Hydrophobic binding magnitude

As the hydrophobic binding is influenced by the reaction solution the hydrolysis has been carried out in several reaction solutions. The increase of the ethanol content in its aqueous solution decreases the magnitude of the hydro-phobic interaction. Table 8 shows the result of the hydrolysis of the negatively charged substrate, NDBA [n - 10 in (8)], by poly(4(5)-vinylimidazole) (II) in an aqueous ethanol solution (24). 

The magnitude of hydrophobic binding free energy has been estimated to be about 0.2 kJ mol per of host-guest contact. This positive contribution will of course be moderated by the loss of entropy on binding, reflecting the loss of translational and rotational freedoms of the separated components. 

There have been numerous synthetic supramolecular structures created to mimic the various aspects of the natural enzymes that catalyze acyl transfers. Here, we only show two with their respective binding geometries and electron pushing for the nucleophilic attack. The first shown below was developed by Lehn, and uses the well precedented binding between crown ethers and ammonium ions to form a complex between the catalyst and the substrate. The second example was developed by Bres-low, where cyclodextrin (the toroid see Chapter 4) is used to drive hydrophobic binding of the substrate to the catalyst. These two examples do indeed catalyze their respective acyl transfers, but with orders of magnitude lower... 

The noncovalent binding of a series of oxo-squaraine dyes 9a-e to BSA was evaluated by measurement of absorption, emission, and circular dichroism [63]. The magnitude of the association constants (Ks) for the dye-BSA complexes depended on the nature of the side chains and ranged from 34 x 103 to 1 x 107 M-1. Depending on the side chains, the Ks increase in the order [R1 = R2 = butyl-phthalimide] < R1 = R2 = cetyl] <[RJ = R2 = ethyl] <<[R = butyl-phthalimide, R2 = butyl-sulfonate] <<[RJ = R2 = butyl-sulfonate]. These dyes seem to interact mainly with a hydrophobic cavity on BSA. However, the association constants Ks increase substantially when the side chains are selected from butyl sulfonate. 

The squaraine probe 9g was tested for its sensitivity to trace the formation of protein-lipid complexes [57]. The binding of dye 9g to model membranes composed of zwitter-ionic lipid phosphatidylcholine (PC) and its mixtures with anionic lipid cardiolipin (CL) in different molar ratios was found to be controlled mainly by hydrophobic interactions. Lysozyme (Lz) and ribonuclease A (RNase) influenced the association of 9g with lipid vesicles. The magnitude of this effect was much higher... 

Errors of this magnitude make the useful prediction of free energies a difficult task, when differences of only one to three kcal/mol are involved. Nevertheless, within the error limits of the computed free energy differences, the trend is that relative to 8-methyl-N5-deazapterin or 8-methyl-pterin, the compounds methyl substituted in the 5, 6 or 7 positions are thermodynamically more stable when bound to DHFR largely by virtue of a hydrophobic effect, i.e. methyl substitution reduces the affinity of the ligand for the solvent more than it reduces affinity for the DHFR active-site. The stability of ligand binding to DHFR appears to be optimal with a 6-methyl substituent additional 5-methyl and/or 7-methyl substitution has little effect... 

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