Proteopedia - User contributions [en]

CBI Molecules

2010-05-01T02:52:32Z

Nilima Kolli:

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]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (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, [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]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (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 ([http://www.biochem.umass.edu/garman/index.html Garman Lab])

'''[[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]]''', Thai lab (Jiaming Zhuang)

'''[[Molecular Playground/Pancreatic Lipase]]''', [http://www.umass.edu/rotellogroup/ Rotello lab] (Rui Tang)

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

'''[[Molecular playground/beta 2 microglobulin]]''', Vachet lab (Nick)

''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Thai lab (Jing Guo)

'''[[Molecular playground/Chymotrypsin]]''', Rotello lab (Brad)

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

2010-05-01T02:51:51Z

Nilima Kolli:

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]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (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, [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]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (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 [http://www.biochem.umass.edu/garman/index.html Garman Lab]

'''[[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]]''', Thai lab (Jiaming Zhuang)

'''[[Molecular Playground/Pancreatic Lipase]]''', [http://www.umass.edu/rotellogroup/ Rotello lab] (Rui Tang)

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

'''[[Molecular playground/beta 2 microglobulin]]''', Vachet lab (Nick)

''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Thai lab (Jing Guo)

'''[[Molecular playground/Chymotrypsin]]''', Rotello lab (Brad)

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/Human PPCA

2010-04-30T16:30:59Z

Nilima Kolli: New page: 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://...

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].

Human protective protein/cathepsin A (PPCA) is a lysosomal serine carboxypeptidase that has a chaperoning function towards two other lysosomal enzymes, lysosomal neuraminidase (Neu1) and beta-galactosidase (Glb1). Deficiency of this enzyme causes the autosomal recessive disease galactosialidosis for which there is no known treatment. Due to the secondary deficiencies of Neu1 and Glb1 in these patients the substrates of PPCA protease activity are not clearly known. PPCA is synthesized as a dimer (each monomer is 54kDa single chain) that undergoes processing in the lysosome to form a dimer of heterodimers, 32kDa and 20kDa subunits. The processing involves the removal of a 2kDa peptide called the excision peptide and consequent conformational changes to form the mature enzyme.

{{Clear}}
<applet load='1ivy' size='[450,338]' frame='true' align='right'
caption='Human Protective Protein/Cathepsin A (PPCA, 1IVY)' scene='User:Nilima_Kolli/sandbox_1/Homodimer_ppca/1'/>

The dimer of <scene name='User:Nilima_Kolli/sandbox_1/PPCA/1'>PPCA</scene> is shown here in cartoon representation. The active site residues are in red with the disulphides in yellow. The catalytically competent active site is blocked by the 'blocking peptide' shown in cyan. The excision peptide shown in dark blue is positioned above the blocking peptide thus completely occluding the active site. The excision peptide is removed during processing which is assumed to result in local conformational changes that then remove the blocking peptide from occluding the active site.

Molecular Playground banner: Human lysosomal protease that exhibits chaperoning function.

CBI Molecules

2010-04-30T16:28:17Z

Nilima Kolli:

CBI Molecules

2010-04-30T16:27:11Z

Nilima Kolli:

CBI Molecules

2010-04-30T16:26:34Z

Nilima Kolli:

Molecular Playground/PPCA

2010-04-30T16:25:03Z

User:Nilima Kolli/sandbox 1

2010-04-30T16:23:25Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-30T16:19:03Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-30T16:11:46Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-30T16:06:21Z

Nilima Kolli:

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].

Human protective protein/cathepsin A (PPCA) is a lysosomal serine carboxypeptidase that has a chaperoning function towards two other lysosomal enzymes, lysosomal neuraminidase (Neu1) and beta-galactosidase (Glb1). Deficiency of this enzyme causes the autosomal recessive disease galactosialidosis for which there is no known treatment. Due to the secondary deficiencies of Neu1 and Glb1 the substrates of PPCA protease activity are not clearly known. It is synthesized as a 54kDa homodimer that undergoes processing in the lysosome to form a dimer of heterodimers, 32kDa and 20kDa subunits. The processing involves the removal of a 2kDa peptide called the excision peptide and consequent conformational changes to form the mature enzyme.

{{Clear}}
<applet load='1ivy' size='[450,338]' frame='true' align='right'
caption='Human Protective Protein/Cathepsin A (PPCA, 1IVY)' scene='User:Nilima_Kolli/sandbox_1/Homodimer_ppca/1'/>

The homodimer of <scene name='User:Nilima_Kolli/sandbox_1/Homodimer_ppca/1'>PPCA</scene> is shown here in cartoon representation. The active site residues are in red with the disulphides in yellow. The catalytically competent active site is blocked by the 'blocking peptide' shown in cyan. The excision peptide shown in dark blue is positioned above the blocking peptide thus completely occluding the active site. The excision peptide is removed during processing which is assumed to result in local conformational changes that then remove the blocking peptide from occluding the active site.

User:Nilima Kolli/sandbox 1

2010-04-28T19:46:22Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-28T19:29:08Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-28T19:19:00Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-28T18:50:56Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-28T18:49:11Z

Nilima Kolli:

User:Nilima Kolli/sandbox 1

2010-04-28T18:45:33Z

Nilima Kolli:

[[Image:intactModelLargeText.jpg|frame|Human Protective Protein/Cathepsin A (PPCA)]]

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].

File:1IVY.pdb

2010-04-28T03:01:28Z

Nilima Kolli: PPCA

PPCA

User:Nilima Kolli/sandbox 1

2010-04-28T02:57:02Z

Nilima Kolli: New page: <applet size='[450,338]' frame='true' align='right' caption='YYY' />