Sandbox 39: Difference between revisions
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In addition, the entirety of the secondary structure of papain can be traced from the <scene name='Sandbox_39/Elemental/3'>N- to C-terminus.</scene> As shown to the left, the red end begins the protein at the | In addition, the entirety of the secondary structure of papain can be traced from the <scene name='Sandbox_39/Elemental/3'>N- to C-terminus.</scene> As shown to the left, the red end begins the protein at the | ||
N-terminus, and can be traced through the colors of the rainbow to the blue end at the C-terminus. | N-terminus, and can be traced through the colors of the rainbow to the blue end at the C-terminus. | ||
== Primary, Secondary, and Tertiary Structure == | == Primary, Secondary, and Tertiary Structure == | ||
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Papain's primary structure causes it to fold into different motifs that make up its secondary structure. These motifs include <scene name='Sandbox_39/Alpha_helices/2'>alpha helices</scene>, shown in green, and <scene name='Sandbox_39/Beta_pleated_sheets/2'>beta pleated sheets</scene>, shown in orange. As shown to the left, papain has 7 alpha helices and 8 beta pleated sheets. All other motifs are nonrandom, structural units, mostly simply turns. | Papain's primary structure causes it to fold into different motifs that make up its secondary structure. These motifs include <scene name='Sandbox_39/Alpha_helices/2'>alpha helices</scene>, shown in green, and <scene name='Sandbox_39/Beta_pleated_sheets/2'>beta pleated sheets</scene>, shown in orange. As shown to the left, papain has 7 alpha helices and 8 beta pleated sheets. All other motifs are nonrandom, structural units, mostly simply turns. | ||
Papain's seconary structures then fold even further to for its three-dimensional structure, which consists of two distinct structural domains with a cleft between them. This cleft contains the catalytic diad discussed above. This tertiary structure is pictured | Papain's seconary structures then fold even further to for its three-dimensional structure, which consists of two distinct structural domains with a cleft between them. This cleft contains the catalytic diad discussed above. This tertiary structure is pictured to the right. | ||
[[Image:9pap moreau 1.jpeg]] | |||
[[Image:9pap moreau 1.jpeg|right]] | |||
<ref>Image from: | <ref>Image from: | ||
http://linus.chem.ku.edu/hewlett/Chem188/Enzyme/enzyme_background.htm</ref>]] | http://linus.chem.ku.edu/hewlett/Chem188/Enzyme/enzyme_background.htm</ref>]] | ||
== Active Site == | |||
Papain has a broad specificity for protein substrates. The active site consists of seven subsites (S1-S4 and S1’-S3’) that can each accommodate one amino acid residue of a protein substrate (P1-P4 and P1’-P3’). | |||
[[Image:Subsites.jpg|right]] | |||
<ref>Image from: | |||
Hans-Hartwig Otto, and Tanja Schirmeister (1997) Cysteine Proteases and Their Inhibitors. Chemical Reviews. No. 97, 133-171.</ref>]] | |||
Specificity is controlled, however, by the <scene name='Sandbox_39/Active_site_revised/1'>catalytic diad</scene>, a hydrophobic pocket that accommodates the side chains of the protein substrate. This diad, shown above in red and clearly visible in the cleft of the enzyme, consists of cysteine25 (after which the protein is categorized as a cysteine protease)and histidine159. Papain exhibits specific substrate preferences for hydrophobic or aromatic residues. | |||
== Polarity and Hydrophobicity == | == Polarity and Hydrophobicity == | ||
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3. Hans-Hartwig Otto, and Tanja Schirmeister (1997) Cysteine Proteases and Their Inhibitors. Chemical Reviews. No. 97, 133-171. | 3. Hans-Hartwig Otto, and Tanja Schirmeister (1997) Cysteine Proteases and Their Inhibitors. Chemical Reviews. No. 97, 133-171. | ||
4. Image from: | |||
5. Image from: http://linus.chem.ku.edu/hewlett/Chem188/Enzyme/enzyme_background.htm | |||
6. Image from: http://www.rcsb.org/pdb/explore/jmol.do?structureId=9PAP&bionumber=1 | |||
7. Image from: http://www.rcsb.org/pdb/explore/explore.do?structureId=1POP | |||
