons become collectively bigger contributors to the interfacial tension than the rarer nonpolar patches on the protein surface. 

Protein-water interaction plays an important role in the determination and maintenance of the three-dimensional structure of proteins. Water modified the physicochemical properties of proteins. Therefore, protein-water interactions have been the subject of intensive study and have provided significant advances in our understanding of the involvement of water in protein functionality, stability, and dynamics [6]. The thermodynamics of protein-water interaction directly affects dispersibility, wettability, swelling, and solubility of proteins. Surface-active properties of proteins are simply the result of the thermodynamically unfavorable interaction of exposed nonpolar patches of proteins with solvent water. 

Iodide (large and poorly hydrated) is found on the remaining nonpolar patches. 

To confirm that different ions also segregate on complex molecular surfaces according to the distribution of charged and nonpolar patches, we... 

Protein-protein association is governed by salt type and concentration as well as the solution pH. Taking into account the patchiness of protein surfaces, the experimental observations can be reproduced using coarse grained molecular simulations. In particular, ion binding to nonpolar patches leads to the observed pH-dependent reversal of the Hofmeister series. 

Most polar groups are on the surfaces of proteins, and those that are not are almost always hydrogen bonded to other groups in the interior 244 While most nonpolar groups are inside proteins, they are also present in the outer surfaces where they are often clustered into hydrophobic regions or "patches." The latter may be sites of interaction with other proteins or with lipid portions of membranes. 

The hydrophobic effect refers to the favorable interactions between nonpolar surfaces immersed in water. These interactions are considered to provide the driving force for protein folding (44) and to make a major contribution to the stability of protein tertiary stractures. The hydrophobic effect also plays an important role in protein interactions (45). The hydrophobicity of protein surfaces has been studied experimentally by affinity partitioning of proteins (46). Theoretical studies have shown that the presence of hydrophobic patches on the surfaces of proteins correlates with protein binding sites (47 9). 

An alternative model has been proposed by Kauzmann (1959), with association areas of proteins considered as surface patches of nonpolar side chains brought together rather like hydrocarbon chains in lipid micelles, making the surfaces complementary. 

In another recent study, Chen and coworkers [11] also investigated the effect of surfece oxygen complexes, introduced by air and ozone treatments, on the adsorption of the commercial surfactants SDS, Darex II (anionics), and Tergitol (nonionic). Results revealed that the surfactant adsorption was strongly suppressed by surface oxidation. These authors proposed that surfactant adsorption primarily occurs on nonpolar carbon surface patches by hydrophobic interactions. Therefore, the oxidative suppression of surfactant adsorption was... 

Another factor besides PrP conformations in strain differences could be differences in PrP /PrP interaction surfaces, as with the models for species barriers discussed previously. For example, Warwicker (1997b) has interpreted his heterodimer model in light of residues important in determining strain differences. In particular, in this case, he focused on conserved and nonpolar residues and proposed that there are two distinct patches on the molecule that can interact with membrane or with a neighboring protein. This hypothesis leads to two different membrane-attached PrP orientations, or faces, that would be presented to an incoming PrP molecule. In a more recent study, Warwicker (1999) discusses how charge interactions between PrP and the membrane may affect scrapie formation. Along these lines, Morillas et al. 

Nonpolar residues formed a hydrophobic patch in the middle of the back side (opposite the active site cleft) of both proteins as can be seen in figure 4 e f. The hydrophobic patch on the human lysozyme appeared to be slightly larger than that on the hen lysozyme. 

Amphiphilic compounds are also surface-active their differently polarized regions cause them to accumulate at interfacial zones in the environment. For example, at the air-water interface, amphiphiles tend to orient themselves in surface microlayers or surface films (see Section l.B.2d), where the polar region of the molecule is associated with the water phase and the nonpolar region is forced out of solution and extends up into the air phase. Often these surface layers are visible by the damping effect they exert on wave action (Figure 1.8) they are apparent as smoother patches among the ripples on a lake or in the ocean. 

---