Papain: Difference between revisions
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===General Structural Features=== | ===General Structural Features=== | ||
Papain is a relatively simple enzyme, consisting of a single 212 residue chain. A majority of papain's residues are <scene name='Papain/Hydrophobicity_papain/1'>hydrophobic</scene> as shown in fuchsia. 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='Papain/Sk_two_domains/2'>domains</scene>, each with its own <scene name='Papain/Sk_hydrophobic_core/2'>hydrophobic core</scene> (surface residues are transparent, hydrophobic-core residues are colored and opaque, and the remaining are polar, non-surface residues).<ref name="Structure">PMID:6502713</ref> | Papain is a relatively simple enzyme, consisting of a single 212 residue chain. A majority of papain's residues are <scene name='Papain/Hydrophobicity_papain/1'>hydrophobic</scene> as shown in fuchsia. 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='Papain/Sk_two_domains/2'>domains</scene>, each with its own <scene name='Papain/Sk_hydrophobic_core/2'>hydrophobic core</scene> (surface residues are transparent, hydrophobic-core residues are colored and opaque, and the remaining are polar, non-surface residues).<ref name="Structure">PMID:6502713</ref> It is between these two domains that the <scene name='Papain/9pap_bindingpocket_wrtdomains/4'>substrate binding pocket</scene> is situated. | ||
In addition to hydrophobic residues, papain contains a variety of <scene name='Papain/Sk_polar_residues/2'>polar residues</scene>, some carrying a <scene name='Papain/Sk_acidic_residues/2'>negative charge</scene>, shown in gray at physiological pH, and are therefore acidic; others a <scene name='Papain/Sk_basic_residues/2'>positive charge</scene>, shown in purple, and are therefore basic. The rest of the <scene name='Papain/Sk_basic_residues/3'>polar residues</scene>, shown in a light gray, are neutral. As expected, the charged <scene name='Papain/Termini/3'>termini</scene> face outward due to their hydrophilic nature. | In addition to hydrophobic residues, papain contains a variety of <scene name='Papain/Sk_polar_residues/2'>polar residues</scene>, some carrying a <scene name='Papain/Sk_acidic_residues/2'>negative charge</scene>, shown in gray at physiological pH, and are therefore acidic; others a <scene name='Papain/Sk_basic_residues/2'>positive charge</scene>, shown in purple, and are therefore basic. The rest of the <scene name='Papain/Sk_basic_residues/3'>polar residues</scene>, shown in a light gray, are neutral. As expected, the charged <scene name='Papain/Termini/3'>termini</scene> face outward due to their hydrophilic nature. | ||
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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). | 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). | ||
<scene name='Papain/Ke_salt_bridges/2'>Salt bridges</scene> strongly contribute to the tertiary structure of papain.<ref name="Sigma Aldrich" /> 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='Papain/9pap_sam_disulfides/1'>disulfide bonds</scene>, which connect <scene name='Papain/9pap_sam_disulfides_22-63/1'>Cys-22 to Cys63</scene>, <scene name='Papain/9pap_sam_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='Papain/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. | ===Intermolecular Forces=== | ||
<scene name='Papain/Ke_salt_bridges/2'>Salt bridges</scene> strongly contribute to the tertiary structure of papain.<ref name="Sigma Aldrich" /> 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='Papain/9pap_sam_disulfides/1'>disulfide bonds</scene>, which connect <scene name='Papain/9pap_sam_disulfides_22-63/1'>Cys-22 to Cys63</scene>, <scene name='Papain/9pap_sam_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='Papain/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. The two subunits are held together with <scene name='Papain/Armcrossing/1'>"arm" linkage</scene>, where each protein domain holds the opposite domain. In papain's case the "arm" crossing primarily occurs on or near the surface.<ref>[http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.2i.html] Jane S. Richardson</ref> The two domains interact with one another via <scene name='Papain/Valine_19/2'>hydrophobic interactions</scene> (illustrated by dotted white lines), <scene name='Papain/Twodomainshbonds/3'>hydrogen bonds</scene> (shown in white), and electrostatic interactions in this cleft. For example, <scene name='Papain/Gln_19/3'>Gln-19</scene> hydrogen bonds multiple times with the oxygen atoms of Ser-176. Electrostatic interactions are seen between <scene name='Papain/Glu_35/1'>Glu-35 and Lys-174</scene> where the carboxyl group of Glu-35 forms an ionic bond with the ammonia group of the Lys-174 residue. Additionally, there are several <scene name='Papain/Clash/1'>clashes</scene> that occur between the two domains, illustrated in orange. The <scene name='Papain/Twodomainsallncbonds/1'>sum total</scene> of interactions within the cleft between the two domains ensures that the lobes do not move with respect to one another. <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] The Structure of Papain </ref> | |||
===Substrate Binding=== | ===Substrate Binding=== | ||