Sandbox 34: Difference between revisions

== Structure ==  

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>: R is shown in purple, and L in gray. A cleft is formed in which the <scene name='Sandbox_34/2subuwithactivesite/4'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" /> A <scene name='Sandbox_34/Rainbown-c/1'>Rainbow-C</scene> illustration of this shows, from the N-terminus in blue to the C-terminus in red, an easy means by which to track the residues through the molecule. Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/2'>backbone</scene>, and between <scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/3'>residues</scene>.  

<scene name='Sandbox_34/Salt_bridges/5'>Salt bridges</scene> also strongly contribute to the stability of the protein structure. In this particular image, clarification of residue coordination is demonstrated by color: paired residues are shown in the same color, oxygen is shown in red, and nitrogen is shown in blue A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized.  Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the hydrophobic and polar residues segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.In a paper entitled, ''The Structure of Papain Refined at 1.65 A Resoltion'', Kamphuis et al. discovered interesting information on <scene name='Sandbox_34/All_bonding_shenanigans/1'>direct protein-protein contacts</scene> between molecules of papain in solution. These contacts, communicated in Table 7 of their paper, consist of nine hydrogen-bond connections and three ionic interactions. The strongest salt bridge exists between <scene name='Sandbox_34/Arg191asp140intraxn/2'>asparagine-140 and arginine-191</scene>.<ref name="Structure" />