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 <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>. 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 ~~[https://en.wikipedia.org/wiki/Glutamic_acid~~ 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 <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> can be a branching point that is able to pass protons via the <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> 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 <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>. 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 and negative charge characteristic of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene>, together with previous mutagenesis experiments, supports the proposal that this glutamate residue is a redox state-dependent mediator of proton transfer to a charge compensation site. 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 <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> can be a branching point that is able to pass protons via the <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> 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 <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB</scene>. 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 <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> 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 <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>, and therefore, the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> is the most accepted source of protons.

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 <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>. 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 [https://en.wikipedia.org/wiki/Glutamic_acid 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 <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> can be a branching point that is able to pass protons via the <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> 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 <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>. 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 and negative charge characteristic of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene>, together with previous mutagenesis experiments, supports the proposal that this glutamate residue is a redox state-dependent mediator of proton transfer to a charge compensation site. 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 <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> can be a branching point that is able to pass protons via the <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> 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 <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB</scene>. 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 <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> 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 <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>, and therefore, the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> is the most accepted source of protons.