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, 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> | 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 two domains interact with one another via hydrophobic interactions, hydrogen bonds, and electrostatic interactions in this cleft. For example, <scene name='Sandbox_36/Papain_intermolecular_interxns/1'>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='Sandbox_36/Papain_intermolecular_interxns/2'>Gln 19 </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='Sandbox_36/Papain_intermolecular_interxns/3'>Glu35 and Lys174</scene> where the carboxyl group of Glu35 forms an ionic bond with the ammonia group of the Lys174 residue. The sum total of interactions within the cleft between the two domains ensure 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 </ref> | ||
In addition to hydrophobic residues, papain contains a variety of<scene name='Sandbox_36/Papain_polar_residues/1'>polar</scene> residues, 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. | In addition to hydrophobic residues, papain contains a variety of<scene name='Sandbox_36/Papain_polar_residues/1'>polar</scene> residues, 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. | ||
