Sandbox 30: Difference between revisions

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==Structure==

The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>. The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain. These secondary structures form as a result of favorable hydrogen bonding interactions within the polypeptide backbone. Meanwhile, secondary structures are kept in place by hydrophobic interactions and hydrogen bonds between sidechains of adjacent structures. For example, the first helix (residues 25-42) is maintained as a result of <scene name='Sandbox_30/Papain_secondary_helices_hbond/2'>hydrogen bonds</scene> between backbone carbonyl atoms and the hydrogen on the amide nitrogen four residues away. However, <scene name='Sandbox_30/Papain_secondary_heliceshbond2/1'>no hydrogen bonds</scene> are present between this helix and the rest of the protein, suggesting that this helix is coordinated entirely by hydrophobic interactions, which is reasonable given its place in the center of the enzyme. As expected, the helix contains many <scene name='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic). The tertiary structure of papain is also maintained by three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,

The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>. The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain. These secondary structures form as a result of favorable hydrogen bonding interactions within the polypeptide backbone. Meanwhile, secondary structures are kept in place by hydrophobic interactions and hydrogen bonds between sidechains of adjacent structures. For example, the first helix (residues 25-42) is maintained as a result of <scene name='Sandbox_30/Papain_secondary_helices_hbond/3'>hydrogen bonds</scene> between backbone carbonyl atoms and the hydrogen on the amide nitrogen four residues away. However, <scene name='Sandbox_30/Papain_secondary_heliceshbond2/1'>no hydrogen bonds</scene> are present between this helix and the rest of the protein, suggesting that this helix is coordinated entirely by hydrophobic interactions, which is reasonable given its place in the center of the enzyme. As expected, the helix contains many <scene name='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic). The tertiary structure of papain is also maintained by three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,

<scene name='Sandbox_30/Papain_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='Sandbox_30/Papain_disulfides_153-200/1'>Cys-153 to Cys-200</scene><ref name="9PAP PDB" />. These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures.

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@@ Line 13: / Line 13: @@
 ==Structure==
-The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>.  The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain.  These secondary structures form as a result of favorable hydrogen bonding interactions within the polypeptide backbone.  Meanwhile, secondary structures are kept in place by hydrophobic interactions and hydrogen bonds between sidechains of adjacent structures.  For example, the first helix (residues 25-42) is maintained as a result of <scene name='Sandbox_30/Papain_secondary_helices_hbond/2'>hydrogen bonds</scene> between backbone carbonyl atoms and the hydrogen on the amide nitrogen four residues away.  However, <scene name='Sandbox_30/Papain_secondary_heliceshbond2/1'>no hydrogen bonds</scene> are present between this helix and the rest of the protein, suggesting that this helix is coordinated entirely by hydrophobic interactions, which is reasonable given its place in the center of the enzyme.  As expected, the helix contains many <scene name='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic).  The tertiary structure of papain is also maintained by three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,
+The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>.  The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain.  These secondary structures form as a result of favorable hydrogen bonding interactions within the polypeptide backbone.  Meanwhile, secondary structures are kept in place by hydrophobic interactions and hydrogen bonds between sidechains of adjacent structures.  For example, the first helix (residues 25-42) is maintained as a result of <scene name='Sandbox_30/Papain_secondary_helices_hbond/3'>hydrogen bonds</scene> between backbone carbonyl atoms and the hydrogen on the amide nitrogen four residues away.  However, <scene name='Sandbox_30/Papain_secondary_heliceshbond2/1'>no hydrogen bonds</scene> are present between this helix and the rest of the protein, suggesting that this helix is coordinated entirely by hydrophobic interactions, which is reasonable given its place in the center of the enzyme.  As expected, the helix contains many <scene name='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic).  The tertiary structure of papain is also maintained by three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,
 <scene name='Sandbox_30/Papain_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='Sandbox_30/Papain_disulfides_153-200/1'>Cys-153 to Cys-200</scene><ref name="9PAP PDB" />.  These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures.