Sandbox 34: Difference between revisions
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<scene name='Sandbox_34/Arg191asp140intraxn/1'>asparagine-140 and arginine-191</scene>.<ref name="Structure" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the | <scene name='Sandbox_34/Arg191asp140intraxn/1'>asparagine-140 and arginine-191</scene>.<ref name="Structure" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the | ||
<scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</scene> segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule. | <scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</scene> segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule. | ||
=== Ligands === | === Ligands === | ||
Papain binds both <scene name='Sandbox_34/Papainwithwaterandmtoh/1'>methanol and water molecules</scene> via hydrogen bonds. This solvent mixture of 62%, (w/w) <scene name='Sandbox_34/Entire_protein_with_ligands/2'>methanol</scene> in <scene name='Sandbox_34/Papainwithwateronly/1'>water</scene> was used in order to obtain a C-type crystal. In addition to the methanol molecules, papain also has an interesting hydrogen bonding with water molecules. A refined crystal structure of papain, involving a restrained least-squares procedure at 1.65 A, with an estimated accuracy of 0.1 A, revealed that water forms something similar to a hydration shell around individual molecules of papain. The interaction of papain with these water molecules leads to less interaction between papain molecules, and contributes to the stability of the crystal structure of papain.<ref name="Structure" /> | Papain binds both <scene name='Sandbox_34/Papainwithwaterandmtoh/1'>methanol and water molecules</scene> via hydrogen bonds. This solvent mixture of 62%, (w/w) <scene name='Sandbox_34/Entire_protein_with_ligands/2'>methanol</scene> in <scene name='Sandbox_34/Papainwithwateronly/1'>water</scene> was used in order to obtain a C-type crystal. In addition to the methanol molecules, papain also has an interesting hydrogen bonding with water molecules. A refined crystal structure of papain, involving a restrained least-squares procedure at 1.65 A, with an estimated accuracy of 0.1 A, revealed that water forms something similar to a hydration shell around individual molecules of papain. The interaction of papain with these water molecules leads to less interaction between papain molecules, and contributes to the stability of the crystal structure of papain.<ref name="Structure" /> | ||
=== Specificity === | === Specificity === | ||
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[[Image:Papainmech6.jpg| | [[Image:Papainmech6.jpg|500px|right|thumb| A general mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]] | ||
