Serine Proteases

Teaching Points Enzymes are biological catalysts that accelerate the rate of a reaction without being modified during the process. Several families of enzymes exist, each with a specific function. For example, proteases are enzymes that catalyze the cleavage of peptide bonds, which are the bonds that join amino acids together to form proteins. Serine proteases are members of this protease family. These enzymes are named after the reactive serine residue located in the active site that is essential for the function of the enzyme.

The active site of serine proteases contains three critical amino acids: serine, histidine and aspartate. These residues are often referred to as the “catalytic triad.” When the linear sequence of amino acids folds into its tertiary structure, these three residues are arranged in such a fashion that enables the sidechain of the serine residue to become negatively charged through the loss of the hydrogen off the hydroxyl R group to histidine. This nucleophile can then make an attack on the carbonyl group of the peptide bond that is to be cleaved.

Included within this collection are three serine proteases: Chymotrypsin, Elastase and Trypsin. Each of these enzymes plays an essential role in digestion. They are secreted by the pancreas as inactive zymogens into the small intestine, where they become active through proteolytic cleavage events. Each of these enzymes contains the catalytic triad within its active site, but they differ with respect to their target cleavage sites. The size and chemical nature of the active sites of these enzymes accommodate different substrates. Chymotrypsin cleaves peptide bonds that are next to aromatic residues (phenylalanine, tyrosine or tryptophan). Trypsin cleaves next to basic residues (lysine or arginine). Elastase is less discriminating, but prefers to cleave bonds near small hydrophobic residues (alanine). The structure of the active site allows for these specific cleavage sites to be positioned near the catalytic triad so that the active serine residue can make the nucleophilic attack on the bond in order to cleave it. This collection includes two versions of each of the enzymes: an α-carbon backbone and a spacefill model. The α-carbon backbone models allow for students to compare the three enzymes on different aspects, including secondary and tertiary structures and characteristics of the active site. The spacefill version of the model allows the student to appreciate how the different sidechains of each amino acid can interact to form the protein. This model is colored using the David Goodsell color scheme that highlights charged residues within the protein structure.

Models in this Collection

• α-carbon backbone models o Chymotrypsin o Elastase o Trypsin • Spacefill models o Chymotrypsin o Elastase o Trypsin

Model Details

• α-carbon backbone models o Backbone format o Color scheme α-helices – red β-sheets – yellow Loops – grey N terminus – green C terminus – cyan o Active site residues (His, Asp, Ser) in ball and stick and in CPK colors (carbon is gray, oxygen is red and nitrogen is blue) o Chymotrypsin Derived from PDB file 4cha Model made of plaster with the ZCorp printer o Elastase Derived from PDB file 4est Model made of plaster with the ZCorp printer o Trypsin Derived from PDB file 4ptc Model made of plaster with the ZCorp printer • Spacefill models o Spacefill format o Color scheme is developed by David Goodsell Oxygen • If neutral, colored pink • If charged, colored bright red Nitrogen • If neutral, colored light blue • If charged, colored bright blue Carbon: white Sulfur: yellow Hydrogen atoms are colored the same color as the atom to which each is attached o Chymotrypsin Derived from PDB file 4cha Model made of plaster with the ZCorp printer o Elastase Derived from PDB file 4est Model made of plaster with the ZCorp printer o Trypsin Derived from PDB file 4ptc Model made of plaster with the ZCorp printer

Documentation included

• Teaching points and inventory • How do the models fit back in the suitcase? • Enzyme Active Sites and Guide for Exploration • Serine Proteases Teaching Exercises • Serine Proteases – distinguishing the models • Images of Serine Proteases

Resources

• Animation: Nucleophilic Attack of Serine o http://www.andrew.cmu.edu/course/03-231/Protease/SerPro.htm o This website provides an animated view of the mechanism of action that serine proteases use in order to catalyze the hydrolysis of the peptide bond. • Chime tutorial of the active site of serine protease: o http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES /serprot.html • Superimposition of three serine proteases in Chime: o http://www.andrew.cmu.edu/course/03-231/ProtStruc/3TCE.htm