Papain: Difference between revisions

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<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. Stefin inhibitors are characterized by M<sub>r</sub> of about 11,000, no disulfide bonds and no associated carbohydrates.

In Stefin B, the Gly-9 residue along with <scene name='Papain/Stf_b_hairpin_loops/2'>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 and a total of 128 intermolecular atom-atom interactions occur. <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 to the enzyme, though not always direct. All residues from the base and both sides of the <scene name='Papain/~~Sk_inhibitor_2~~/1'>active site cleft</scene> are involved in the complex with the ~~inhibtor (Trp-177, Ser-21, Cys-63, Cys-25, Asp-158 and His-159)~~.

In Stefin B, the Gly-9 residue along with <scene name='Papain/Stf_b_hairpin_loops/2'>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 and a total of 128 intermolecular atom-atom interactions occur. <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 to the enzyme, though not always direct. All residues from the base and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene> 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~~. 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>

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>

</StructureSection>

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@@ Line 55: / Line 55: @@
 <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.  Stefin inhibitors are characterized by M<sub>r</sub> of about 11,000, no disulfide bonds and no associated carbohydrates.
-In Stefin B, the Gly-9 residue along with <scene name='Papain/Stf_b_hairpin_loops/2'>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 and a total of 128 intermolecular atom-atom interactions occur. <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 to the enzyme, though not always direct.  All residues from the base and both sides of the <scene name='Papain/Sk_inhibitor_2/1'>active site cleft</scene> are involved in the complex with the inhibtor (Trp-177, Ser-21, Cys-63, Cys-25, Asp-158 and His-159).
+In Stefin B, the Gly-9 residue along with <scene name='Papain/Stf_b_hairpin_loops/2'>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 and a total of 128 intermolecular atom-atom interactions occur. <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 to the enzyme, though not always direct.  All residues from the base and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene> 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.  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>
+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>
 </StructureSection>