Sandbox 22: Difference between revisions
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[[Image:Domains of Papain.png|200px|left|thumb|Contacts between Papain Subunits.<ref name="Richardson">[http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.2i.html] Jane S. Richardson</ref>.]] | [[Image:Domains of Papain.png|200px|left|thumb|Contacts between Papain Subunits.<ref name="Richardson">[http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.2i.html] Jane S. Richardson</ref>.]] | ||
Papain is a relatively simple enzyme, consisting of a single 212 residue chain. A majority of papain's residues, shown in purple in the link, are <scene name='Sandbox_35/Hydrophobicity_papain/3'>hydrophobic</scene>. As with all proteins, it is primarily the exclusion of these residues by water that leads to papain's assumption of a globular form. Despite its apparent simplicity and small size, papain folds into two distinct, evenly sized <scene name='Sandbox_36/Papain_domains/2'>domains</scene>, each with its own <scene name='Sandbox_35/Nonpolar_papain/2'>hydrophobic core</scene>. | Papain is a relatively simple enzyme, consisting of a single 212 residue chain. A majority of papain's residues, shown in purple in the link, are <scene name='Sandbox_35/Hydrophobicity_papain/3'>hydrophobic</scene>. As with all proteins, it is primarily the exclusion of these residues by water that leads to papain's assumption of a globular form. Despite its apparent simplicity and small size, papain folds into two distinct, evenly sized <scene name='Sandbox_36/Papain_domains/2'>domains</scene>, each with its own <scene name='Sandbox_35/Nonpolar_papain/2'>hydrophobic core</scene>. | ||
These two subunits are held together with "arm" linkage where one end of the protein chain holds the opposite domain. In papain's case the "arm crossing" primarily occurs on or near the surface.<ref name="Richardson" /> It is between these two domains that the | These two subunits are held together with "arm" linkage, pictured to the left, where one end of the protein chain holds the opposite domain. In papain's case the "arm crossing" primarily occurs on or near the surface.<ref name="Richardson" /> It is between these two domains that the <scene name='Sandbox_22/9pap_bindingpocket_wrtdomains/1'>substrate binding pocket</scene> is situated.<ref>http://books.google.com/books?hl=en&lr=&id=fk1hbZdPTEgC&oi=fnd&pg=PA79&dq=aromatic+residues+in+papain&ots=L8SvlkQaZU&sig=xZ2l8kj52PD7DzuiAQ1zah0CU2M#v=onepage&q=aromatic%20residues%20in%20papain&f=false</ref> The remaining residues are <scene name='Sandbox_36/Papain_polar_residues/1'>polar</scene>, some carrying a <scene name='Sandbox_36/Papain_polar_residues_acidic/1'>negative charge</scene> (acidic) at physiological pH, others a <scene name='Sandbox_36/Papain_polar_residues_basic/1'>positive charge</scene> (basic), the rest of the polar residues are neutral. As expected, the charged <scene name='Sandbox_31/Termini/4'>Termini</scene> face outward due to their hydrophilic nature. | ||
Papain's secondary structure is composed of 21% <scene name='Sandbox_34/Betasheets/1'>beta sheets</scene> (45 residues comprising 7 sheets) and 25% <scene name='Sandbox_34/Alphahelices/1'>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</ref> These secondary structures may be traced from the N- to C-terminus by means of <scene name='Sandbox_39/Elemental/3'>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='9pap/Papain_sam_centralhelix/1'>first helix</scene> (residues 25-42) is maintained as a result of <scene name='9pap/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='9pap/Papain_sb_helix1_hydrophobic/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='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic). | Papain's secondary structure is composed of 21% <scene name='Sandbox_34/Betasheets/1'>beta sheets</scene> (45 residues comprising 7 sheets) and 25% <scene name='Sandbox_34/Alphahelices/1'>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</ref> These secondary structures may be traced from the N- to C-terminus by means of <scene name='Sandbox_39/Elemental/3'>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='9pap/Papain_sam_centralhelix/1'>first helix</scene> (residues 25-42) is maintained as a result of <scene name='9pap/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='9pap/Papain_sb_helix1_hydrophobic/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='Sandbox_30/Papain_secondary_helix1_phobic/1'>hydrophobic residues</scene> (red residues are hydrophilic). | ||
<scene name='Sandbox_34/Salt_bridges/5'>Salt bridges</scene> strongly contribute to the tertiary structure of papain. 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. The tertiary structure of papain is also maintained by three <scene name='9pap/9pap_sam_disulfides/1'>disulfide bonds</scene>, which connect <scene name='9pap/9pap_sam_disulfides_22-63/1'>Cys-22 to Cys63</scene>, <scene name='9pap/9pap_sam_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='9pap/9pap_sam_disulfides_153-200/1'>Cys-153 to Cys-200</scene><ref name="9PAP PDB" />. These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures. | <scene name='Sandbox_34/Salt_bridges/5'>Salt bridges</scene> strongly contribute to the tertiary structure of papain. 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. The tertiary structure of papain is also maintained by three <scene name='9pap/9pap_sam_disulfides/1'>disulfide bonds</scene>, which connect <scene name='9pap/9pap_sam_disulfides_22-63/1'>Cys-22 to Cys63</scene>, <scene name='9pap/9pap_sam_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='9pap/9pap_sam_disulfides_153-200/1'>Cys-153 to Cys-200</scene><ref name="9PAP PDB" />. These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures. | ||
