Proteopedia - User contributions [en]

User:Jing Huang/Sandbox 1

2012-12-21T00:05:58Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]

----

<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-63/2'>PA-63</scene> (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state under a low pH condition and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-21T00:05:15Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]

----

<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-63/2'>PA-63</scene> (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state under a low pH condition and translocates LF/EF into the cell.

<scene name='User:Jing_Huang/Sandbox_1/Ligand/1'>Ligand</scene>

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

CBI Molecules

2012-12-14T17:23:38Z

Jing Huang: /* Molecules */

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).

==Molecules==
'''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''

Bhatia Lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

[http://openwetware.org/wiki/Chien Chien Lab]

: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau
:: Best CBI Molecule 2011

: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang

: '''[[Molecular Playground/RBP]]''', Jan Panteli

: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon

: '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy
:: Best Overall CBI Molecule 2010

: '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez
(compare this to the previous version above to see what's new)

: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani
:: Best CBI Molecule 2012

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao

: ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay

: '''[[Molecular Playground/Caspase-7 Dynamics]]'''

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano

[http://people.chem.umass.edu/mholden/ Holden Lab]

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas
:: Best CBI Molecule Proteopedia Page 2010

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu
: New Fall 2012!! '''[[Molecular Playground/HypA]]''', Heidi Hu

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia
:: Best CBI Molecule 2011
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

Peyton Lab
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman

[http://roberts.openwetware.org/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson

: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino

: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang

: '''[[Molecular playground/Chymotrypsin]]''', Brad

: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

[https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab]

: '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde

Thayumanavan Lab

: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez

: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura

: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi

: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy

: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado

: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang

: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo

: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang

: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''

Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.

1. If you don't already have one, request a Proteopedia account and log in.

2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).

3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.

You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.

4. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished.

==Links to HELP pages==
Overview at [[Help:Contents ]]

See also [[Help:Getting_Started_in_Proteopedia]]

Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

Molecular Playground/Protective Antigen

2012-12-14T17:09:36Z

Jing Huang: New page: One of the CBI Molecules being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at th...

User:Jing Huang/Sandbox 1

2012-12-14T17:09:07Z

Jing Huang:

User:Jing Huang/Sandbox 1

2012-12-14T17:08:40Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----

<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-63/2'>PA-63</scene> (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state under a low pH condition and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:35:35Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----
<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-63/2'>PA-63</scene> (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state under a low pH condition and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:34:01Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----
<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-63/2'>PA-63</scene> (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:32:22Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----
<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-63/2'>PA-63</scene> (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:30:42Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----
<table align="right" width="400" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:29:29Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----
<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment <scene name='User:Jing_Huang/Sandbox_1/Pa-20/1'>PA-20</scene> (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003) Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:24:24Z

Jing Huang:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
----
<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

= Reference =
#R.John Collier and John A.T.Young. (2003)Anthrax Toxin., Annu. Rev. Cell Dev. Biol.19:45-70

User:Jing Huang/Sandbox 1

2012-12-13T15:18:46Z

Jing Huang:

<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TZO 1TZO])' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T15:17:56Z

Jing Huang:

<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]), PA-63 prepore (PDB ID: [[1TZO]])' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T15:13:18Z

Jing Huang:

<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]PA)' scene='Insert optional scene name here' />
</td></tr></table>

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T15:09:26Z

Jing Huang:

= Anthrax Protective Antigen =

<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]PA)' scene='Insert optional scene name here' />

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T15:07:42Z

Jing Huang:

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (<scene name='User:Jing_Huang/Sandbox_1/Pa-63/1'>PA</scene>), lethal factor ([http://en.wikipedia.org/wiki/Anthrax_lethal_factor_endopeptidase LF]), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]PA)' scene='Insert optional scene name here' />

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T15:03:52Z

Jing Huang:

= Anthrax Protective Antigen =

[http://en.wikipedia.org/wiki/Anthrax_toxin Anthrax toxin] complex consists of three nontoxic proteins: protective antigen (PA), lethal factor (LF), and endema factor (EF). PA forms pore and delivers LF and EF, which lead to lethal shock and edema of the host separately, to the cytosol. Formation of the toxin complex starts when PA binds to the cellular receptors and is cleaved into two fragments. The smaller fragment PA-20 (20 kDa) dissociates and the remaining receptor-bound fragment PA-63 (63 kDa) self-assemblies to a ring-shaped heptameric oligomer, a pore precursor (<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>). LF and/or EF binds to the PA63 prepore to form a toxic complex. Oligomerization of PA-63 causes the endocytosis and the complex is trafficked to an acidic compartment. The PA-63 heptamer converts from the prepore to the pore state and translocates LF/EF into the cell.

<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC]PA)' scene='Insert optional scene name here' />

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T15:00:08Z

Jing Huang:

= Anthrax Protective Antigen =

<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC])' scene='Insert optional scene name here' />

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T14:34:17Z

Jing Huang:

'''Anthrax Protective Antigen'''

<Structure load='1ACC' size='500' frame='true' align='right' caption='Anthrax Protective Atigen (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=1acc 1ACC])' scene='Insert optional scene name here' />

<scene name='User:Jing_Huang/Sandbox_1/Prepore/1'>prepore</scene>

User:Jing Huang/Sandbox 1

2012-12-13T03:56:31Z

Jing Huang:

User:Jing Huang/Sandbox 1

2012-12-13T03:55:56Z

Jing Huang:

User:Jing Huang/Sandbox 1

2012-12-12T22:46:46Z

Jing Huang:

'''Anthrax Protective Antigen'''

<Structure load='1ACC' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

<scene name='User:Jing_Huang/Sandbox_1/N_to_c_rainbow/1'>structure of PA-63</scene>
{{Template:ColorKey_N52C3Rainbow}}

User:Jing Huang/Sandbox 1

2012-12-12T22:31:46Z

Jing Huang:

User:Jing Huang/Sandbox 1

2012-12-12T19:05:28Z

Jing Huang:

'''Anthrax Protective Antigen'''

<Structure load='1ACC' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

User:Jing Huang/Sandbox 1

2012-12-12T18:32:33Z

Jing Huang:

'''Anthrax Protective Antigen'''

<Structure load='1ACC' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

User:Jing Huang/Sandbox 1

2012-12-12T18:16:13Z

Jing Huang:

'''Anthrax Protective Antigen'''

<Structure load='1acc' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

User:Jing Huang/Sandbox 1

2012-10-10T17:00:41Z

Jing Huang: New page: 200px {{STRUCTURE_1h5d| PDB=1h5d | SCENE= }} ===X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (0-11% DOSE)=== {{ABSTRACT_PUBMED_1202421...

[[Image:1h5d.png|left|200px]]

{{STRUCTURE_1h5d| PDB=1h5d | SCENE= }}

===X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (0-11% DOSE)===

{{ABSTRACT_PUBMED_12024218}}

==About this Structure==
[[1h5d]] is a 1 chain structure of [[Horseradish peroxidase]] with sequence from [http://en.wikipedia.org/wiki/Armoracia_rusticana Armoracia rusticana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H5D OCA].

==See Also==
*[[Horseradish peroxidase|Horseradish peroxidase]]

==Reference==
<ref group="xtra">PMID:012024218</ref><ref group="xtra">PMID:010574977</ref><ref group="xtra">PMID:009406554</ref><ref group="xtra">PMID:002198290</ref><references group="xtra"/>
[[Category: Armoracia rusticana]]
[[Category: Peroxidase]]
[[Category: Berglund, G I.]]
[[Category: Carlsson, G H.]]
[[Category: Hajdu, J.]]
[[Category: Henriksen, A.]]
[[Category: Smith, A T.]]
[[Category: Szoke, H.]]
[[Category: Compound iii]]
[[Category: Horseradish]]
[[Category: Oxidoreductase]]
[[Category: Oxyperoxidase]]
[[Category: Peroxidase]]
[[Category: X-ray induced reduction]]

User:Jing Huang

2012-10-10T15:29:40Z

Jing Huang:

* Full Real Name:
Jing Huang
* Position:
Graduate student
* Institution (NO ABBREVIATIONS):
University of Massachusetts Amherst
* City, State/Province, Country:
Sunderland, MA, USA
* Field of Expertise or Study:
Model membrane and membrane protein
*[[User:Jing Huang/Sandbox 1]]