Sandbox Reserved 1066 - Revision history

Kyle Colston at 21:28, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 21:28:57 GMT

←Older revision		Revision as of 21:28, 29 March 2017
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	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.		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 <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.	+	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<sup>2+</sup> Induced Conformation Change===		===Zn<sup>2+</sup> 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>. 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_5/1'>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 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.		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.

Kyle Colston at 21:20, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 21:20:26 GMT

←Older revision		Revision as of 21:20, 29 March 2017
Line 11:		Line 11:

	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.		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 perplasmic/outward-facing conformation 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<sup>2+</sup> Induced Conformation Change===		===Zn<sup>2+</sup> 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>. 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_5/1'>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> ~~and causes~~ Zn<sup>2+</sup> ~~to leave~~ site A ~~which then favors~~ change back to inward-facing conformation.	+	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_5/1'>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.		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.

Kyle Colston at 20:58, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 20:58:04 GMT

←Older revision		Revision as of 20:58, 29 March 2017
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	===Zn<sup>2+</sup> Induced Conformation Change===		===Zn<sup>2+</sup> 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>. 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 site A which then favors change back to inward-facing conformation.	+	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_5/1'>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> and causes Zn<sup>2+</sup> to leave site A 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 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.		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.

Kyle Colston at 20:22, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 20:22:50 GMT

←Older revision		Revision as of 20:22, 29 March 2017
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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 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 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.

Kyle Colston at 20:19, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 20:19:30 GMT

←Older revision		Revision as of 20:19, 29 March 2017
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	==Zn<sup>2+</sup> Transporter YiiP==		==Zn<sup>2+</sup> Transporter YiiP==
-	<StructureSection load='3h90' size='340' side='right' caption='~~Zn<sup>2+</sup>~~ Transporter YiiP' 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 < and > signs.		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.		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==		==Structure==

Kyle Colston at 19:16, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 19:16:38 GMT

←Older revision		Revision as of 19:16, 29 March 2017
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	===Zn<sup>2+</sup> Induced Conformation Change===		===Zn<sup>2+</sup> 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 are focused around the charge interlocking mechanism that holds the dimer together. This is because a flexible loop that likes the CTD and the TMD which acts as a hinge for	+	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 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 site A which then favors change back to inward-facing conformation.
-	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 site A 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 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.		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.

Kyle Colston at 16:22, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 16:22:00 GMT

←Older revision		Revision as of 16:22, 29 March 2017
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	==Zn<sup>2+</sup> 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='Zn<sup>2+</sup> 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 < and > signs.		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.		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.

Kyle Colston at 16:20, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 16:20:55 GMT

←Older revision		Revision as of 16:20, 29 March 2017
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-	==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='Zn Transporter' 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 < and > signs.		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.
Line 13:		Line 13:
	==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 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 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.

-	===Zn Induced Conformation Change===	+	===Zn<sup>2+</sup> 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 are focused around the charge interlocking mechanism that holds the dimer together. This is because a flexible loop that likes the CTD and the TMD which acts as a hinge for		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 are focused around the charge interlocking mechanism that holds the dimer together. This is because a flexible loop that likes the CTD and the TMD which acts as a hinge for

Kyle Colston at 16:16, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 16:16:11 GMT

←Older revision		Revision as of 16:16, 29 March 2017
Line 13:		Line 13:
	==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 ~~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 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.

	===Zn Induced Conformation Change===		===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	+	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 are focused around the charge interlocking mechanism that holds the dimer together. This is because a flexible loop that likes the CTD and the TMD which acts as a hinge for
-	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.	+	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 site A 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~~.	+	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.

-	===Allosteric Inhibition===
-
-	Zn binding to Active Site C causes a conformation change that reduces the affinity for Zn at Active Site A.
-
-	== 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.		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.

Kyle Colston at 15:50, 29 March 2017

Kyle Colston — Wed, 29 Mar 2017 15:50:38 GMT

←Older revision		Revision as of 15:50, 29 March 2017
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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 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. ~~The energy for inducing the conformation change from inward to outward~~ is ~~postulated to come from the binding energy of each substrate. The binding of~~ Zn<sup>2+</sup> ~~favors~~ the outward-facing conformation~~, but the outward facing conformation does not favor the binding of Zn~~<sup>2+</sup>~~. The same is observed with~~ the inward-facing conformation ~~and H~~<sup>+</sup>. Although YiiP exists as a homodimer both monomers can undergo conformation change independent of one other to produce the alternating access mechanism~~. The main driving force behind exporting Zn<sup>2+</sup> from the cytoplasm is the proton motive force~~.	+	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.
		+	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.

	===Zn Induced Conformation Change===		===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===		===Allosteric Inhibition===