Proteopedia - User contributions [en]

CBI Molecules

2010-04-30T20:20:09Z

Ankit Vahia:

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

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez, Thayumanavan Research Group

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

'''[[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

'''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

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

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia ([http://www.chem.umass.edu/~cmartin/ Martin] lab)

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

'''[[Molecular Playground/Alginate]]''', David Griffin

'''[[Molecular Playground/Glutamate Receptor]]''', [http://chamberslab.com/wp/ Chambers Lab] (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

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

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

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

'''[[Molecular Playground/Pancreatic Lipase]]''', Rotello lab (Rui Tang)

'''[[Molecular Playground/Trypsin]]''', Thai-Vachet lab (Murage, Gladys)

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). With your chosen Jmol scene for the Molecular Playground, specify a "banner", which will be projected with the molecule on the Molecular Playground. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

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. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too. 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

2010-04-30T20:18:40Z

Ankit Vahia:

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

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez, Thayumanavan Research Group

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

'''[[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

'''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

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

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia (Martin Lab : http://www.chem.umass.edu/~cmartin/)

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

'''[[Molecular Playground/Alginate]]''', David Griffin

'''[[Molecular Playground/Glutamate Receptor]]''', [http://chamberslab.com/wp/ Chambers Lab] (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

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

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

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

'''[[Molecular Playground/Pancreatic Lipase]]''', Rotello lab (Rui Tang)

'''[[Molecular Playground/Trypsin]]''', Thai-Vachet lab (Murage, Gladys)

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). With your chosen Jmol scene for the Molecular Playground, specify a "banner", which will be projected with the molecule on the Molecular Playground. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

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. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too. 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/T7 RNA Polymerase (7 mer int)

2010-04-30T20:17:27Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

The initiation phase continues until the enzyme synthesizes ~8 base RNA after which it loses promoter contacts and transitions into the stable elongation phase. The initiation phase in T7 RNA polymerase like all other single and multi subunit RNA polymerases is characterized by inherent instability leading to the release of small RNA (3-8 bases long). In addition to the crystal structure of the enzyme with a 3 base DNA-RNA hybrid (PDB ID:1QLN) this 7 base intermediate structure provides a insight into the structural changes within the enzyme has it synthesizes RNA during initiation and the mechanism which eventually leads to the release of the promoter contacts and the transition into elongation.

In the image below, the template strand (blue) has been separated from the non-template strand (green) and forms a 7 base hybrid with the RNA (red).

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='T7 RNA polymerase with a 7 base DNA-RNA hybrid (3E2E)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

CBI Molecules

2010-04-30T15:52:48Z

Ankit Vahia:

Molecular Playground/T7 RNA Polymerase (7 mer int)

2010-04-30T15:49:47Z

Ankit Vahia: New page: [Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase] A CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amher...

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

The initiation phase continues until the enzyme synthesizes ~8 base RNA after which it loses promoter contacts and transitions into the stable elongation phase. The initiation phase in T7 RNA polymerase like all other single and multi subunit RNA polymerases is characterized by inherent instability leading to the release of small RNA (3-8 bases long). In addition to the crystal structure of the enzyme with a 3 base DNA-RNA hybrid (PDB ID:1QLN) this 7 base intermediate structure provides a insight into the structural changes within the enzyme has it synthesizes RNA during initiation and the mechanism which eventually leads to the release of the promoter contacts and the transition into elongation.

In the image below, the template strand (blue) has been separated from the non-template strand (green) and forms a 7 base hybrid with the RNA (red).

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

User:Ankit Vahia/sandbox1

2010-04-30T15:46:11Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

The initiation phase continues until the enzyme synthesizes ~8 base RNA after which it loses promoter contacts and transitions into the stable elongation phase. The initiation phase in T7 RNA polymerase like all other single and multi subunit RNA polymerases is characterized by inherent instability leading to the release of small RNA (3-8 bases long). In addition to the crystal structure of the enzyme with a 3 base DNA-RNA hybrid (PDB ID:1QLN) this 7 base intermediate structure provides a insight into the structural changes within the enzyme has it synthesizes RNA during initiation and the mechanism which eventually leads to the release of the promoter contacts and the transition into elongation.

In the image below, the template strand (blue) has been separated from the non-template strand (green) and forms a 7 base hybrid with the RNA (red).

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

User:Ankit Vahia/sandbox1

2010-04-30T15:45:48Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

The initiation phase continues until the enzyme synthesizes ~8 base RNA after which it loses promoter contacts and transitions into the stable elongation phase. The initiation phase in T7 RNA polymerase like all other single and multi subunit RNA polymerases is characterized by inherent instability leading to the release of small RNA (3-8 bases long). In addition to the crystal structure of the enzyme with a 3 base DNA-RNA hybrid (PDB ID:1QLN) this 7 base intermediate structure provides a insight into the structural changes within the enzyme has it synthesizes RNA during initiation and the mechanism which eventually leads to the release of the promoter contacts and the transition into elongation.

In the image below, the template strand (blue) has been separated from the non-template strand (green) and forms a 7 base hybrid with the RNA (red).

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

User:Ankit Vahia/sandbox1

2010-04-29T16:02:53Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

The initiation phase continues until the enzyme synthesizes ~8 base RNA after which it loses promoter contacts and transitions into the stable elongation phase. The initiation phase in T7 RNA polymerase like all other single and multi subunit RNA polymerases is characterized by inherent instability leading to the release of small RNA (3-8 bases long). In addition to the crystal structure of the enzyme with a 3 base DNA-RNA hybrid (PDB ID:1QLN) this 7 base intermediate structure provides an insight into the structural changes within the enzyme has it synthesizes RNA during initiation and provides an insight into the mechanism that eventual culminates into the release of the promoter contacts and the transition into elongation

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

User:Ankit Vahia/sandbox1

2010-04-28T20:39:01Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

The initiation phase continues until the enzyme synthesizes ~8 base RNA after which it loses promoter contacts and transitions into the stable elongation phase. The initiation phase in T7 RNA polymerase like all other single and multi subunit RNA polymerases is characterized by inherent instability leading to the release of small RNA (3-8 bases long). In addition to the crystal structure of the enzyme with a 3 base DNA-RNA hybrid (PDB ID:1QLN) this 7 base intermediate structure provides an insight into the structural changes within the enzyme has it synthesizes RNA during initiation and provides an insight into the mechanism that eventual culminates into the release of the promoter contacts and the transition into elongation

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T20:23:27Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/2'>TextToBeDisplayed</scene>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T20:22:10Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T20:20:35Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T20:18:21Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/1'>TextToBeDisplayed</scene>' size='[450,338]' frame='true' align='right'
caption='T7 RNA Polymerase with a 7 base DNA-RNA hybrid (3E2E)' <scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/1'>TextToBeDisplayed</scene>>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T20:04:45Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='T7 RNA Polymerase with a 7 base DNA-RNA hybrid (3E2E)' <scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/1'>TextToBeDisplayed</scene>>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T20:03:58Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

T7 RNA polymerase is a a single sub-unit DNA dependent RNA polymerase from the T7 RNA bacteriophage. Like most RNA polymerase T7 RNA polymerase transcribes DNA through three phases
-Initiation
-Elongation
-Termination

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' <scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/1'>TextToBeDisplayed</scene>>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:45:13Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' <scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_2/1'>TextToBeDisplayed</scene>>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:42:02Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='3E2E' size='[450,338]' frame='true' align='right'

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:40:57Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:39:31Z

Ankit Vahia:

[Image:intactModelLargeText.jpg|frame|T7 RNA Polymerase in the Late Initiation Phase]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:38:31Z

Ankit Vahia:

[[Image:intactModelLargeText.jpg|frame|T7 RNA polymerase in the late initiation phase]]

A [[CBI Molecule]] 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].

T7 RNA Polymerase is a single sub-unit DNA dependent RNA polymerase.

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:37:01Z

Ankit Vahia:

[[Image:intactModelLargeText.jpg|frame|T7 RNA polymerase in the late initiation phase]]

A [[CBI Molecule]] 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].

T7 RNA Polymerase is a single sub-unit DNA dependent RNA polymerase.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='T7 RNA polymerase with a 7 base DNA-RNA hybrid'

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is T7 RNA polymerase with a 7 base DNA-RNA hybrid

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:32:33Z

Ankit Vahia:

[[Image:intactModelLargeText.jpg|frame|T7 RNA polymerase in the late initiation phase]]

A [[CBI Molecule]] 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].

T7 RNA Polymerase is a single sub-unit DNA dependent RNA polymerase.

=== 7 base DNA-RNA hybrid ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) shows a 7 mer DNA-RNA hybrid as the enzyme is about to loose promoter contacts and transition into the more stable elongation phase.

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:29:31Z

Ankit Vahia: /* Ligand-binding domain */

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:27:39Z

Ankit Vahia: /* Ligand-binding domain */

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein <scene name='User:Ankit_Vahia/sandbox1/T7-7mer_rna_scene_1/1'>TextToBeDisplayed</scene> is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.

User:Ankit Vahia/sandbox1

2010-04-28T19:06:02Z

Ankit Vahia: New page: Bacterial chemotaxis receptor A CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Bi...

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

A [[CBI Molecule]] 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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A receptor protein used by bacteria to "smell" their environment.