Proteopedia - User contributions [en]

Molecular Playground/ERMan1

2010-04-30T14:31:58Z

Johan Sunryd:

==ERMan1==
Alpha-mannosidases I(ERMan1) is a human protein that resides in the endoplasmic reticulum(ER). ERMan1 is a member of the class 1 glycosylhydrolase family 47 group proteins and sports a Tim-barrel fold. Asparagine(N)-linked glycans are common covalent modifiers in the ER that aid in protein folding and trafficking. ERMan1 trims N-linked glycans to target a misfolded protein for degradation. The slow acting kinetics of ERMan1 have been proposed to act as a timer for protein degradation, creating a discrete window for protein folding followed by degradation if the substrate protein cannot reach the native state.

{{STRUCTURE_1x9d | PDB=1x9d | SCENE= }}

"Molecular Playground banner: A catalytic timer for protein degradation."

[http://proteopedia.org/wiki/index.php/CBI_Molecules]
[http://proteopedia.org/wiki/index.php/1x9d]

Molecular Playground/ERMan1

2010-04-30T14:22:08Z

Johan Sunryd:

==ERMan1==
Alpha-mannosidases I(ERMan1) is a human protein that reside in the endoplasmic reticulum(ER). ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. Asparagine(N)-linked glycans are common covalent modifiers in the ER that aid in protein folding and trafficking. ERMan1 trims N-linked glycans to make the client protein targeted for degradation. The slow acting kinetics of ERMan1 has been proposed to give at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{STRUCTURE_1x9d | PDB=1x9d | SCENE= }}

"Molecular Playground banner: A catalytic timer for protein degradation."

[http://proteopedia.org/wiki/index.php/CBI_Molecules]
[http://proteopedia.org/wiki/index.php/1x9d]

Molecular Playground/ERMan1

2010-04-30T14:21:44Z

Johan Sunryd:

==This is a placeholder==
Alpha-mannosidases I(ERMan1) is a human protein that reside in the endoplasmic reticulum(ER). ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. Asparagine(N)-linked glycans are common covalent modifiers in the ER that aid in protein folding and trafficking. ERMan1 trims N-linked glycans to make the client protein targeted for degradation. The slow acting kinetics of ERMan1 has been proposed to give at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{STRUCTURE_1x9d | PDB=1x9d | SCENE= }}

"Molecular Playground banner: A catalytic timer for protein degradation."

[http://proteopedia.org/wiki/index.php/CBI_Molecules]
[http://proteopedia.org/wiki/index.php/1x9d]

Molecular Playground/ERMan1

2010-04-30T14:17:20Z

Johan Sunryd:

==This is a placeholder==
Alpha-mannosidases I(ERMan1) is a human protein that reside in the endoplasmic reticulum(ER). ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In N-linked glycans are common covalent modifiers in the ER that aid in protein folding and trafficking. ERMan1 trims N-linked glycans to make the client protein targeted for degradation. The slow acting kinetics of ERMan1 has been proposed to give at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{STRUCTURE_1x9d | PDB=1x9d | SCENE= }}

"Molecular Playground banner: A catalytic timer for protein degradation."

[http://proteopedia.org/wiki/index.php/CBI_Molecules]
[http://proteopedia.org/wiki/index.php/1x9d]

CBI Molecules

2010-04-30T14:06:28Z

Johan Sunryd:

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]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Thompson & Weis laboratories

'''[[User:Tsung-Yi_Lin/6-deoxyerythronolide_B_synthase|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez

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

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

'''[[Molecular Playground/Taxol]]''', Rohan Patil

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

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

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

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

[http://proteopedia.org/wiki/index.php/Molecular_Playground/ERMan1], Johan Sunryd

Instructions:

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]).

3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Follow instructions at [[Molecular Playground/Procedures]] as well. But don't "capture the state script for your scene"; that will be done for you (see #7).

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.

CBI Molecules

2010-04-30T14:05:13Z

Johan Sunryd:

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]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Thompson & Weis laboratories

'''[[User:Tsung-Yi_Lin/6-deoxyerythronolide_B_synthase|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez

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

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

'''[[Molecular Playground/Taxol]]''', Rohan Patil

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

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

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

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

'''[[User:Johan Sunryd|Molecular Playground/ERMan1]]''', Johan Sunryd

Instructions:

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]).

3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Follow instructions at [[Molecular Playground/Procedures]] as well. But don't "capture the state script for your scene"; that will be done for you (see #7).

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.

Molecular Playground/ERMan1

2010-04-30T14:04:44Z

Johan Sunryd: New page: ==This is a placeholder== Alpha-mannosidases I(ERMan1) is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 grou...

==This is a placeholder==
Alpha-mannosidases I(ERMan1) is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as indicators of how well a client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{STRUCTURE_1x9d | PDB=1x9d | SCENE= }}

"Molecular Playground banner: A catalytic timer for protein degradation."

[http://proteopedia.org/wiki/index.php/CBI_Molecules]

User talk:Johan sunryd/sandbox 1

2010-04-30T02:07:08Z

Johan Sunryd: Molecular Playground/ ER mannosidases 1

Alpha-mannosidases I(ERMan1) is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as indicators of how well a client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{Clear}}
<applet load='1X9D' size='[450,338]' frame='true' align='right'
caption='ERMan1 (1X9D)' <scene name='User_talk:Johan_sunryd/sandbox_1/Catalytic_site_of_erman_1/1'>TextToBeDisplayed</scene>

=== Catalytic Site ===

The spinning protein (<scene name='User_talk:Johan_sunryd/sandbox_1/Erman1_full_length/1'>TextToBeDisplayed</scene>) ) is a highlight of the catalytic residues of ERMan1.

"Molecular Playground banner: A catalytic timer for protein degradation."

User talk:Johan sunryd/sandbox 1

2010-04-30T02:02:54Z

Johan Sunryd: Molecular Playground/ERMan1

Alpha-mannosidases I is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as indicators of how well a client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{Clear}}
<applet load='1X9D' size='[450,338]' frame='true' align='right'
caption='ERMan1 (1X9D)' scene='User:Johan_Sunryd/Sandbox_1/Loadedfrompdb/4'/>

=== Catalytic Site ===

The spinning protein (<scene name='User_talk:Johan_sunryd/sandbox_1/Erman1_full_length/1'>TextToBeDisplayed</scene>) ) is a highlight of the catalytic residues of ERMan1.

"Molecular Playground banner: A catalytic timer for protein degradation."

User talk:Johan sunryd/sandbox 1

2010-04-30T01:55:59Z

Johan Sunryd:

User talk:Johan sunryd/sandbox 1

2010-04-26T02:03:24Z

Johan Sunryd:

Alpha-mannosidases I is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as indicators of how well a client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{Clear}}
<applet load='1X9D' size='[450,338]' frame='true' align='right'
caption='ERMan1 (1X9D)' scene='User:Johan_Sunryd/Sandbox_1/Loadedfrompdb/4'/>

=== Catalytic Site ===

The spinning protein (<scene name='User_talk:Johan_sunryd/sandbox_1/Erman1_full_length/1'>TextToBeDisplayed</scene>) ) is a highlight of the catalytic residues of ERMan1.

Molecular Playground banner: A catalytic timer for protein degradation.

User talk:Johan sunryd/sandbox 1

2010-04-26T02:00:54Z

Johan Sunryd:

[<scene name='User_talk:Johan_sunryd/sandbox_1/Side_view_of_erman1/1'>TextToBeDisplayed</scene>]

Alpha-mannosidases I is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as indicators of how well a client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{Clear}}
<applet load='1X9D' size='[450,338]' frame='true' align='right'
caption='ERMan1 (1X9D)' scene='User:Johan_Sunryd/Sandbox_1/Loadedfrompdb/4'/>

=== Catalytic Site ===

The spinning protein (<scene name='User_talk:Johan_sunryd/sandbox_1/Erman1_full_length/1'>TextToBeDisplayed</scene>) ) is a highlight of the catalytic residues of ERMan1.

Molecular Playground banner: A catalytic timer for protein degradation.

User talk:Johan sunryd/sandbox 1

2010-04-26T01:39:25Z

Johan Sunryd:

[[Image:intactModelLargeText.jpg|frame|ER Man 1]]

Alpha-mannosidases I is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47 group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as indicators of how well a client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein can be targeted for degradation by other ER proteins.

{{Clear}}
<applet load='1X9D' size='[450,338]' frame='true' align='right'
caption='ERMan1 (1X9D)' scene='User:Johan_Sunryd/Sandbox_1/Loadedfrompdb/4'/>

=== Catalytic Site ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is a highlight of the catalytic residues of ERMan1.

Molecular Playground banner: A catalytic timer for protein degradation.

User talk:Johan sunryd/sandbox 1

2010-04-26T01:34:35Z

Johan Sunryd: New page: ER Man 1 ER Mannosidase 1 is a type II ER membrane protein that. EMechanism of class 1 (glycosylhydrolase family 47) Alpha-mannosidases involved ...

[[Image:intactModelLargeText.jpg|frame|ER Man 1]]

ER Mannosidase 1 is a type II ER membrane protein that. EMechanism of class 1 (glycosylhydrolase family 47) Alpha-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control.

Alpha-mannosidases I is a human protein that reside in the endoplasmic reticulum(ER) lumen. ERMan1 is part of the class 1 glycosylhydrolase family 47, group of proteins and sports a Tim-barrel fold. In the ER N-linked glycans are used as a indicator of how wella client protein is folded. ERMan1 functions by slowly trimming N-linked glycans, giving the protein at hand a defined window of time before the client protein will be detected as misfolded by other ER proteins.

{{Clear}}
<applet load='1X9D' size='[450,338]' frame='true' align='right'
caption='ERMan1 (1X9D)' scene='User:Johan_Sunryd/Sandbox_1/Loadedfrompdb/4'/>

=== Catalytic Site ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is a highlight of the catalytic residues of ERMan1.

Molecular Playground banner: A catalytic timer for protein degradation.