CHEM2052 Tutorial: Difference between revisions
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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'''''! | 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'''''! | ||
*<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/2'>Chymotrypsin</scene> | *<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/2'>Chymotrypsin</scene> | ||
*<scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/4'>Trypsin</scene> | *<scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/4'>Trypsin</scene> | ||
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== '''Understanding the Mechanism''' == | == '''Understanding the Mechanism''' == | ||
==== '''Catalytic Mechanism''' ==== | ==== '''Catalytic Mechanism''' ==== | ||
Lehninger's Principles of Biochemistry (5th edition)describes the catalytic mechanism of chymotrypsin on pages 208-209. An [http://bcs.whfreeman.com/lehninger5e/pages/bcs-main.asp?v=&s=06000&n=00010&i=06010.01&o=|00610|00580|00590|00510|00540|00600|00550|00570|00630|00010|00020|00030|00040|00070|00080|00090|00100|01000|02000|03000|04000|05000|06000|07000|08000|09000|10000|11000|12000|13000|14000|15000|16000|17000|18000|19000|20000|21000|22000|23000|24000|25000|26000|27000|28000|99000| animated version] of the enzyme-catalyzed hydrolysis reaction is also available on the textbook's website. <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/10'> | |||
This representation</scene> was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/11'>binding pocket residues</scene> that were highlighted above. (Or you can <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/16'>label the catalytic triad and Gly193</scene>.) | This representation</scene> was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/11'>binding pocket residues</scene> that were highlighted above. (Or you can <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/16'>label the catalytic triad and Gly193</scene>.) | ||
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== '''Additional PDB Structures''' == | == '''Additional PDB Structures''' == | ||
In 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 | In 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 chymotrypsin== | ==3D structures of chymotrypsin== | ||