Proteopedia - User contributions [en]

Molecular Playground/Pancreatic Lipase

2010-04-30T21:19:14Z

Rui Tang:

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }}
==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Coupled with two <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>non-amino acid ligands</scene>, Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary triglycerides. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:18:12Z

Rui Tang:

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }}
==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Coupled with two<scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>special ligands</scene>, Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary triglycerides. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:13:53Z

Rui Tang:

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }}
==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:12:45Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }}
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:12:21Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }} <scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:10:42Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }}

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:10:17Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

{{STRUCTURE_1lpa| PDB=1lpa | SCENE='User:Rui_Tang/Sandbox_1/Description/1' size='[450,338]' align='right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' }}
<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:07:04Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:06:37Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<STRUCTURE_3hvt| PDB=3jyt | scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T21:05:52Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<applet STRUCTURE_3hvt| PDB=3jyt | size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

CBI Molecules

2010-04-30T20:26:09Z

Rui Tang:

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]]''', 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]]''', [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.

CBI Molecules

2010-04-30T20:09:57Z

Rui Tang:

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

'''[[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

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

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

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

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

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

'''[[Molecular Playground/Glutamate Receptor]]''', 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)

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/Pancreatic Lipase

2010-04-30T20:05:52Z

Rui Tang:

==Pancreatic Lipase==
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 in [http://www.umass.edu/rotellogroup/ Rotello's Group] and on display at the [http://www.molecularplayground.org/ Molecular Playground].

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

CBI Molecules

2010-04-30T20:04:08Z

Rui Tang:

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

'''[[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

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

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

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

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

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

'''[[Molecular Playground/Glutamate Receptor]]''', 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]]''', Rui Tang

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

2010-04-30T20:03:41Z

Rui Tang:

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

'''[[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

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

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

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

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

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

'''[[Molecular Playground/Glutamate Receptor]]''', 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]]''', Rui Tang
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/Pancreatic Lipase

2010-04-30T19:57:14Z

Rui Tang:

==Pancreatic Lipase==
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].

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T19:54:04Z

Rui Tang:

==Pancreatic Lipase==
<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

Molecular Playground/Pancreatic Lipase

2010-04-30T19:53:27Z

Rui Tang: New page: ==Pancreatic Lipase== 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 ...

==Pancreatic Lipase==
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= }}

User:Rui Tang/Sandbox 1

2010-04-30T19:10:13Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats in our bodies' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

User:Rui Tang/Sandbox 1

2010-04-30T17:08:10Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase: an enzyme help us digest the fats' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than that of the bulk ones.

User:Rui Tang/Sandbox 1

2010-04-30T17:05:46Z

Rui Tang:

User:Rui Tang/Sandbox 1

2010-04-30T04:46:40Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emulsified by bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of the emulsions of fat than the bulk ones.

User:Rui Tang/Sandbox 1

2010-04-30T04:45:43Z

Rui Tang:

User:Rui Tang/Sandbox 1

2010-04-30T04:45:14Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene>, which can hydrolyze the ester bond in a wide range of ester compounds, is a 46KD, water-soluble enzyme secreted from pancreas.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>. triglycerides are firstly emusified by Bile salts in the duodenum. And then, the lipase can break them into fat acids and glycerol more efficiently due to larger surface area of emusion of fat than the bulk ones.

User:Rui Tang/Sandbox 1

2010-04-30T04:36:56Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene> is a 46KD enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.

Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>.

User:Rui Tang/Sandbox 1

2010-04-30T04:36:03Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene> is a 46KD enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.Pancreatic lipase is clearly essential for the efﬁcient digestion of dietary <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>triglycerides</scene>.

User:Rui Tang/Sandbox 1

2010-04-30T04:32:15Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene> is a 46KD enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.

The <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>active site</scene> of this enzyme includes one serine, one glutamate and one histidine.

User:Rui Tang/Sandbox 1

2010-04-30T04:31:32Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene> is a 46KD enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.
The <scene name='User:Rui_Tang/Sandbox_1/Substrate/2'>active site</scene> of this enzyme includes one serine, one glutamate and one histidine.

User:Rui Tang/Sandbox 1

2010-04-30T04:21:10Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/3'>Pancreatic lipase</scene> is a type of enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.
<scene name='User:Rui_Tang/Sandbox_1/Description/4'>TextToBeDisplayed</scene>

User:Rui Tang/Sandbox 1

2010-04-30T04:15:18Z

Rui Tang:

User:Rui Tang/Sandbox 1

2010-04-30T04:12:54Z

Rui Tang:

<applet size'[450, 338]' load='1lpa' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/1'>Pancreatic lipase</scene> is a type of enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.

User:Rui Tang/Sandbox 1

2010-04-30T04:11:12Z

Rui Tang:

<applet size'[450, 338]' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/1'>Pancreatic lipase</scene> is a type of enzyme secreted pancreas which can hydrolyze the ester bond in a wide range of ester compounds.

User:Rui Tang/Sandbox 1

2010-04-30T03:38:22Z

Rui Tang:

<applet size'[450, 338]' frame='true' align= 'right' caption='Pancreatic lipase' />
<scene name='User:Rui_Tang/Sandbox_1/Description/1'>Description</scene>

User:Rui Tang/Sandbox 1

2010-04-30T03:33:25Z

Rui Tang: New page: <applet size'[450, 338]' frame='true' align= 'right' caption='Pancreatic lipase' />

User:Rui Tang/Building

2010-04-29T18:42:06Z

Rui Tang:

hello, World!

<applet load= '3HAK' size='[445,338]' frame='true' align='center' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/3/5'>TextToBeDisplayed</scene>

User:Rui Tang/Building

2010-03-16T15:44:03Z

Rui Tang:

hello, World!

<applet load= '3HAK' size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/3/5'>TextToBeDisplayed</scene>

User:Rui Tang/Building

2010-03-16T15:34:17Z

Rui Tang:

User:Rui Tang/Building

2010-03-16T15:25:37Z

Rui Tang:

hello, World!

<applet size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/1/4'>Part 1</scene>

<scene name='User:Rui_Tang/Building/2/1'>Part 2</scene>

<scene name='User:Rui_Tang/Building/3/1'>Part 3</scene>

<scene name='User:Rui_Tang/Building/3/4'>TextToBeDisplayed</scene>

User:Rui Tang/Building

2010-03-16T15:24:17Z

Rui Tang:

hello, World!

<applet size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/1/4'>Part 1</scene>

<scene name='User:Rui_Tang/Building/2/1'>Part 2</scene>

<scene name='User:Rui_Tang/Building/3/1'>Part 3</scene>
<scene name='User:Rui_Tang/Building/3/3'>TextToBeDisplayed</scene>

User:Rui Tang/Building

2010-03-16T15:11:37Z

Rui Tang:

User:Rui Tang/Building

2010-03-16T15:11:21Z

Rui Tang:

hello, World!

<apple size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/1/4'>Part 1</scene>

<scene name='User:Rui_Tang/Building/2/1'>Part 2</scene>

User:Rui Tang/Building

2010-03-16T15:11:06Z

Rui Tang:

hello, World!

<apple' size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/1/1'>Part 1</scene>

<scene name='User:Rui_Tang/Building/2/1'>Part 2</scene>

User:Rui Tang/Building

2010-03-16T15:08:30Z

Rui Tang:

User:Rui Tang/Building

2010-03-16T15:07:20Z

Rui Tang:

User:Rui Tang/Building

2010-03-16T15:02:05Z

Rui Tang:

User:Rui Tang/Building

2010-03-16T15:00:00Z

Rui Tang:

User:Rui Tang/Building

2010-03-16T14:58:06Z

Rui Tang:

hello, World!

<size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/1/2'>Part 1</scene>

User:Rui Tang/Building

2010-03-16T14:49:24Z

Rui Tang:

hello, World!

<applet load='3HAK' size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

<applet load='3HAF' size='[445,338]' frame='true' align='right' caption='Human prion protein variant V129 domain swapped dimer' />

This is the first part of this demo.

<scene name='User:Rui_Tang/Building/1/2'>Part 1</scene>

User:Rui Tang/Building

2010-03-16T14:48:33Z

Rui Tang:

hello, World!

<applet load='3HAK' size='[445,338]' frame='true' align='left' caption='Human prion protein variant V129' />

<applet load='3HAF' size='[445,338]' frame='true' align='right' caption='Human prion protein variant V129 domain swapped dimer' />

Copy and paste the following line where you want the scene link to appear (scroll down if needed) and edit the TextToBeDisplayed:

<scene name='User:Rui_Tang/Building/1/2'>TextToBeDisplayed</scene>

User:Rui Tang/Building

2010-03-16T14:46:33Z

Rui Tang:

hello, World!

<applet load='3HAK' size='[445,338]' frame='false' align='left' caption='Human prion protein variant V129' />

<applet load='3HAF' size='[445,338]' frame='false' align='right' caption='Human prion protein variant V129 domain swapped dimer' />