Sandbox 38

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. 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. Papain Introduction Cartoon Peak at Pepsin DID YOU KNOW? Papain. Meat tenderizer. Old time home remedy for insect, jellyfish, and stingray stings. Who would have thought that a sulfhydryl protease from the latex of the papaya fruit, Carica papaya and Vasconcellea cundinamarcensis would have such a practical application beyond proteopedia? This protease belongs to an extended family of aminopeptidases, dipeptidyl peptidases, endopeptidases, and other enzymes having both exo- and endo-peptidase activity. The inactivated zymogen with N-terminal propeptide regions - helping to stabilize against alkalinity and enabling proper folding - is activated through removal of the propeptide regions . spinqualitylabelsall models Structure of Papain (PDB entry 9PAP) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structure Its polypeptide chain consists of 212 amino acid residues folded to form a groove between its two domains containing the active site. secondary structure beta sheets alpha helix active site TextToBeDisplayed Distribution of Residues acidic and basic residues polar and non-polar residue polar residues non-polar residues Ligands interactions Cathepsin L specific inhibitor Primarily hydrogen bonds with non-water and hydrophobic interactions interaction Catalytic Mechanism General mechanism of papain catalysis. References https://www.pdb.org/pdb/explore/explore.do?structureId=2PAD • Show the secondary structures. • Compare the distribution of polar residues to that of nonpolar residues. • Highlight the active site. • If you can find a PDB file of the enzyme that contains a pseudo-substrate (may be inhibitor), highlight it. • Show the contacts or attractions that are present between the pseudo-substrate and the protein, and if the enzyme has multiple subunits, show the contacts between the subunits. • Identify any other ligands that are present in the structure and the types of contacts that are present between them and the protein https://proteopedia.org/wiki/index.php/Sandbox_55#cite_note-18 Table of contents Pictures References (cross links)