Papain: Difference between revisions

Papain's secondary structure is composed of 21% <scene name='Papain/Ke_betasheets/2'>beta sheets</scene> (45 residues comprising 17 sheets) and 25% <scene name='Papain/Ke_alphahelices/2'>alpha helices</scene> (51 residues comprising 7 helices).  The rest of the residues, accounting for over 50% of the enzymes structure, make up ordered non-repetative sequences.<ref name="RSCB PDB">[http://www.rcsb.org/pdb/explore/explore.do?structureId=9PAP] RCSB PDB</ref>  These secondary structures may be traced from the N- to C-terminus by means of <scene name='Papain/Lm_elemental/2'>differential coloration</scene>.  As shown in this scene, the red end begins the protein at the N-terminus, and can be traced through the colors of the rainbow to the blue end at the C-terminus.  These secondary structures form as a result of favorable hydrogen bonding interactions within the polypeptide backbone.  Meanwhile, secondary structures are kept in place by hydrophobic interactions and hydrogen bonds between sidechains of adjacent structures. For example, the <scene name='Papain/Papain_sam_centralhelix/1'>first helix</scene> (residues 25-42) is maintained as a result of <scene name='Papain/Papain_sb_helix1_hbonds/1'>hydrogen bonds</scene> between backbone carbonyl atoms and the hydrogen on the amide nitrogen four residues away.  However, <scene name='Papain/Papain_sam_nohbondswhelix1/1'>no hydrogen bonds</scene> are present between this helix and the rest of the protein, suggesting that this helix is coordinated primarily by hydrophobic interactions.  This is reasonable given its central location in the enzyme.  As expected, the helix contains many <scene name='Papain/Papain_sb_helix1_hydrophobic/1'>hydrophobic residues</scene> (red residues are hydrophilic).