Interactions chain-hydrophobic site

Lysine also may form complexes with anionic ligands and thereby increase Am values. In addition, lysine may have an unfavorable effect on protein structure. Because it has a considerable hydrophobic moment, it may interact with hydrophobic sites on the protein, leading to perturbation of structure. Compatible solutes lack a propensity for interacting with peptide backbone linkages or amino acid side-chains, as discussed later. 

As stated earlier, the primary site of association of [ H]MDA with brain synaptosomes is with membrane components, not with the intrasynaptic space. While the phenolic ends of these compounds may enable them to interact with hydrophobic environments of brain membrane components, their polar side chains may inhibit the ability of these compounds to move freely across the membranes, thus inhibiting internalization. The pKa of... 

Modification or enhancement of interaction of CDs with hydrophobic drugs arising from the high number of long aliphatic chains and by increasing the number of hydrophobic sites for possible interactions with hydrophobic molecules... 

In the pH range close to the protein s lEP an interesting phenomenon of non-uniform redistribution of protein molecules among polysaccharide chains occurs (Tolstoguzov et al. 1985). The reason is that in the vicinity of the protein lEP the hydrophobic protein-protein and electrostatic protein-polysaccharide interactions can be energetically comparable with each other. Protein-protein association on the anionic polysaccharide matrix (or self-association of proteins), which is mainly due to hydrophobic interactions, is usually enhanced when the pH approaches the protein lEP. Accordingly, under conditions of a relatively weak protein-polysaccharide interaction, each free site situated near the site on the polysaccharide chain already occupied by a protein molecule becomes thermodynamically preferable for further binding of protein molecules. This leads to cooperative protein adsorption on an anionic polysaccharide. Some parts of polysaccharide chains tend to be completely covered by protein molecules (as in a virus) while other parts are completely free of protein. 

The hydrophobic site is usually a non polar group like a hydrocarbon chain. If a molecule contains both non-polar and polar groups then in an aqueous medium it will take up a configuration or associate in such a way that the hydrophobic (nonpolar) parts are in contact with one other so as to maximize the number of attractive interactions (mainly by dispersion forces) and that the hydrophilic (polar) parts are turned toward the aqueous phase to participate in hydrogen bonds or other polar interactions. Both enthalpy and entropy considerations are important in this respect and wc refer to Nemethy and Scheraga for a detailed discussion of the problem. 

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