Papain: Difference between revisions

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==='''Stefin B'''===

<scene name='Papain/Stefin_b/1'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases - it binds tightly but reversibly to the Papain active site. Its interaction is much more complicated than many other cysteine protease inhibitors, such as those illustrated above. Stefin inhibitors are characterized by an M<sub>r</sub> of about 11,000, with no disulfide bonds and no associated carbohydrates.

<scene name='Papain/Stefin_b/4'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases - it binds tightly but reversibly to the Papain active site. Its interaction is much more complicated than many other cysteine protease inhibitors, such as those illustrated above. Stefin inhibitors are characterized by an M<sub>r</sub> of about 11,000, with no disulfide bonds and no associated carbohydrates.

In Stefin B, the Gly-9 residue along with <scene name='Papain/Stefin_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of Papain. This wedge makes extensive and tight interactions with Papain which involves the embedding of 16% of Stefin B into Papain with a total of 128 intermolecular atom-atom interactions occurring. <scene name='Papain/Stefin_b/2'>Residue segments</scene> Met-6 - Pro-11, Gln-53 - Asn-59, Gln-101 - His-104, Tyr-124 and Phe-125 on the wedge all have some interaction with the enzyme, though Cys-25 is the only one to form a direct contact. All residues from the base of Stefin B, shown in ball-and-stick form, and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene>, shown in gray, are involved in the complex with the inhibitor.

In Stefin B, the Gly-9 residue along with <scene name='Papain/Stefin_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of Papain. This wedge makes extensive and tight interactions with Papain which involves the embedding of 16% of Stefin B into Papain with a total of 128 intermolecular atom-atom interactions occurring. <scene name='Papain/Stefin_b/3'>Residue segments</scene> Met-6 - Pro-11, Gln-53 - Asn-59, Gln-101 - His-104, Tyr-124 and Phe-125 on the wedge all have some interaction with the enzyme, though Cys-25 is the only one to form a direct contact. All residues from the base of Stefin B, shown in ball-and-stick form, and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene>, shown in gray, are involved in the complex with the inhibitor.

There are a small number of <scene name='Papain/Sk_inhibitor_3/1'>direct hydrogen bonds</scene> between Stefin B and Papain, however there are many more polar interactions mediated by <scene name='Papain/Sk_inhibitor_4/3'>solvent bridges</scene>. Thirteen solvent molecules bridge polar residues of the enzyme and inhibitor. Seventeen hydrogen bonds are made with a solvent molecule and Stefin B. Fourteen of these bridges form a Papain contact. The rest of the interactions are largely hydrophobic-- involving apolar <scene name='Papain/Sk_inhibitor_5/3'>Van der Waals interactions</scene>.<ref> PMID:2347312 </ref>

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 ==='''Stefin B'''===
-<scene name='Papain/Stefin_b/1'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases - it binds tightly but reversibly to the Papain active site. Its interaction is much more complicated than many other cysteine protease inhibitors, such as those illustrated above.  Stefin inhibitors are characterized by an M<sub>r</sub> of about 11,000, with no disulfide bonds and no associated carbohydrates.
+<scene name='Papain/Stefin_b/4'>Stefin B</scene> acts as a competitive inhibitor to cysteine proteases - it binds tightly but reversibly to the Papain active site. Its interaction is much more complicated than many other cysteine protease inhibitors, such as those illustrated above.  Stefin inhibitors are characterized by an M<sub>r</sub> of about 11,000, with no disulfide bonds and no associated carbohydrates.
-In Stefin B, the Gly-9 residue along with <scene name='Papain/Stefin_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of Papain.  This wedge makes extensive and tight interactions with Papain which involves the embedding of 16% of Stefin B into Papain with a total of 128 intermolecular atom-atom interactions occurring. <scene name='Papain/Stefin_b/2'>Residue segments</scene> Met-6 - Pro-11, Gln-53 - Asn-59, Gln-101 - His-104, Tyr-124 and Phe-125 on the wedge all have some interaction with the enzyme, though Cys-25 is the only one to form a direct contact.  All residues from the base of Stefin B, shown in ball-and-stick form, and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene>, shown in gray, are involved in the complex with the inhibitor.
+In Stefin B, the Gly-9 residue along with <scene name='Papain/Stefin_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of Papain.  This wedge makes extensive and tight interactions with Papain which involves the embedding of 16% of Stefin B into Papain with a total of 128 intermolecular atom-atom interactions occurring. <scene name='Papain/Stefin_b/3'>Residue segments</scene> Met-6 - Pro-11, Gln-53 - Asn-59, Gln-101 - His-104, Tyr-124 and Phe-125 on the wedge all have some interaction with the enzyme, though Cys-25 is the only one to form a direct contact.  All residues from the base of Stefin B, shown in ball-and-stick form, and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene>, shown in gray, are involved in the complex with the inhibitor.
 There are a small number of <scene name='Papain/Sk_inhibitor_3/1'>direct hydrogen bonds</scene> between Stefin B and Papain, however there are many more polar interactions mediated by <scene name='Papain/Sk_inhibitor_4/3'>solvent bridges</scene>.  Thirteen solvent molecules bridge polar residues of the enzyme and inhibitor.  Seventeen hydrogen bonds are made with a solvent molecule and Stefin B.  Fourteen of these bridges form a Papain contact.  The rest of the interactions are largely hydrophobic-- involving apolar <scene name='Papain/Sk_inhibitor_5/3'>Van der Waals interactions</scene>.<ref> PMID:2347312 </ref>