Proteopedia - User contributions [en]

CBI Molecules

2010-04-30T20:29:23Z

Krishna Reddy Ragupathi:

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, [http://www.biochem.umass.edu/garman/index.html Garman Research Group]

'''[[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]]''', Thai lab (Krishna Reddy Raghupathi)

'''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Thai lab (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]]''', [http://www.umass.edu/rotellogroup/ 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.

User:Krishna Reddy Ragupathi

2010-04-30T01:03:46Z

Krishna Reddy Ragupathi:

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].

<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>CBI Carbonic Anhydrase Model</scene>

<applet size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' scene='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

Shown is the enzyme Carbonic Anhydrase II which falls under α-Family of Carbonic Anhydrases. As the name suggest Carbonic Anhydrases are a class of enzymes which catalyze the reversible conversion of carbondioxide to the bicarbonate and proton. Due to this unique property they play a key role in maintaining the acid-base balance of blood and several other tissues.

The active site of the enzyme is depicted here, which has three histidine residues coordinated to the zinc metal.

User:Krishna Reddy Ragupathi

2010-04-29T23:42:46Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>CBI Carbonic Anhydrase Model</scene>

<applet size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' scene='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

Shown is the enzyme Carbonic Anhydrase II which falls under α-Family of Carbonic Anhydrases. As the name suggest Carbonic Anhydrases are a class of enzymes which catalyze the reversible conversion of carbondioxide to the bicarbonate and proton. Due to this unique property they play a key role in maintaining the acid-base balance of blood and several other tissues.

The active site of the enzyme is depicted here, which has three histidine residues coordinated to the zinc metal.

User:Krishna Reddy Ragupathi

2010-04-29T23:42:07Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.
<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>CBI Carbonic Anhydrase Model</scene>

<applet size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' scene='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

Shown is the enzyme Carbonic Anhydrase II which falls under α-Family of Carbonic Anhydrases. As the name suggest Carbonic Anhydrases are a class of enzymes which catalyze the reversible conversion of carbondioxide to the bicarbonate and proton. Due to this unique property they play a key role in maintaining the acid-base balance of blood and several other tissues.

The active site of the enzyme is depicted here, which has three histidine residues coordinated to the zinc metal.

User:Krishna Reddy Ragupathi

2010-04-29T23:41:25Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<applet size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' scene='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

Shown is the enzyme Carbonic Anhydrase II which falls under α-Family of Carbonic Anhydrases. As the name suggest Carbonic Anhydrases are a class of enzymes which catalyze the reversible conversion of carbondioxide to the bicarbonate and proton. Due to this unique property they play a key role in maintaining the acid-base balance of blood and several other tissues.

The active site of the enzyme is depicted here, which has three histidine residues coordinated to the zinc metal.

<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>CBI Carbonic Anhydrase Model</scene>

User:Krishna Reddy Ragupathi

2010-04-29T23:40:24Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<applet size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' scene='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

Shown is the enzyme Carbonic Anhydrase II which falls under α-Family of Carbonic Anhydrases. As the name suggest Carbonic Anhydrases are a class of enzymes which catalyze the reversible conversion of carbondioxide to the bicarbonate and proton. Due to this unique property it plays a key role in maintaining the acid-base balance of blood and several other tissues.

The active site of the enzyme is depicted here, which has three histidine residues coordinated to the zinc metal.

<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>CBI Carbonic Anhydrase Model</scene>

User:Krishna Reddy Ragupathi

2010-04-29T20:05:19Z

Krishna Reddy Ragupathi:

CBI Molecules

2010-04-29T20:03:43Z

Krishna Reddy Ragupathi:

User:Krishna Reddy Ragupathi

2010-04-29T20:00:57Z

Krishna Reddy Ragupathi:

User:Krishna Reddy Ragupathi

2010-04-29T20:00:05Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<applet load=1ca2 size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>CBI Carbonic Anhydrase Model</scene>

User:Krishna Reddy Ragupathi

2010-04-29T19:58:30Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<applet load=1ca2 size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

<scene name='User:Krishna_Reddy_Ragupathi/Test/1'>First Test</scene>
<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>Carbonic_Anhydrase</scene>

User:Krishna Reddy Ragupathi

2010-04-29T19:57:42Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<applet load=1ca2 size='[450,338]' frame='true' align='right'
caption='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2' />

<scene name='User:Krishna_Reddy_Ragupathi/Test/1'>First Test</scene>
<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>Carbonic_Anhydrase</scene>

User:Krishna Reddy Ragupathi

2010-04-27T13:40:09Z

Krishna Reddy Ragupathi:

Gaduate student in Chemistry at University of Massachuesetts (Amherst).
In the CBI program.

<applet size='[450,338]' frame='true' align='right'
caption='Carbonic Anhydrase' />

<scene name='User:Krishna_Reddy_Ragupathi/Test/1'>First Test</scene>
<scene name='User:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/2'>Carbonic_Anhydrase</scene>

User talk:Krishna Reddy Ragupathi

2010-04-27T04:47:54Z

Krishna Reddy Ragupathi: Carbonic Anhydrase

'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! [[User:Eran Hodis|Eran Hodis]] 15:42, 16 March 2010 (IST)

== Carbonic Anhydrase ==

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />
<scene name='User_talk:Krishna_Reddy_Ragupathi/Carbonic_anhydrase/1'>CA</scene>

User:Krishna Reddy Ragupathi

2010-04-27T01:41:22Z

Krishna Reddy Ragupathi:

User:Krishna Reddy Ragupathi/Sandbox 1

2010-04-26T18:21:18Z

Krishna Reddy Ragupathi: Replacing page with 'Krishna Reddy Ragupathi'

Krishna Reddy Ragupathi

User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T15:51:25Z

Krishna Reddy Ragupathi:

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caption='YYY' />
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User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T15:25:36Z

Krishna Reddy Ragupathi:

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caption='YYY' />
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User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T15:15:52Z

Krishna Reddy Ragupathi:

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caption='YYY' />
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User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T15:10:52Z

Krishna Reddy Ragupathi:

User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T15:03:31Z

Krishna Reddy Ragupathi:

User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T14:50:52Z

Krishna Reddy Ragupathi:

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caption='YYY' />
<scene name='User:Krishna_Reddy_Ragupathi/Sandbox_1/Ca/4'>TextToBeDisplayed</scene>

User:Krishna Reddy Ragupathi/Sandbox 1

2010-03-16T14:30:08Z

Krishna Reddy Ragupathi: New page: Krishna

Krishna