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The rise in pH can change the protein conformation by changing the ionic interactions and hydrogen bonds between two polypeptide chains. This is a fact that I understand very well because the change in amino-acid ionization with pH. I would like to know if by changing the pH value the hydrophobic interactions between two chains can also be changed. If yes, what is the mechanism? Article: a pH Induced increase in hydrophobicity...

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Here is one possible mechanism:

In tightly folded, compact, "globular" protein structures, the most hydrophobic bits of the protein tend to be in the core of the structure, away from the surface.

If the pH changes, then by mechanisms you mention in your question, this structure can be disrupted. If it is side chain interactions among surface-oriented, polar residues that "hold together" the globular structure, then a pH change can disrupt those interactions, allowing the previously isolated hydrophobic "core" to become exposed. This core can now bind more surfactant molecules, aggregate with itself, or do any number of other "hydrophobic" things.

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