Sandbox Reserved 1069: Difference between revisions
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==Mechanism of Transport== | ==Mechanism of Transport== | ||
YiiP's ability to export Zn<sup>2+</sup> from the cytoplasm is best described as an alternating access mechanism with Zn<sup>2+</sup>/H<sup>+</sup> antiport. YiiP has 2 major structural conformations as shown by the crystallized structures [http://proteopedia.org/wiki/index.php/3h90 3H90] and [http://proteopedia.org/wiki/index.php/3j1z 3J1Z]<ref>PMID:23341604</ref> (a YiiP homolog derived from ''Shewanella oneidensis''). 3H90 shows YiiP in its outward-facing conformation and 3J1Z shows the YiiP homolog in an inward-facing conformation. | YiiP's ability to export Zn<sup>2+</sup> from the cytoplasm is best described as an alternating access mechanism with Zn<sup>2+</sup>/H<sup>+</sup> antiport. YiiP has 2 major structural conformations as shown by the crystallized structures [http://proteopedia.org/wiki/index.php/3h90 3H90]<ref>PMID:19749753</ref> | ||
and [http://proteopedia.org/wiki/index.php/3j1z 3J1Z]<ref>PMID:23341604</ref> (a YiiP homolog derived from ''Shewanella oneidensis''). 3H90 shows YiiP in its outward-facing conformation and 3J1Z shows the YiiP homolog in an inward-facing conformation. | |||
When YiiP is saturated with Zn<sup>2+</sup> it seems to favor the <scene name='69/694233/Outward-facing_conformation/2'>outward-facing conformation</scene> whereas when active sites are either empty or bound to H<sup>+</sup> the <scene name='69/694233/Outward-facing_conformation/1'>inward-facing conformation</scene> is favored. This drives the export of Zn<sup>2+</sup> from the cytoplasm and enhances the coupling of the proton-motive force. Although YiiP exists as a homodimer both monomers can undergo conformation change independent of one other to | When YiiP is saturated with Zn<sup>2+</sup> it seems to favor the <scene name='69/694233/Outward-facing_conformation/2'>outward-facing conformation</scene> whereas when active sites are either empty or bound to H<sup>+</sup> the <scene name='69/694233/Outward-facing_conformation/1'>inward-facing conformation</scene> is favored. This drives the export of Zn<sup>2+</sup> from the cytoplasm and enhances the coupling of the proton-motive force. Although YiiP exists as a homodimer both monomers can undergo conformation change independent of one other to | ||
produce the alternating access mechanism. | produce the alternating access mechanism. | ||
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Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn<sup>2+</sup>. The conformation change directly involved with Zn<sup>2+</sup>/H<sup>+</sup> antiport occurs in the TMD as helix pivoting controls what environment site A is available to. Conformation change occurs when the transmembrane helix pairs TM1, TM2, TM4, and TM5 pivot around cation binding site.<ref>PMID:23341604</ref> It is believed that the energy for TMD conformation change comes from energy of binding each substrate. Changing to the outward from the inward-facing conformation causes a shift in <scene name='69/694233/Transmembrane_helix_5/2'>TM5</scene> which disrupts the tetrahedral geometry of active site A. This in turn decreases binding affinity site A has for Zn<sup>2+</sup> making export to the periplasm possible. After Zn<sup>2+</sup> is exported and site A is either empty or bound to hydrogen change back to the inward-facing conformation is favored. | Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn<sup>2+</sup>. The conformation change directly involved with Zn<sup>2+</sup>/H<sup>+</sup> antiport occurs in the TMD as helix pivoting controls what environment site A is available to. Conformation change occurs when the transmembrane helix pairs TM1, TM2, TM4, and TM5 pivot around cation binding site.<ref>PMID:23341604</ref> It is believed that the energy for TMD conformation change comes from energy of binding each substrate. Changing to the outward from the inward-facing conformation causes a shift in <scene name='69/694233/Transmembrane_helix_5/2'>TM5</scene> which disrupts the tetrahedral geometry of active site A. This in turn decreases binding affinity site A has for Zn<sup>2+</sup> making export to the periplasm possible. After Zn<sup>2+</sup> is exported and site A is either empty or bound to hydrogen change back to the inward-facing conformation is favored. | ||
In contrast the main purpose of conformation change in the CTD is to stabilize the YiiP dimer and to act as a Zn<sup>2+</sup> sensor. This is possible because of the flexible loop that links the TMD and the CTD. This loop harbors the charge interlock which serves as a hinge that allows movement of the CTD. Using [https://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer FRET] to measure the distance between the CTD of each monomer fluorescence quenching was observed as the concentration Zn<sup>2+</sup> increased, which supports that idea that Zn<sup>2+</sup> induces a stabilizing conformation change in the CTD. | In contrast the main purpose of conformation change in the CTD is to stabilize the YiiP dimer and to act as a Zn<sup>2+</sup> sensor. This is possible because of the flexible loop that links the TMD and the CTD. This loop harbors the charge interlock which serves as a hinge that allows movement of the CTD. Using [https://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer FRET] to measure the distance between the CTD of each monomer fluorescence quenching was observed as the concentration Zn<sup>2+</sup> increased, which supports that idea that Zn<sup>2+</sup> induces a stabilizing conformation change in the CTD.<ref>PMID:19749753</ref> | ||
