Why does trypsin cleave peptide bonds after lysine or arginine, while chymotrypsin cleaves after large hydrophobic residues?
Answer
Trypsin has a negatively charged aspartate in its binding pocket forming an ionic bond with basic residues.
Trypsin's specificity is conferred by a negatively charged aspartate residue within its binding pocket, enabling it to form ionic interactions with the positively charged side chains of basic amino acids like lysine or arginine, while chymotrypsin's hydrophobic pocket recognizes nonpolar residues.
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