CHEM2052 Tutorial
From Proteopedia
Chem2052: Example 3 - Serine ProteasesSerine proteases account for over one-third of all known proteolytic enzymes [1],[2]. Within the diverse collection of serine proteases, the most famous members are trypsin, chymotrypsin and elastase. Aside from their key roles in digestion (and other physiological processes) [2], the unique specificities of these enzymes make them useful tools in biochemistry and molecular biology to ascertain protein sequences. Looking at the structures below, it is apparent that these three enzymes have similar folds. This conservation of tertiary structure is due to extensive similarities at the level of primary amino acid sequence. However, there are small differences in amino acid sequence among the proteins, which are reflected in their different specificities. Each protein cleaves the peptide backbone after (or on the carbonyl side) of a specific type of sidechain. After examining the molecular basis for these functional similarities and differences, you will hopefully see why serine proteases are a classic example of how structure dictates function! Active SitesSerine proteases perform their catalytic roles using three key residues, which are commonly referred to as the catalytic triad: . The elements are color coded as follows: C, O, N.
This arrangement of amino acids is also called a charge relay system [3]. Now compare the active site residues of chymotrypsin to the . Substrate Binding PocketsThe next links examine the binding pockets of each protein. The spacefilled residues have been color coded according to hydrophobicity (residues are indicated as: Hydrophobic or Polar, with Aspartate highlighted further ).
Understanding the MechanismCatalytic MechanismLehninger's Principles of Biochemistry (5th edition)describes the catalytic mechanism of chymotrypsin on pages 208-209. An animated version of the enzyme-catalyzed hydrolysis reaction is also available on the textbook's website. was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the that were highlighted above. (Or you can .)
Additional PDB StructuresIn order to easily compare the proteins shown on this page, some portions of the crystal structures have been masked. Although each of these serine proteases functions as a monomer, they are often observed as dimers or even tetramers in crystal structures. These higher-order multimers are not the physiological state of the serine protease, but rather a consequence of the experimental method, which requires high protein concentrations. However, some proteins are only functional in the tetrameric state, such as hemoglobin. Therefore, it is important to recognize that one cannot necessarily determine the physiological state from a crystal structure alone. 3D structures of chymotrypsin3D structures of trypsin3D structures of elastase
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