Sandbox 37: Difference between revisions
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==Structure== | ==Structure== | ||
<StructureSection load='9PAP' size='400' align='left' caption='Papain (9PAP)' scene=''></StructureSection> | <StructureSection load='9PAP' size='400' align='left' caption='Papain (9PAP)' scene=''></StructureSection> | ||
Papain's three-dimensional structure is at 1.65 Angstrom resolution. It consists of one polypepetide chain that is made up of 212 amino acids residues. There are three <scene name='Sandbox_37/Papain_disulfide_bonds/1'>disulfide bonds</scene> present in the enzyme that maintains the protein's structure. Papain consists of 25% alpha helices and 21% beta sheets within its <scene name='Sandbox_37/Papain_beta-alpha/1'>secondary structure</scene>. Alpha helices are shown in red and beta sheets are shown in green. The enzyme's structure has a mixture of <scene name='Sandbox_37/Papain_hydrophobic/7'>hydrophobic residues</scene> shown in yellow and hydrophilic residues shown in purple. This corresponds to the protein's <scene name='Sandbox_37/Papain_polar/1'>polar residues</scene> shown in orange and nonpolar residues shown in green. Papain is naturally found with many <scene name='Sandbox_37/Ligand/3'>ligands</scene>. The majority are methanol molecules because the crystallization medium is 62% (w/w) methanol in water and only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules.<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref> Here, the enzyme's sulfhydryl group can also be seen which is necessary for the activity of the enzyme. <scene name='Sandbox_37/Papain_van_der_waals/1'>Van der Waals interactions</scene> and <scene name='Sandbox_37/Papain_hydrogen_bonds/1'>hydrogen bonds</scene> between the ligands and protein maintain the structural domains of papain. Water molecules are depicted as pink spheres. | Papain's three-dimensional structure is at 1.65 Angstrom resolution. It consists of one polypepetide chain that is made up of 212 amino acids residues. There are three <scene name='Sandbox_37/Papain_disulfide_bonds/1'>disulfide bonds</scene> present in the enzyme that maintains the protein's structure. Papain consists of 25% alpha helices and 21% beta sheets within its <scene name='Sandbox_37/Papain_beta-alpha/1'>secondary structure</scene>. Alpha helices are shown in red and beta sheets are shown in green. The enzyme's structure has a mixture of <scene name='Sandbox_37/Papain_hydrophobic/7'>hydrophobic residues</scene> shown in yellow and hydrophilic residues shown in purple. This corresponds to the protein's <scene name='Sandbox_37/Papain_polar/1'>polar residues</scene> shown in orange and nonpolar residues shown in green. Papain is naturally found with many <scene name='Sandbox_37/Ligand/3'>ligands</scene>. The majority are methanol molecules because the crystallization medium is 62% (w/w) methanol in water and only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules.<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref> Here, the enzyme's sulfhydryl group can also be seen which is necessary for the activity of the enzyme. <scene name='Sandbox_37/Papain_van_der_waals/1'>Van der Waals interactions</scene> and <scene name='Sandbox_37/Papain_hydrogen_bonds/1'>hydrogen bonds</scene> between the ligands and protein maintain the structural domains of papain. Water molecules are depicted as pink spheres.Twenty-one water molecules are located in contact areas between adjacent papain molecules. It seems as if the enzyme is trapped in a grid of water molecules with only a limited number of direct interactions between the protein molecules.<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref> | ||
[[Image:Ramachandran plot.JPG| right| thumb| Ramachandran plot of papain amino acid residues]] | [[Image:Ramachandran plot.JPG| right| thumb| Ramachandran plot of papain amino acid residues]] | ||
Revision as of 01:28, 14 November 2011
Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013.
PapainIntroductionPapain is a cysteine protease that is stable and active under a wide range of conditions. The enzyme present in the leaves, latex, roots, and fruit of the papaya plant (Carica papaya).[1] The papain proteins are synthesized as inactive precursors that become active within two minutes of the plant being wounded and the latex is expelled.[2] The latex is dried and then purified to extract the active papain enzme. The enzyme was first studied and isolated in the 1960's. It has a 23.4kDa theoretical molecular weight and works at an optimum pH of 6-7 and optimum temperature of 60-70 degrees Celsius. Structure
Papain's three-dimensional structure is at 1.65 Angstrom resolution. It consists of one polypepetide chain that is made up of 212 amino acids residues. There are three disulfide bonds present in the enzyme that maintains the protein's structure. Papain consists of 25% alpha helices and 21% beta sheets within its secondary structure. Alpha helices are shown in red and beta sheets are shown in green. The enzyme's structure has a mixture of hydrophobic residues shown in yellow and hydrophilic residues shown in purple. This corresponds to the protein's polar residues shown in orange and nonpolar residues shown in green. Papain is naturally found with many ligands. The majority are methanol molecules because the crystallization medium is 62% (w/w) methanol in water and only 29 out of 224 solvent molecules can be regarded with any certainty as methanol molecules.[3] Here, the enzyme's sulfhydryl group can also be seen which is necessary for the activity of the enzyme. Van der Waals interactions and hydrogen bonds between the ligands and protein maintain the structural domains of papain. Water molecules are depicted as pink spheres.Twenty-one water molecules are located in contact areas between adjacent papain molecules. It seems as if the enzyme is trapped in a grid of water molecules with only a limited number of direct interactions between the protein molecules.[4] MechanismFunctionInhibitionReferences
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