Proteopedia - User contributions [en]

CBI Molecules

2010-04-30T20:41:07Z

Rohan Patil:

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, [http://robertsgroup.ecs.umass.edu/ Roberts Research Group]

'''[[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, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

'''[[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.

Molecular Playground/Taxol

2010-04-30T00:35:30Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. Paclitaxel is a complex diterpenoid product, with a bulky, fused ring system as well as a number of hydrophobic substituents. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (also known as Taxol)' /> <scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Molecular Playground Banner: "Paclitaxel (Taxol),a plant-derived natural product to treat cancer"

Molecular Playground/Taxol

2010-04-29T21:23:02Z

Rohan Patil:

Molecular Playground/Taxol

2010-04-29T21:20:42Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''.Paclitaxel is a complex diterpenoid product, with a bulky, fused ring system as well as a number of hydrophobic substituents. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (also known as Taxol)' /> <scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Molecular Playground Banner: "Paclitaxel (Taxol), a natural product with anti-cancer activity"

Rohan Patil/Sandbox1

2010-04-29T21:14:27Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

Link to Roberts Lab: http://robertsgroup.ecs.umass.edu/

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (also known as Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel [Molecular formula :C47H51NO14] </scene>

Molecular Playground Banner : "Paclitaxel (Taxol), a natural product with anti-cancer activity"

Rohan Patil/Sandbox1

2010-04-29T21:13:49Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

Link to Roberts Lab: http://robertsgroup.ecs.umass.edu/

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel ( also known as Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel [Molecular formula :C47H51NO14] </scene>

Molecular Playground Banner : "Paclitaxel (Taxol), a natural product with anti-cancer activity"

Rohan Patil/Sandbox1

2010-04-29T20:53:33Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

Link to Roberts Lab: http://robertsgroup.ecs.umass.edu/

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Molecular Playground Banner : "Paclitaxel (Taxol), a natural product with anti-tumor activity"

Rohan Patil/Sandbox1

2010-04-29T20:43:39Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

Link to Roberts Lab: http://robertsgroup.ecs.umass.edu/

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Molecular Playground Banner : "Paclitaxel (Taxol),

CBI Molecules

2010-04-29T20:38:56Z

Rohan Patil:

CBI Molecules

2010-04-28T20:01:49Z

Rohan Patil:

Molecular Playground/Taxol

2010-04-28T19:59:59Z

Rohan Patil: New page: Paclitaxel (Taxol) A CBI Molecule being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] a...

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Rohan Patil/Sandbox1

2010-04-28T18:14:29Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Rohan Patil/Sandbox1

2010-04-28T18:13:59Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, ''Taxus brevifolia''. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through ''Taxus'' cell suspension cultures. ''Taxus'' cell suspension culture is an alternative to stripping bark from ''Taxus'' trees and extracting precursors from needles.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

File:Taxol.png

2010-04-28T18:03:42Z

Rohan Patil: uploaded a new version of "Image:Taxol.png"

Rohan Patil/Sandbox1

2010-04-28T18:01:16Z

Rohan Patil:

[[Image:taxol.png|frame|Paclitaxel (Taxol)]]

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].

Paclitaxel, also called as Taxol, is a plant derived anticancer drug. It was first isolated from the bark of Pacific yew tree, Taxus brevifolia. It has been FDA approved for the treatment of ovarian, breast and non-small cell lung cancer. Taxol binds to the ends of microtubules and inhibits further microtubule elongation. This prevents the cell from dividing and causes the cell to die. Because cancer cells divide much quicker than normal cells, taxol predominantly attacks tumors.

Presently, taxol supply is made available either through a semi-synthetic route using precursors isolated from needles of yew species or through Taxus cell suspension cultures. Taxus cell suspension culture is an alternative to stripping bark from Taxus trees and extracting precursors from needles.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Rohan Patil/Sandbox1

2010-04-28T17:43:44Z

Rohan Patil:

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.

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Rohan Patil/Sandbox1

2010-04-28T17:43:04Z

Rohan Patil:

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>Paclitaxel</scene>

Rohan Patil/Sandbox1

2010-04-28T17:33:54Z

Rohan Patil:

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>TextToBeDisplayed</scene>

Rohan Patil/Sandbox1

2010-04-28T17:26:37Z

Rohan Patil:

<applet size='[450,338]' frame='true' align='right'
caption='Paclitaxel (Taxol)' />

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>TextToBeDisplayed</scene>

Rohan Patil/Sandbox1

2010-04-28T17:25:40Z

Rohan Patil:

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

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>TextToBeDisplayed</scene>

Rohan Patil/Sandbox1

2010-04-28T17:23:10Z

Rohan Patil:

<scene name='Rohan_Patil/Sandbox1/Taxol/6'>TextToBeDisplayed</scene>

File:Taxol.png

2010-04-28T05:40:10Z

Rohan Patil:

Rohan Patil/Sandbox1

2010-04-27T22:02:47Z

Rohan Patil: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...

==This is a placeholder==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3cin | PDB=3cin | SCENE= }}

File:Pdb 3926740124834-0.pdb

2010-04-27T21:57:36Z

Rohan Patil: