Sandbox 39: Difference between revisions
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Proteins only consist of certain elements: carbon, hydrogen, nitrogen, oxygen, and sulfur. Enzymes' primary structures allow them to fold optimally and interact with their substrates maximally in order to efficiently catalyze biological reactions. The <scene name='Sandbox_39/Elemental_composition/1'>elemental composition of papain</scene> shows carbon atoms outlined in grey, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow. | Proteins only consist of certain elements: carbon, hydrogen, nitrogen, oxygen, and sulfur. Enzymes' primary structures allow them to fold optimally and interact with their substrates maximally in order to efficiently catalyze biological reactions. The <scene name='Sandbox_39/Elemental_composition/1'>elemental composition of papain</scene> shows carbon atoms outlined in grey, oxygen atoms in red, nitrogen atoms in blue, and sulfur atoms in yellow. | ||
In addition, the entirety of the secondary structure of papain can be traced from the <scene name='Sandbox_39/N_to_c_rainbow/1'>N- to the 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/N_to_c_rainbow/1'>N- to the 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 purple end at the C-terminus. | N-terminus, and can be traced through the colors of the rainbow to the purple end at the C-terminus. | ||
== Active Site == | |||
Papain has a broad specificity for protein substrates. The active site consists of seven subsites that can each accommodate one amino acid residue of a substrate. Specificity is controlled, however, by the <scene name='Sandbox_39/Catalytic_triad/1'>catalytic triad</scene>, a hydrophobic pocket that accommodates the side chains of the protein substrate. This triad consists of a histidine, asparagine, and a cysteine, after which the protein is categorized as a cysteine protease. Papain exhibits specific substrate preferences for hydrophobic or aromatic residues. | |||
== Secondary Structure == | == Secondary Structure == | ||
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/1'>alpha helices</scene>, shown in blue, and <scene name='Sandbox_39/Beta_pleated_sheets/1'>beta pleated sheets</scene>, shown in green. All other motifs are nonrandom, structural units, mostly simply turns. As shown to the left, papain has 7 alpha helices and 8 beta pleated sheets. | 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/1'>alpha helices</scene>, shown in blue, and <scene name='Sandbox_39/Beta_pleated_sheets/1'>beta pleated sheets</scene>, shown in green. All other motifs are nonrandom, structural units, mostly simply turns. As shown to the left, papain has 7 alpha helices and 8 beta pleated sheets. | ||
== Polarity and Hydrophobicity == | == Polarity and Hydrophobicity == | ||
