The purpose of pepsin is to bind protein chains deep in the active site groove of pepsin so that they can be broken up into smaller pieces and eventually become absorbed by cells (Goodsell 2000).
Pepsin uses a pair of aspartate residues (shown in green) to perform the protein cleavage reaction. The active site (shown above) relies on two acidic aspartate amino acids, ASP - 32 and ASP - 215, that activate a water molecule (shown in red) and use it to cleave protein chains (Goodsell 2000).
The pair of aspartate residues (shown in green) are dicarboxylic amino acids that have a negatively charged hydrophilic side chain. It is due to this negatively charged side chain that pepsin is attracted to positively charged protein ions and only reacts with proteins that are positive (Northrop 1922).
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