Ligand binding, solvent effects

As shown in Figure 6, the solvent molecules tend to be ordered around the molecules and when the protein and the ligand bind, several of these molecules are liberated and become disordered (entropic effect). Therefore, upon complex formation water molecules are released, receptor and ligand lose degrees of freedom and the interaction between the ligand and the receptor is calculated. 

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... 

First, we remove the solvent and consider only the system of adsorbent and ligand molecules. We make this simplification not because solvent effects are unimportant or negligible. On the contrary, they are very important and sometimes can dominate the behavior of the systems. We do so because the development of the theory of cooperativity of a binding system in a solvent is extremely complex. One could quickly lose insight into the molecular mechanism of cooperativity simply because of notational complexity. On the other hand, as we shall demonstrate in subsequent chapters, one can study most of the aspects of the theory of cooperativity in unsolvated systems. What makes this study so useful, in spite of its irrelevance to real systems, is that the basic formalism is unchanged by introducing the solvent. The theoretical results obtained for the unsolvated system can be used almost unchanged, except for reinterpretation of the various parameters. We shall discuss solvated systems in Chapter 9. 

Figure 8.1. Lock and key model (a) geometrical fit, (b) complementary pattern of functional groups, (c) site preference due to the solvent effect. The ligand L may better fit site A, but it binds preferentially to site B due to the solvent effect...

Effects due to solvent dielectric constant in terms of the contribution AGb (equation I) have already been considered. The destabilization effect due to a decrease in dielectric constant is relatively small as long as s S 10. On the other hand, during the complexation process the ligand binding sites have to be set free by breaking intermolecular solvent-ligand bonds. This is more difficult in polar solvents of high than for solvents of low e (5, 16). 

It is also possible to make some inferences about the nature of the transition state. Fast association rates imply stepwise removal of the solvation shell of the cation by consecutive replacement of each solvent molecule by a ligand binding site, so as to minimize the loss of binding energy in the transition state. The fact that the association rates differ less than the dissociation rates (which follow the stability sequence) could indicate that the transition state is nearer to the reagents than to the complex. Furthermore the slowness of the association could be explained by the operation of the following effects on the way to the transition state ... 

Effects of solvent mixtures can be seen in biochemical systems. Ligand binding to myoglobin in aqueous solution involves two kinetic components, one extramolecular and one intramolecular, which have been interpreted in terms of two sequential kinetic barriers. In mixed solvents and subzero temperatures, the outer barrier increases and the inner barrier splits into several components, giving rise to fast intramolecular recombination. Measurements of the corresponding solvent structural relaxation rates by frequency resolved calorimetry allows the discrimination between solvent composition and viscosity-related effects. The inner barrier and its coupling to structural relaxation appear to be independent of viscosity but change with solvent composition (Kleinert et al., 1998). 

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