Papain: Difference between revisions

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===General Structural Features===

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='Papain/Hydrophobicity_papain/1'>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='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 purple. 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>

These 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> It is between these two domains that the <scene name='Papain/9pap_bindingpocket_wrtdomains/4'>substrate binding pocket</scene> is situated. The two domains interact with one another via hydrophobic interactions, <scene name='Papain/Twodomainshbonds/2'>hydrogen bonds</scene> (shown in white), and electrostatic interactions in this cleft. For example, <scene name='Papain/Sk_domain_contact_valine/2'>Valine-32</scene> from the L Domain hydrophobically interacts with the carbon atoms on residues Lys174, Ala162 and Pro129 of the R Domain. <scene name='Papain/Sk_domain_contact_glutamine/3'>Gln19</scene> hydrogen bonds multiple times with the oxygen atoms of Ser176 and also with the oxygen atom on Tyr88. Electrostatic interactions are seen between <scene name='Papain/Sk_domain_contact_glu_and_lys/2'>Glu35 and Lys174</scene> where the carboxyl group of Glu35 forms an ionic bond with the ammonia group of the Lys174 residue. 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>

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@@ Line 10: / Line 10: @@
 ===General Structural Features===
-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='Papain/Hydrophobicity_papain/1'>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='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 purple.  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>
 These 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>  It is between these two domains that the <scene name='Papain/9pap_bindingpocket_wrtdomains/4'>substrate binding pocket</scene> is situated. The two domains interact with one another via hydrophobic interactions, <scene name='Papain/Twodomainshbonds/2'>hydrogen bonds</scene> (shown in white), and electrostatic interactions in this cleft.  For example, <scene name='Papain/Sk_domain_contact_valine/2'>Valine-32</scene> from the L Domain hydrophobically interacts with the carbon atoms on residues Lys174, Ala162 and Pro129 of the R Domain.  <scene name='Papain/Sk_domain_contact_glutamine/3'>Gln19</scene> hydrogen bonds multiple times with the oxygen atoms of Ser176 and also with the oxygen atom on Tyr88.  Electrostatic interactions are seen between <scene name='Papain/Sk_domain_contact_glu_and_lys/2'>Glu35 and Lys174</scene> where the carboxyl group of Glu35 forms an ionic bond with the ammonia group of the Lys174 residue.  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>