Sandbox 35: Difference between revisions
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<Structure load='9pap' size='500' frame='true' align='right' caption='Structure of Papain (PDB entry [[9PAP]])' scene='Sandbox_35/Papain/1'/> | <Structure load='9pap' size='500' frame='true' align='right' caption='Structure of Papain (PDB entry [[9PAP]])' scene='Sandbox_35/Papain/1'/> | ||
==Structure== | ==Structure== | ||
Papain's polypeptide chain consists of 212 amino acid residues which fold to form a groove containing the active site between its two domains. Its | Papain's single polypeptide chain consists of 212 amino acid residues which fold to form a groove containing the active site between its two domains. Its | ||
<scene name='Sandbox_35/Secondary_structure_papain/2'>secondary structure</scene> consists of 17 <scene name='Sandbox_35/2nd_struc_papain_beta/2'>beta sheet</scene> strands and 7 <scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helices</scene> giving it a composition 21% and 25% respectively. <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref> The hydrogen bonds within the alpha helices are shorter than the typical alpha helix because of C=O being directed further away from the helical axis. Moreover, the beta sheet hydrogen bonding constraints and structural angles show great variation; hydrogen bonds in the sheets' central tend to be shorter than on the fringes. Three disulfide bonds, for example <scene name='Sandbox_35/Papain_cys_bond/1'>Cys 22-Cys 63</scene>, serve to hold papain's tertiary structure together. <ref>PMID: 6502713</ref> | <scene name='Sandbox_35/Secondary_structure_papain/2'>secondary structure</scene> consists of 17 <scene name='Sandbox_35/2nd_struc_papain_beta/2'>beta sheet</scene> strands and 7 <scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helices</scene> giving it a composition 21% and 25% respectively. <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref> The hydrogen bonds within the alpha helices are shorter than the typical alpha helix because of C=O being directed further away from the helical axis. Moreover, the beta sheet hydrogen bonding constraints and structural angles show great variation; hydrogen bonds in the sheets' central tend to be shorter than on the fringes. Three disulfide bonds, for example <scene name='Sandbox_35/Papain_cys_bond/1'>Cys 22-Cys 63</scene>, serve to hold papain's tertiary structure together. <ref>PMID: 6502713</ref> | ||
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Although Papain has a scattered distribution of <scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>, it can be seen to have more basic residues than acidic, shedding understanding into the application of its use as a digestive supplement. <ref>[http://www.webmd.com/vitamins-supplements/ingredientmono-69-PAPAIN.aspx?activeIngredientId=69&activeIngredientName=PAPAIN] WebMD</ref> Seeing its <scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residues</scene> further shows <scene name='Sandbox_35/Papain_polar/1'>polar residues</scene> remaining mostly on the exterior while <scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene> sequestering near the center. Observations have revealed that the proteins atomic positions are more ordered going from outside toward the center and also disclose the hydrophobic core of the enzyme. <ref>PMID: 6502713 </ref> | Although Papain has a scattered distribution of <scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>, it can be seen to have more basic residues than acidic, shedding understanding into the application of its use as a digestive supplement. <ref>[http://www.webmd.com/vitamins-supplements/ingredientmono-69-PAPAIN.aspx?activeIngredientId=69&activeIngredientName=PAPAIN] WebMD</ref> Seeing its <scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residues</scene> further shows <scene name='Sandbox_35/Papain_polar/1'>polar residues</scene> remaining mostly on the exterior while <scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene> sequestering near the center. Observations have revealed that the proteins atomic positions are more ordered going from outside toward the center and also disclose the hydrophobic core of the enzyme. <ref>PMID: 6502713 </ref> | ||
==== | ====Ligand interactions and Pseudo Substrates==== | ||
Papain is said to have 29 methanol molecules that encircle around it as <scene name='Sandbox_35/Papain_ligand/1'>ligands</scene>. The polarity of the ligands result in hydrogen bonding interactions, possibly providing further stability for papain structure. <ref>PMID: 6502713</ref> | Papain is said to have 29 methanol molecules that encircle around it as <scene name='Sandbox_35/Papain_ligand/1'>ligands</scene>. The polarity of the ligands result in hydrogen bonding interactions, possibly providing further stability for papain structure. <ref>PMID: 6502713</ref> | ||
