Papain: Difference between revisions
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===Intermolecular Forces=== | ===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, defined above, 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 with dotted white lines), <scene name='Papain/Twodomainshbonds/3'>hydrogen bonds</scene> (shown in white), and <scene name='Papain/Ke_salt_bridges/ | <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, defined above, 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 with dotted white lines), <scene name='Papain/Twodomainshbonds/3'>hydrogen bonds</scene> (shown in white), and <scene name='Papain/Ke_salt_bridges/3'>salt bridges</scene> (shown as above) in the cleft formed between the two domains. 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 too much 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=== | ||
