Proteopedia - User contributions [en]

Sandbox - Stephen Everse

2025-04-22T14:57:50Z

Stephen Everse:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>

== Mechanisms ==
<scene name='78/786628/Frag_D/1'>Enjoy Fragment D from human fibrinogen</scene>

----
<scene name='78/786628/Highlights/2'>And now this should auto rotate!</scene>
== References ==
More text here!

----
<scene name='78/786628/Apo_Transferrin_Electrostatics/3'>TextToBeDisplayed</scene>

----

<scene name='78/786628/Test/1'>TextToBeDisplayed</scene>
</ReferencesSection>

File:1bp5-electro.pse

2025-04-22T14:55:17Z

Stephen Everse:

Sandbox - Stephen Everse

2025-04-22T14:52:27Z

Stephen Everse:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>

== Mechanisms ==
<scene name='78/786628/Frag_D/1'>Enjoy Fragment D from human fibrinogen</scene>

----
<scene name='78/786628/Highlights/2'>And now this should auto rotate!</scene>
== References ==
More text here!

<scene name='78/786628/Test/1'>TextToBeDisplayed</scene>
</ReferencesSection>

Sandbox - Stephen Everse

2025-04-22T13:15:31Z

Stephen Everse:

Sandbox - Stephen Everse

2025-04-22T13:07:49Z

Stephen Everse:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>

== Mechanisms ==
<scene name='78/786628/Frag_D/1'>Enjoy Fragment D from human fibrinogen</scene>

----

<scene name='78/786628/Highlights/1'>Now lets see if we can use a highlighted PSE file</scene>

== References ==
More text here!

Sandbox - Stephen Everse

2025-04-22T13:06:11Z

Stephen Everse:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>

== Mechanisms ==
<scene name='78/786628/Frag_D/1'>Enjoy Fragment D from human fibrinogen</scene>
<scene name='78/786628/Highlights/1'>TextToBeDisplayed</scene>

== References ==
More text here!

File:Tester.pse

2025-04-22T13:04:07Z

Stephen Everse: testing PSE upload

testing PSE upload

File:Gamma-electrostatics.pse

2025-04-22T12:29:01Z

Stephen Everse: Frag D -- gamma chain electrostatics

Frag D -- gamma chain electrostatics

File:Abc-electrostatics.pse

2025-04-22T12:23:14Z

Stephen Everse: Frag D with electrostatics at the gamma binding site for GPR--

Frag D with electrostatics at the gamma binding site for GPR--

Sandbox - Stephen Everse

2025-04-22T12:18:12Z

Stephen Everse:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>

== Mechanisms ==
<scene name='78/786628/Frag_D/1'>Enjoy Fragment D from human fibrinogen</scene>
</MechanismsSection>
== References ==
More text here!
</ReferencesSection>

Sandbox - Stephen Everse

2025-04-22T12:17:16Z

Stephen Everse:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>

== Mechanisms ==
<scene name='78/786628/Frag_D/1'>Enjoy Fragment D from human fibrinogen</scene>
</MechanismSection>
== References ==
More text here!
</ReferencesSection>

Sandbox - Stephen Everse

2025-04-22T12:16:18Z

Stephen Everse:

Sandbox - Stephen Everse

2025-04-22T12:13:24Z

Stephen Everse:

File:Abc.pse

2025-04-22T12:12:31Z

Stephen Everse:

Sandbox - Stephen Everse

2025-04-21T12:00:18Z

Stephen Everse:

Sandbox - Stephen Everse

2025-04-21T11:56:28Z

Stephen Everse:

===Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==
<scene name='78/786628/1lhs_-_myoglobin_-_consurf/1'>Time to test consurf with myoglobin!</scene>

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>
== References ==
<references/>

Sandbox - Stephen Everse

2025-04-21T02:36:09Z

Stephen Everse: /* Disease */

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==
<scene name='78/786628/1a8e_structure_-_zoom/1'>Hopefully this spins and zooms on click!</scene>

== Relevance ==

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>
== References ==
<references/>

Sandbox - Stephen Everse

2022-04-11T16:07:05Z

Stephen Everse: /* Function */

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
 
Testing to upload a PNG image
[[Image:APpocket.png]]

== Disease ==

== Relevance ==

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>
== References ==
<references/>

File:APpocket.png

2022-04-11T16:05:36Z

Stephen Everse: PNG image

== Summary ==
PNG image
== Licensing ==
{{subst:No license from license selector|Don't know}}

File:Pocket.jpg

2022-04-11T16:04:58Z

Stephen Everse: Testimage3 jpg

== Summary ==
Testimage3 jpg
== Licensing ==
{{subst:No license from license selector|Don't know}}

Sandbox - Stephen Everse

2022-04-11T16:00:49Z

Stephen Everse: /* Function */

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>

Testing to upload a PNG image

== Disease ==

== Relevance ==

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>
== References ==
<references/>

File:Test (1).mp4

2020-04-28T18:37:50Z

Stephen Everse: compressed PyMOL movie convert to mp4 for testing

== Summary ==
compressed PyMOL movie convert to mp4 for testing
== Licensing ==
{{self|cc-by-sa-3.0|GFDL}}

File:Test.mp4

2020-04-28T18:35:09Z

Stephen Everse: test of PyMOL movie converted to mp4

== Summary ==
test of PyMOL movie converted to mp4
== Licensing ==
{{self|cc-by-sa-3.0|GFDL}}

Sandbox - Stephen Everse

2020-04-24T21:17:13Z

Stephen Everse:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
== Disease ==

== Relevance ==

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />
<scene name='78/786628/Nlobe/2'>So what happens with you click on this link?</scene>
== References ==
<references/>

Sandbox - Stephen Everse

2020-04-24T21:15:24Z

Stephen Everse:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
== Disease ==

== Relevance ==

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<Structure load='1a8e' size='350' frame='true' align='right' caption='This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed.' scene='78/786628/Nlobe/1' />

== References ==
<references/>

Sandbox - Stephen Everse

2020-04-24T20:19:55Z

Stephen Everse:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox - Stephen Everse'''. 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.

== Function ==
Testing to insert a movie!
<qt>file=test.mp4|width=700|height=410|autoplay= false |controller=true|loop=false</qt>
== Disease ==

== Relevance ==

== 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.
[[1a8e]]
[[1sdd]]
</StructureSection>
== Test scene load from pymol.pse file ==
<scene name='78/786628/Nlobe/1'>This is the N-lobe of human serum transferrin -- unfortunately the PyMOL upload failed...I/scene>
== References ==
<references/>

Sandbox - Stephen Everse

2018-04-30T15:29:53Z

Stephen Everse:

Sandbox - Stephen Everse

2018-04-27T17:53:26Z

Stephen Everse:

Sandbox - Stephen Everse

2018-04-27T17:53:06Z

Stephen Everse:

Sandbox - Stephen Everse

2018-04-27T17:51:45Z

Stephen Everse: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

Triose Phosphate Isomerase

2009-04-15T19:11:28Z

Stephen Everse:

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

<scene name='Triose_Phosphate_Isomerase/Morph_tpi/1'>TextToBeDisplayed</scene>

[[Image:triosejpg.jpg|right|thumb|TPI]]

[[Image:cartoon-small.gif]]

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis]. TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase]. In addition to its relevance in glycolysis, TPI is also involved in metabolic biological processes such as gluconeogenesis, pentose phosphate shunt, fatty acid biosynthesis among others.

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits each consisting of 247 amino acids. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[http://en.wikipedia.org/wiki/Triose_Phosphate_Isomerase_deficiency Triose Phosphate Isomerase Deficiency], initially described in 1965, is an autosomal recessive inherited disease with characteristics ranging from chronic haemolytic anaemia, increased suseptibility to infections, severe neurological dysfunction, and often times death in early childhood. TPI has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

'''Role in Alzeihmer's Disease''': Recent discoveries in Alzeihmer Disease research has indicated that amyloid Beta-peptide induced nitro-oxidative damage promotes the nitrotyrosination of the glycolytic enzyme triosephosphate isomerase in human neuroblastoma cells.<ref name="nitrotyrosination induces glycation">[http://www.ncbi.nlm.nih.gov/pubmed/19251756]. </ref> Nitro-triosephosphate isomerase was found to be present in brain slides from double transgenic mice overexpressing human amyloid precursor protein as well as in Alzeihmer's disease patients. Specifically, the nitrotyrosination occurs on <scene name='Triose_Phosphate_Isomerase/Two_tyrosine_tesidues/2'>Tyrosine 164 and 208 residues</scene> , which are located in close proximity to the catalytic center, and this modification correlates with a reduced isomerase activity. Additionally, according to work done by Francesc Guix and colleagues, nitro-triosphosphate isomerase contributed to the formation of large beta-sheet aggregates ''in vitro'' and ''in vivo''.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz
Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain: A Journal of Neurobiology. Authors....

Triose Phosphate Isomerase

2009-04-15T19:04:33Z

Stephen Everse:

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

<applet load='TPI_combined.pdb' size='500' frame='true' align='right' caption='Test morph' scene='' />

[[Image:triosejpg.jpg|right|thumb|TPI]]

[[Image:cartoon-small.gif]]

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis]. TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase]. In addition to its relevance in glycolysis, TPI is also involved in metabolic biological processes such as gluconeogenesis, pentose phosphate shunt, fatty acid biosynthesis among others.

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits each consisting of 247 amino acids. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[http://en.wikipedia.org/wiki/Triose_Phosphate_Isomerase_deficiency Triose Phosphate Isomerase Deficiency], initially described in 1965, is an autosomal recessive inherited disease with characteristics ranging from chronic haemolytic anaemia, increased suseptibility to infections, severe neurological dysfunction, and often times death in early childhood. TPI has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

'''Role in Alzeihmer's Disease''': Recent discoveries in Alzeihmer Disease research has indicated that amyloid Beta-peptide induced nitro-oxidative damage promotes the nitrotyrosination of the glycolytic enzyme triosephosphate isomerase in human neuroblastoma cells.<ref name="nitrotyrosination induces glycation">[http://www.ncbi.nlm.nih.gov/pubmed/19251756]. </ref> Nitro-triosephosphate isomerase was found to be present in brain slides from double transgenic mice overexpressing human amyloid precursor protein as well as in Alzeihmer's disease patients. Specifically, the nitrotyrosination occurs on <scene name='Triose_Phosphate_Isomerase/Two_tyrosine_tesidues/2'>Tyrosine 164 and 208 residues</scene> , which are located in close proximity to the catalytic center, and this modification correlates with a reduced isomerase activity. Additionally, according to work done by Francesc Guix and colleagues, nitro-triosphosphate isomerase contributed to the formation of large beta-sheet aggregates ''in vitro'' and ''in vivo''.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz
Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain: A Journal of Neurobiology. Authors....

Triose Phosphate Isomerase

2009-04-15T19:03:17Z

Stephen Everse:

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

<applet load='TPI_combined.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />

[[Image:triosejpg.jpg|right|thumb|TPI]]

[[Image:cartoon-small.gif]]

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis]. TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase]. In addition to its relevance in glycolysis, TPI is also involved in metabolic biological processes such as gluconeogenesis, pentose phosphate shunt, fatty acid biosynthesis among others.

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits each consisting of 247 amino acids. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[http://en.wikipedia.org/wiki/Triose_Phosphate_Isomerase_deficiency Triose Phosphate Isomerase Deficiency], initially described in 1965, is an autosomal recessive inherited disease with characteristics ranging from chronic haemolytic anaemia, increased suseptibility to infections, severe neurological dysfunction, and often times death in early childhood. TPI has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

'''Role in Alzeihmer's Disease''': Recent discoveries in Alzeihmer Disease research has indicated that amyloid Beta-peptide induced nitro-oxidative damage promotes the nitrotyrosination of the glycolytic enzyme triosephosphate isomerase in human neuroblastoma cells.<ref name="nitrotyrosination induces glycation">[http://www.ncbi.nlm.nih.gov/pubmed/19251756]. </ref> Nitro-triosephosphate isomerase was found to be present in brain slides from double transgenic mice overexpressing human amyloid precursor protein as well as in Alzeihmer's disease patients. Specifically, the nitrotyrosination occurs on <scene name='Triose_Phosphate_Isomerase/Two_tyrosine_tesidues/2'>Tyrosine 164 and 208 residues</scene> , which are located in close proximity to the catalytic center, and this modification correlates with a reduced isomerase activity. Additionally, according to work done by Francesc Guix and colleagues, nitro-triosphosphate isomerase contributed to the formation of large beta-sheet aggregates ''in vitro'' and ''in vivo''.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz
Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain: A Journal of Neurobiology. Authors....

Triose Phosphate Isomerase

2009-04-15T18:59:39Z

Stephen Everse:

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

{{STRUCTURE_2ypi| PDB=TPI_combined.pdb | SCENE= }}

[[Image:triosejpg.jpg|right|thumb|TPI]]

[[Image:cartoon-small.gif]]

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis]. TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase]. In addition to its relevance in glycolysis, TPI is also involved in metabolic biological processes such as gluconeogenesis, pentose phosphate shunt, fatty acid biosynthesis among others.

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits each consisting of 247 amino acids. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[http://en.wikipedia.org/wiki/Triose_Phosphate_Isomerase_deficiency Triose Phosphate Isomerase Deficiency], initially described in 1965, is an autosomal recessive inherited disease with characteristics ranging from chronic haemolytic anaemia, increased suseptibility to infections, severe neurological dysfunction, and often times death in early childhood. TPI has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

'''Role in Alzeihmer's Disease''': Recent discoveries in Alzeihmer Disease research has indicated that amyloid Beta-peptide induced nitro-oxidative damage promotes the nitrotyrosination of the glycolytic enzyme triosephosphate isomerase in human neuroblastoma cells.<ref name="nitrotyrosination induces glycation">[http://www.ncbi.nlm.nih.gov/pubmed/19251756]. </ref> Nitro-triosephosphate isomerase was found to be present in brain slides from double transgenic mice overexpressing human amyloid precursor protein as well as in Alzeihmer's disease patients. Specifically, the nitrotyrosination occurs on <scene name='Triose_Phosphate_Isomerase/Two_tyrosine_tesidues/2'>Tyrosine 164 and 208 residues</scene> , which are located in close proximity to the catalytic center, and this modification correlates with a reduced isomerase activity. Additionally, according to work done by Francesc Guix and colleagues, nitro-triosphosphate isomerase contributed to the formation of large beta-sheet aggregates ''in vitro'' and ''in vivo''.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz
Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain: A Journal of Neurobiology. Authors....

File:TPI combined.pdb

2009-04-15T18:58:19Z

Stephen Everse:

Triose Phosphate Isomerase

2009-03-25T13:40:03Z

Stephen Everse:

[[Image:triosejpg.jpg|center|thumb|TPI]]

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis].

TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase].

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop acts as a lid on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[[Triose Phosphate Isomerase Deficiency]] has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz

Triose Phosphate Isomerase

2009-03-25T13:39:28Z

Stephen Everse:

[[Image:triosejpg.jpg|left|thumb|TPI]]

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis].

TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase].

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop acts as a lid on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[[Triose Phosphate Isomerase Deficiency]] has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz

Triose Phosphate Isomerase

2009-03-25T13:39:07Z

Stephen Everse:

[[Image:triosejpg.jpg|thumb|TPI]]

{{STRUCTURE_2ypi| PDB=2ypi | SCENE= }}

== Overview ==

'''Triose Phosphate Isomerase''' (TPI or TIM) catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate ([http://en.wikipedia.org/wiki/DHAP DHAP]) and D-glyceraldehyde-3-phosphate <scene name='Triose_Phosphate_Isomerase/Pga/1'>(GAP)</scene>, an essential process in the glycolytic pathway. More simply, the enzyme catalyzes the [http://en.wikipedia.org/wiki/Isomerization isomerization] of a ketose (DHAP) to an aldose [http://en.wikipedia.org/wiki/Glycerate_3-phosphate GAP] also referred to as PGA. In regards to the two isomers, at equilibrium, roughly 96% of the triose phosphate is in the DHAP isomer form; however, the isomerization reaction proceeds due to the rapid removal of GAP from the subsequent reactions of [http://en.wikipedia.org/wiki/Glycolysis glycolysis].

TPI is an example of a [http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme catalytically perfect enzyme], indicating that for almost every enzyme substrate encounter, a product is formed and that this interaction is only limited by the substrate diffusion rate. Other catalytically perfect enzymes include [http://en.wikipedia.org/wiki/Carbonic_anhydrase carbonic anhydrase], [http://en.wikipedia.org/wiki/Acetylcholinesterase acetylcholinesterase], [http://en.wikipedia.org/wiki/Catalase catalase] and [http://en.wikipedia.org/wiki/Fumarase fumarase].

== Mechanism ==

TPI catalyzes the transfer of a hydrogen atom from carbon 1 to carbon 2, an intramolecular [http://en.wikipedia.org/wiki/Oxidation_reduction oxidation-reduction] reaction. This isomerization of a ketose to an aldose proceeds through an enediol intermediate.

=== Acid Base Catalysis ===

TPI carries out the isomerization reaction through acid base chemistry involving <scene name='Triose_Phosphate_Isomerase/Three_catalytic_residues/1'>three catalytic residues </scene>. First the PGA molecule is held in place by <scene name='Triose_Phosphate_Isomerase/Lys12/1'>Lysine 12</scene>, which provides a positive charge to the active site. <scene name='Triose_Phosphate_Isomerase/Glu165/2'>Glutamate 165</scene>, which plays the role of the general base catalyst in a proton abstraction mechanism , abstracts a proton from carbon 1. However, the [http://en.wikipedia.org/wiki/Carboxylate carboxylate group] of Glutamate 165 alone is not basic enough to abstract a proton and requires <scene name='Triose_Phosphate_Isomerase/His95/4'>Histidine 95</scene>, the general acid, to donate a proton to C-2 to stabilize the negatively charge C-2 carbonyl group, effectively forming the endediol intermediate. At this point in the reaction, Glutamate 165 acts as a general acid by donating its proton the C-2, while Histidine 95 now acts as a general base by abstracting a proton from the [http://en.wikipedia.org/wiki/Hydroxyl hydroxyl group] of C-1. The final step in the reaction is the formation of the GAP isomer product while glutamate and histidine are returned to their original forms.

[[Image:TPImechanism.jpg]]

== Structure & Function ==

Triose Phosphate Isomerase is part of the all alpha and beta(a/b)class of proteins and it is a dimer consisting of two identical subunits. Each subunit contains <scene name='Triose_Phosphate_Isomerase/Helices/1'>8 exterior alpha helices</scene> surrounding 8 interior <scene name='Triose_Phosphate_Isomerase/Beta_sheet/1'>beta sheets</scene>, which form a structural motif called a closed alpha/beta barrel or more specifically a <scene name='Triose_Phosphate_Isomerase/Tim_barrel/3'>TIM Barrel</scene>. Characteristic of most all [http://en.wikipedia.org/wiki/TIM_barrel TIM barrel] domains, the active site is located in a similar position, in the loop regions created by the eight loops that connect the C-terminus of the [http://en.wikipedia.org/wiki/Beta_strand beta strands] with the N-terminus of the [http://en.wikipedia.org/wiki/Alpha_helix alpha helices]. As mentioned earlier, TPI is a catalytically perfect enzyme and accomplishes this largely due to its ability to suppress or prevent undesired side reactions such as the decomposition of the enediol intermediate into [http://en.wikipedia.org/wiki/Methyl_glyoxal methyl glyoxal] and [http://en.wikipedia.org/wiki/Orthophosphate orthophosphate], a process which is 100 fold faster in solution than the desired isomerization. TPI is able to prevent this undesired reaction by trapping the intermediate in the active site through the use of a 10 residue loop. This loop acts as a lid on the active site, which shuts when the enediol is present and reopens when the isomerization is complete.

== Disease ==
[[Triose Phosphate Isomerase Deficiency]] has been most closely linked to a point mutation at the <scene name='Triose_Phosphate_Isomerase/Glu104/1'>Glutamate 104</scene> residue which results in the Glu104Asp mutation. A common marker for TPI deficiency is the increased accumulation of dihydroxyacetone phosphate in erythrocyte extracts as a result in the inability of the mutant enzyme to catalyze the isomerization to D-glyceraldehyde-3-phosphate.

== References ==
Stryer, L.; Berg, J. M.; Tymoczko, J. L. (2007), Biochemistry (6th ed.), New York: W. H. Freeman, ISBN 0716746840
Introduction to Protein Structure Second Edition. Carl Branden & John Tooz