Sandbox Reserved 1600: Difference between revisions

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Because there is no proton pump present, the proton transfer mechanism is facilitated by <scene name='83/838655/Bdoxidase_proton_pathways/1'>2 potential proton pathways</scene> via intracellular water molecules.

One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> in the structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle <ref name =”Safarian” />. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu101/1'>Glu101 residue</scene>, which is the last residue in this pathway, could be the protonatable group eventually used upon ~~heme b595~~ reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether Glu108 can be a branching point that is able to pass protons via the ~~heme b595~~ propionates to the oxygen-binding site. <ref name=”Safarian”>PMID:27126043</ref>

One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> in the structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle <ref name =”Safarian” />. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu101/1'>Glu101 residue</scene>, which is the last residue in this pathway, could be the protonatable group eventually used upon Heme B595 reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether Glu108 can be a branching point that is able to pass protons via the Heme B595 propionates to the oxygen-binding site. <ref name=”Safarian”>PMID:27126043</ref>

Another potential entry site is related to the <scene name='83/838655/Bdoxidase_cydb_subunit_b1-4/1'>a1-4 four-helix bundle</scene> of CydB. Therefore, this is called the <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. In this pathway, <scene name='83/838655/Bdoxidase_cydb_pathway_asp25/1'>Asp25</scene> is thought to be the equivalent of the Glu108 in the CydA pathway <ref name =”Safarian” />. The other residues help facilitate the movement of the proton very similarly to the CydA pathway. There is less known about the CydB pathway, and therefore, the CydA pathway is the most accepted source of protons.

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As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, and having the overall reaction of O₂ + 4H+ + 4e- → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to Heme D. This pathway is depicted in orange in Figure 4.

The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The potential pathways utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to Heme ~~b595~~. in the active site. The CydA pathway passes through the CydA subunit, and is shown in purple in Figure 4. THe CydB pathway proceeds through the CydB subunit, and is shown in green in Figure 4.

The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The potential pathways utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to Heme B595. in the active site. The CydA pathway passes through the CydA subunit, and is shown in purple in Figure 4. THe CydB pathway proceeds through the CydB subunit, and is shown in green in Figure 4.

As shown above, the electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the Q-loop and gets oxidized giving 4e- to Heme B558. Once at Heme B558 the 4e- will be shuttled directly to Heme D to be used in the reduction of O₂. The electron pathway is depicted in blue in Figure 4.

Sandbox Reserved 1600: Difference between revisions

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@@ Line 40: / Line 40: @@
 Because there is no proton pump present, the proton transfer mechanism is facilitated by <scene name='83/838655/Bdoxidase_proton_pathways/1'>2 potential proton pathways</scene> via intracellular water molecules.
-One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> in the structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle <ref name =”Safarian” />. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu101/1'>Glu101 residue</scene>, which is the last residue in this pathway, could be the protonatable group eventually used upon heme b595 reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether Glu108 can be a branching point that is able to pass protons via the heme b595 propionates to the oxygen-binding site. <ref name=”Safarian”>PMID:27126043</ref>
+One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> in the structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle <ref name =”Safarian” />. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu101/1'>Glu101 residue</scene>, which is the last residue in this pathway, could be the protonatable group eventually used upon Heme B595 reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether Glu108 can be a branching point that is able to pass protons via the Heme B595 propionates to the oxygen-binding site. <ref name=”Safarian”>PMID:27126043</ref>
 Another potential entry site is related to the <scene name='83/838655/Bdoxidase_cydb_subunit_b1-4/1'>a1-4 four-helix bundle</scene> of CydB. Therefore, this is called the <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. In this pathway, <scene name='83/838655/Bdoxidase_cydb_pathway_asp25/1'>Asp25</scene> is thought to be the equivalent of the Glu108 in the CydA pathway <ref name =”Safarian” />. The other residues help facilitate the movement of the proton very similarly to the CydA pathway. There is less known about the CydB pathway, and therefore, the CydA pathway is the most accepted source of protons.
@@ Line 48: / Line 48: @@
 As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, and having the overall reaction of O₂ + 4H<sup>+</sup> + 4e<sup>-</sup> → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to Heme D. This pathway is depicted in <font color='orange'><b>orange</b></font> in Figure 4.
-The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The potential pathways utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to Heme b595. in the active site. The CydA pathway passes through the CydA subunit, and is shown in <font color='purple'><b>purple</b></font> in Figure 4. THe CydB pathway proceeds through the CydB subunit, and is shown in <font color='green'><b>green</b></font> in Figure 4.
+The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The potential pathways utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to Heme B595. in the active site. The CydA pathway passes through the CydA subunit, and is shown in <font color='purple'><b>purple</b></font> in Figure 4. THe CydB pathway proceeds through the CydB subunit, and is shown in <font color='green'><b>green</b></font> in Figure 4.
 As shown above, the electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the Q-loop and gets oxidized giving 4e<sup>-</sup> to Heme B558.  Once at Heme B558 the 4e<sup>-</sup> will be shuttled directly to Heme D to be used in the reduction of O₂. The electron pathway is depicted in <font color='blue'><b>blue</b></font> in Figure 4.