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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This arrangement of amino acids is also called a '''charge relay system''' <ref>PMID: 7016210</ref>. | This arrangement of amino acids is also called a '''charge relay system''' <ref>PMID: 7016210</ref>. | ||
Now compare the active site residues of chymotrypsin to the <scene name=' | Now compare the active site residues of chymotrypsin to the <scene name='59/596400/Morph/3'>trypsin catalytic triad and the elastase catalytic triad</scene> (<span style="color:lightblue;background-color:black;font-weight:bold;">trypsin is in light blue</span>, PDB code [[1aq7]] and <span style="color:pink;background-color:black;font-weight:bold;">elastase is in pink</span>, PDB code [[4est]]). <jmol><jmolButton><script>frame next</script><text>Click this button</text></jmolButton></jmol> to flip between structures. | ||
== '''Substrate Binding Pockets''' == | == '''Substrate Binding Pockets''' == | ||
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== '''Understanding the Mechanism''' == | == '''Understanding the Mechanism''' == | ||
==== '''Catalytic Mechanism''' ==== | ==== '''Catalytic Mechanism''' ==== | ||
The following animation describes the catalytic mechanism of chymotrypsin [http://www.sumanasinc.com/webcontent/animations/content/chymotrypsin.html]. <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== | ||
Latest revision as of 03:19, 18 August 2015
<StructureSection load= size='450' side='right' scene='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/2' caption='α-chymoptrypsin (PDB code 2cha)'>
Chem2052: Example 3 - Serine ProteasesChem2052: Example 3 - Serine Proteases
Serine 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 SitesActive Sites
Serine 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.
- Mouse over or click on the structure to determine the residue numbers for the catalytic residues. (The residue code will appear near the mouse pointer or in the lower left-hand corner of the browser window.)
- You can adjust the zoom in each image by holding down the shift key while you click and drag on the structure. Alternatively, you can click on the Jmol symbol in the lower right-hand corner of each image and select a different zoom percentage from the main menu.
This arrangement of amino acids is also called a charge relay system [3].
Now compare the active site residues of chymotrypsin to the (trypsin is in light blue, PDB code 1aq7 and elastase is in pink, PDB code 4est). to flip between structures.
Substrate Binding PocketsSubstrate Binding Pockets
The 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 ).
- The . This structure shows the binding pocket using , a bound inhibitor.
- The contains Asp189. Consider the peptide-based inhibitor called , which is now shown in balls and sticks, which residue of this inhibitor is interacting with Asp189?
- The .
Understanding the MechanismUnderstanding the Mechanism
Catalytic MechanismCatalytic Mechanism
The following animation describes the catalytic mechanism of chymotrypsin [1]. 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 .)
- () Note that the would be in approximately the same location as the carbonyl group of the substrate peptide.
Additional PDB StructuresAdditional 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 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 chymotrypsin
3D structures of trypsin3D structures of trypsin
3D structures of elastase3D structures of elastase
ReferencesReferences
- ↑ Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ. MEROPS: the peptidase database. Nucleic Acids Res. 2008 Jan;36(Database issue):D320-5. Epub 2007 Nov 8. PMID:17991683 doi:10.1093/nar/gkm954
- ↑ 2.0 2.1 Di Cera E. Serine proteases. IUBMB Life. 2009 May;61(5):510-5. PMID:19180666 doi:10.1002/iub.186
- ↑ Banacky P, Linder B. Model of serine proteases charge relay system -- PCILO study. Biophys Chem. 1981 Jun;13(3):223-31. PMID:7016210