From Proteopedia
(Difference between revisions)
proteopedia linkproteopedia link
|
|
| (27 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | <!-- PLEASE DO NOT DELETE THIS TEMPLATE --> |
| | {{Template:Oberholser_Sandbox_Reservation}} | | {{Template:Oberholser_Sandbox_Reservation}} |
| | + | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> |
| | + | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Matt's Beautiful Protein' /> |
| | | | |
| - | ='''Papain'''= | + | 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). |
| | | | |
| - | ==Introduction==
| + | 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. |
| - | [[Image:Papaya.jpg | right| thumb| ''Carica papaya'']]
| + | |
| - | <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. | + | |
| | | | |
| - | ==Structure==
| + | The <scene name='Sandbox_37/Matt_hydrogen_bonds_good/1'>Hydrogen Bonds</scene> of chain A of the protein are highlighted in orange here. |
| - | <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.Twenty-one water molecules are located in contact areas between adjacent papain molecules.
| + | |
| | | | |
| - | ==Mechanism==
| + | The <scene name='Sandbox_37/Matt_hydrophobic_good/1'>Hydrophobic Interactions</scene> are shown here in red. |
| - | [[Image:Papain mechanism.jpg | right| thumb| Mechanism of papain catalysis]]
| + | |
| - | Papain cleaves peptide bonds of basic amino acids, leucine, or glycine. It also hydrolyzes esters and amides.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> Its mechanism of breaking peptide bonds takes place in its <scene name='Sandbox_37/Papain_active_site/1'>active site</scene>. The active site is in a cleft formed by the two distinct structural domains of the protein. The active site contains a catalytic dyad of residues cysteine-25 on an alpha helix and histidine-159 on a beta sheet. The catalytic dyad is similar to the catalytic triad seen in most serine proteases. This ion pair of cysteine and histidine is the powerhouse of papain's catalytic mechanism. The other residue of the active site is asparagine-175, which helps with orientation during catalysis. For catalysis, His-159 deprotonates cys-25, then cys-25 attacks the carbonyl of the peptide as a nucleophile. A water molecule then deacylates the enzyme and releases the peptide.
| + | |
| | | | |
| - | ==Inhibition==
| + | The <scene name='Sandbox_37/Matt_hydrophilic_good/1'>Hydrophilic Interactions</scene> are shown here in black. |
| - | <Structure load='1pop' size='400' frame='true' align='right' caption='Papain with leupeptin inhibitor (1POP)' scene='' />
| + | |
| - | One inhibitor of papain is leupeptin. The carbonyl carbon of this <scene name='Sandbox_37/Papain_inhibitor/3'>inhibitor</scene> (seen in blue) is covalently bound by the Cys-25 sulphur atom of papain and is tetrahedrally coordinated. The carbonyl oxygen atom of the inhibitor faces the oxyanion hole and makes hydrogen bond contacts with Gln-19 and Cys-25.<ref>http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1POP¶ms.chainEntityStrategyStr=all</ref> The <scene name='Sandbox_37/Papain_inhibitor_van_der_waals/2'>van der Waals interactions</scene> and <scene name='Sandbox_37/Papain_inhibitor_hydrogen_bond/1'>hydrogen bonds</scene> between papain and leupeptin keep the active site closed and the residues (shown in brown) can no longer catalyze.
| + | |
| | | | |
| - | ==Function== | + | 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. |
| - | Papain is used as a powdered meat tenderizer because of its ability to break down tough meat fibers. It can also be used as a treatment for jellyfish and bee stings because it can break down the protein toxins in the venom.<ref>http://en.wikipedia.org/wiki/Papain</ref> Papain can also digest immunoglobulins (antibodies) by breaking the two Fab fragments from the Fc fragment. This prevents the immunoglobulin's ability to promote agglutination.
| + | |
| | | | |
| - | [[Image:Ramachandran plot.JPG| right| thumb| Ramachandran plot of papain amino acid residues]]
| + | 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. |
| | | | |
| - | ==References== | + | The <scene name='Sandbox_37/Matt_catalytic_residues/1'>catalytic residues</scene> of this protein are shown here in lime green. |
| - | <references /> | + | |
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. |
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.
