Sandbox 35: Difference between revisions
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==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 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> | <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 (yellow) serve to hold papain's tertiary structure together. | ||
The <scene name='Sandbox_35/Active_site_papain/3'>active site</scene> | The <scene name='Sandbox_35/Active_site_papain/3'>active site</scene> primarily consist of three main residues Cys25-His159-Asn175 that resemble the catalytic triad of chymotrypsin <ref>PMID: 8140097</ref><ref>PMID: 2397208</ref> | ||
<scene name='Sandbox_35/Active_site_asp_158_papain/1'>Asp 158</scene> | <scene name='Sandbox_35/Active_site_asp_158_papain/1'>Asp 158</scene> | ||
Crystallization of the protease under conditions of 62% (w/w) methanol in water reveals water playing a crucial role in providing structural stability. The 21 internal water molecules surrounding adjacent papain molecules appear to form an encasement that limit protein to protein interaction <ref>PMID: 6502713</ref>. | |||
===Distribution of Residues=== | ===Distribution of Residues=== | ||
Papain has a scattered distribution of <scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>, but can be seen to have more basic residues than acidic shedding light 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> Its <scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residues</scene> build on this picture with <scene name='Sandbox_35/Papain_polar/1'>polar residues</scene> resting more on the outside and <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 the center | Papain has a scattered distribution of <scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>, but can be seen to have more basic residues than acidic shedding light 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> Its <scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residues</scene> build on this picture with <scene name='Sandbox_35/Papain_polar/1'>polar residues</scene> resting more on the outside and <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 the center toward the outside <ref>PMID: 6502713 </ref> | ||
===Ligands interactions=== | ===Ligands interactions=== | ||
