Changing the pH level can change the shape of a protein. This process is called "denaturing" the protein. When a protein becomes denatured, it does not function optimally or it does not function at all.
A protein has a certain structure that affects its function. For example, proteins such as enzymes can no longer bind to substrates if their structures change; similarly, antibodies cannot bind to foreign substances called antigens if their structure has been changed.
Interactions between the side chains in the amino acids making up proteins causes them to fold into a unique three-dimensional shape. Changing the pH level alters these side-chain interactions, leading to a change in protein shape. According to Brooklyn College, some proteins can return to their original shapes if the pH level returns to optimal conditions.