Hydrophobic forces, substrate

The surface forces apparatus (SEA) can measure the interaction forces between two surfaces through a liquid [10,11]. The SEA consists of two curved, molecularly smooth mica surfaces made from sheets with a thickness of a few micrometers. These sheets are glued to quartz cylindrical lenses ( 10-mm radius of curvature) and mounted with then-axes perpendicular to each other. The distance is measured by a Fabry-Perot optical technique using multiple beam interference fringes. The distance resolution is 1-2 A and the force sensitivity is about 10 nN. With the SEA many fundamental interactions between surfaces in aqueous solutions and nonaqueous liquids have been identified and quantified. These include the van der Waals and electrostatic double-layer forces, oscillatory forces, repulsive hydration forces, attractive hydrophobic forces, steric interactions involving polymeric systems, and capillary and adhesion forces. Although cleaved mica is the most commonly used substrate material in the SEA, it can also be coated with thin films of materials with different chemical and physical properties [12]. 

As we have just seen, the initial encounter complex between an enzyme and its substrate is characterized by a reversible equilibrium between the binary complex and the free forms of enzyme and substrate. Hence the binary complex is stabilized through a variety of noncovalent interactions between the substrate and enzyme molecules. Likewise the majority of pharmacologically relevant enzyme inhibitors, which we will encounter in subsequent chapters, bind to their enzyme targets through a combination of noncovalent interactions. Some of the more important of these noncovalent forces for interactions between proteins (e.g., enzymes) and ligands (e.g., substrates, cofactors, and reversible inhibitors) include electrostatic interactions, hydrogen bonds, hydrophobic forces, and van der Waals forces (Copeland, 2000). 

At present, a wide range of solid substrates are available for protein immobilization. According to the protein attachment strategies, namely, adsorption, affinity binding, and covalent binding, all these substrates can be separated into three main parts. Surfaces like ploy(vinylidene fluoride) (PVDF), poly(dimethylsiloxane) (PDMS), nitrocellulose, polystyrene, and poly-1-lysine coated glass can adsorb proteins by electrostatic or hydrophobic forces. A potential drawback of such substrates is the difficulty... 

The predominant interaction of CYP3A4 is via hydrophobic forces and the overall lowering of lipophilicity can reduce metabolic lability to the enzyme. Figure 7.14 shows the relationship between unboimd intrinsic clearance in man and lipophilicity for a variety of CYP3A4 substrates. The substrates are cleared by a variety of metabolic routes including N-dealkylation, aromatization and aromatic and aliphatic hydroxylation. The trend for lower metabolic lability with lower lipophilicity is maintained regardless of structure or metabolic route. 

Fig. 22 a Measured force curves of linear segmented poly(N-isopropylacrylamide-seg-styrene) (PNIPAM-seg-St) copolymer chains adsorbed on a hydrophobic PS substrate in water, b Statistics of the distance between two adjacent peaks in the measured force curves [97]... 

Polymer acids or polyanions can catalyze the acid hydrolyss of esters, amides, and ethers. This is because the local proton concentration in the polymer domain is hi r than that in the bulk phase. The rate acceleration caused by this effect is moderate. However, when substrate molecules are attracted to the polymer molecule by electrostatic and hydrophobic forces, the catalytic efficiency increases (up to ca. 100 fold compared with mineral acids). Similar results were obtained for the alkali hydrolysis in the presence of polycations. 

Compound 8, which was synthesized by Schmidtchen (49). This receptor provides a fixed-binding site for anions that operates through a combination of electrostatic and hydrophobic forces (50). The absence of donor protons prevents any opportunity for hydrogen bonding, but the crystal structure of the iodide complex still indicated that the anion-binding site was in the center of the cavity (51). Zwitterionic hosts such as 9, have also been reported (52, 53). These net neutral hosts prevent the need for the substrate to compete against a... 

Andrews [76] reported that plasteins were formed by an association of predominantly hydrophobic peptides via hydrophobic and possibly ionic bonding. Aso and coworkers [77,78] concluded that hydrophobic forces were a major factor in plastein chain assembly. They found that, compared with the substrate, the water-insoluble product contained smaller ratios of hydrophilic and larger ratios of hydrophobic amino acid residues. The results of Sukan and Andrews [58] showed that hydrophobic amino acids such as phenylalanine, leucine, isoleucine, tyrosine, valine, and proline were preferentially incorporated into plastein at the expense of hydrophilic amino acids. Also others have reported on a trend of preferential incorporation of hydrophobic amino acids into the protein product in enzyme-catalyzed reactions [46,60,79,80,81]. 

Covalent attachment is often preferred over other types of immobilization modules, such as those based on noncovalent bonds, including van der Waals forces, hydrogen bonds, hydrophobic forces, and ionic bonds in aqueous solutions, and various affinity-based binding reactions. Covalent bond formation provides a more stable linkage between the carbohydrate and the array substrate. Since the coupling efficiencies of the carbohydrate moieties are more readily controlled, the immobilization reproducibility is likely independent of the differences in the structures of carbohydrate probes. 

Hydrophobic forces represent one of the most significant kinds of force binding a substrate with a catalyst [27]. Let us consider two cases in which (1) a polymeric catalyst contains hydrophobic binding sites (polysoaps) besides active nucleophyllic centers, and (2) a substrate has long hydrophobic sites. In the former case, an increase in the hydrolysis rate is observed for long-chained esters [28]. Such specificity is at-... 

All enzymes are proteins, which are linear sequences of amino acids linked by peptide bonds. The folding of these sequences determined the secondary structure (such as a-helix, p-sheet or p-turn) and tertiary structure. Therefore, the properties of an en me are actually presumed from its sequence of amino acids. Some amino acids, dubbed hot spots , especially the ones in the active site where substrate binds, are sensitive to catalytic properties of an enzyme. Substitution of these important amino acids can significantly improve the activity or enantioselectivity toward a certain reaction. Protein stability is also maintained by the intramolecular and intermolecular interactions between residues of amino acids, including van der Waals forces, hydrophobic forces, electrostatic forces, hydrogen bonds and disulfide bonds. Detailed analysis of these amino acids, usually located in the protein surface, sheds light on the protein design for better thermostability. 

FIGURE 30.9. Measured force curves of linear segment PNI-PAM-seg-PS chains adsorbed on a hydrophobic polystyrene substrate in water. Reproduced from Macromolecules (2003) with permission from American Chemical Society [50]. 

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