Sandbox 37

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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Matt's Beautiful Protein' />
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='''Papain'''=
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The <scene name='Sandbox_37/Matt_adenylate_kinase_37/1'>Adenylate Kinase</scene> protein is shown here with alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange).
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==Introduction==
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The <scene name='Sandbox_37/Matt_helix_beta_colored/1'>Secondary Structure</scene> of the protein is shown here with alpha helices (green) and beta sheets (blue) highlighted appropriately.
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[[Image:Papaya.jpg | right| thumb| ''Carica papaya'']]
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<scene name='Sandbox_37/Main_scene/1'>Papain</scene> 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'').<ref>http://www.britannica.com/EBchecked/topic/441803/papain</ref> The papain proteins are synthesized as inactive precursors that become active within two minutes of the plant being wounded and the latex is expelled.<ref>http://www.worthington-biochem.com/pap/default.html</ref> 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.
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==Structure==
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The <scene name='Sandbox_37/Matt_hydrogen_bonds_good/1'>Hydrogen Bonds</scene> of chain A of the protein are highlighted in orange here.
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[[Image:Ramachandran plot.JPG| left| thumb| Ramachandran plot of papain amino acid residues]]
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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.
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<StructureSection load='9PAP' size='400' align='left' caption='Papain (9PAP)' scene=''></StructureSection>
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The <scene name='Sandbox_37/Matt_hydrophobic_good/1'>Hydrophobic Interactions</scene> are shown here in red.
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<scene name='Sandbox_37/Ligand/3'>ligands</scene>
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The <scene name='Sandbox_37/Matt_hydrophilic_good/1'>Hydrophilic Interactions</scene> are shown here in black.
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<scene name='Sandbox_37/Papain_van_der_waals/1'>van der Waals interactions</scene>
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The <scene name='Sandbox_37/Matt_solvent/1'>Solvent</scene> , which is water, is shown here in red. Water's primary location is on the outer parts of the protein, or the hydrophilic regions.
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<scene name='Sandbox_37/Papain_hydrogen_bonds/1'>hydrogen bonds</scene>
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The side chains that interact with the <scene name='Sandbox_37/Matt_ligand/1'>ligand</scene> are shown here in crimson. The interactions occur with the hydrophobic side chains. The rest of the protein is faded blue.
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The <scene name='Sandbox_37/Matt_catalytic_residues/1'>catalytic residues</scene> of this protein are shown here in lime green.
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==Mechanism==
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[[Image:Papain mechanism.jpg | right| thumb| Mechanism of papain catalysis]]
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<scene name='Sandbox_37/Papain_active_site/1'>active site</scene>
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==Function==
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==Inhibition==
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<scene name='Sandbox_37/Papain_inhibitor/3'>inhibitor</scene>
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<scene name='Sandbox_37/Papain_inhibitor_van_der_waals/2'>van der Waals</scene>
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<scene name='Sandbox_37/Papain_inhibitor_hydrogen_bond/1'>hydrogen bonds</scene>
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<ref>http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1POP&params.chainEntityStrategyStr=all</ref>
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<ref>http://en.wikipedia.org/wiki/Papain</ref>
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<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref>
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<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref>
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==References==
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<references />
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Current revision

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.

Adenylate Kinase

Drag the structure with the mouse to rotate

The protein is shown here with alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange).

The of the protein is shown here with alpha helices (green) and beta sheets (blue) highlighted appropriately.

The of chain A of the protein are highlighted in orange here.

The are shown here in red.

The are shown here in black.

The , which is water, is shown here in red. Water's primary location is on the outer parts of the protein, or the hydrophilic regions.

The side chains that interact with the are shown here in crimson. The interactions occur with the hydrophobic side chains. The rest of the protein is faded blue.

The of this protein are shown here in lime green.

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