Sandbox Reserved 1066: Difference between revisions

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==Zn Transporter YiiP==

==Zn2+ Transporter YiiP==

This is a default text for your page '''Kyle Colston/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

~~==Organism==~~

~~This protein is found in ''E. coli''~~

==Structure==

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==Mechanism of Transport==

YiiP's ability to export Zn2+ from the cytoplasm is best described as an alternating access mechanism with Zn2+/H+ antiport. YiiP has 2 major structural conformations ~~which is supported~~ by the crystallized structures 3H90 and 3J1Z (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 Zn2+ from the cytoplasm is best described as an alternating access mechanism with Zn2+/H+ antiport. YiiP has 2 major structural conformations as shown by the crystallized structures [[3H90]] and [[3J1Z]] (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 Zn2+ it seems to favor the ~~perplasmic~~/outward-facing conformation whereas when active sites are either empty or bound to H+ the inward facing conformation is favored. This drives the export of Zn2+ 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.

When YiiP is saturated with Zn2+ 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+ the <scene name='69/694233/Outward-facing_conformation/1'>inward-facing conformation</scene> is favored. This drives the export of Zn2+ 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.

~~===Zn Induced Conformation Change===~~

~~Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn2+.Both of these conformation changes~~

The conformation change directly involved with Zn2+/H+ antiport occurs in the TMD as helix pivoting controls what environment site A is available to. Conformation change occurs when the transmembrane helix pairs TM3-TM6 pivot around cation binding site. 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 TM5 which disrupts the tetrahedral geometry of active site A. This in turn decreases binding affinity site A has for Zn2+ and causes Zn2+ to leave which then favors change back to inward-facing conformation.

In contrast the main purpose of conformation change in the CTD is to stabilize the YiiP dimer and act a Zn2+ sensor. Using FRET to measure the distance between the CTD of each monomer showed fluorescence quenching as the concentration Zn2+ increased. It is not probable that Zn2+ bound at site C works it way up to sites A or B, as C binds Zn2+ with a much greater affinity.

===~~Allosteric Inhibition~~===

===Zn2+ Induced Conformation Change===

Zn binding to ~~Active Site C~~ causes a conformation change that ~~reduces~~ the ~~affinity for~~ Zn ~~at Active Site A~~.

Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn2+. The conformation change directly involved with Zn2+/H+ antiport occurs in the TMD as helix pivoting controls what environment site A is available to. Conformation change occurs when the transmembrane helix pairs TM3-TM6 pivot around cation binding site. 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 Zn2+ making export to the periplasm possible. After Zn2+ 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 acts as a Zn2+ 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 FRET to measure the distance between the CTD of each monomer fluorescence quenching was observed as the concentration Zn2+ increased, which supports that idea that Zn2+ induces a stabilizing conformation change in the CTD.

~~== Structural highlights ==~~

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

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@@ Line 1: / Line 1: @@
-==Zn Transporter YiiP==
+==Zn<sup>2+</sup> Transporter YiiP==
-<StructureSection load='3h90' size='340' side='right' caption='Zn Transporter' scene=''>
+<StructureSection load='3h90' size='340' side='right' caption='Zinc Transporter YiiP' scene=''>
 This is a default text for your page '''Kyle Colston/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
 You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
-==Organism==
-This protein is found in ''E. coli''
 ==Structure==
@@ Line 13: / Line 10: @@
 ==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 which is supported by the crystallized structures 3H90 and 3J1Z (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 [[3H90]] and [[3J1Z]] (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 perplasmic/outward-facing conformation whereas when active sites are either empty or bound to H<sup>+</sup> the inward facing conformation 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.
+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.
-===Zn Induced Conformation Change===
-Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn<sup>2+</sup>.Both of these conformation changes
-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 TM3-TM6 pivot around cation binding site. 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 TM5 which disrupts the tetrahedral geometry of active site A. This in turn decreases binding affinity site A has for Zn<sup>2+</sup> and causes Zn<sup>2+</sup> to leave which then favors change back to inward-facing conformation.
-In contrast the main purpose of conformation change in the CTD is to stabilize the YiiP dimer and act a Zn<sup>2+</sup> sensor. Using FRET to measure the distance between the CTD of each monomer showed fluorescence quenching as the concentration Zn<sup>2+</sup> increased. It is not probable that Zn<sup>2+</sup> bound at site C works it way up to sites A or B, as C binds Zn<sup>2+</sup> with a much greater affinity.
-===Allosteric Inhibition===
+===Zn<sup>2+</sup> Induced Conformation Change===
-Zn binding to Active Site C causes a conformation change that reduces the affinity for Zn at Active Site A.
+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 TM3-TM6 pivot around cation binding site. 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 acts 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 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.
-== Structural highlights ==
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.