Proteopedia - User contributions [en]

CBI Molecules

2011-12-16T20:02:32Z

Whitney Stoppel:

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] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.

Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries.

==Molecules==
Bhatia Lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://openwetware.org/wiki/Chien Chien Lab]

: '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau
:: Best CBI Molecule 2011

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang

: '''[[Molecular Playground/RBP]]''', Jan Panteli

: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon

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

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy
:: Best Overall CBI Molecule 2010

: NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/Caspase-7 Dynamics]]'''

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin
:: Best CBI Molecule Proteopedia Page 2010

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia
:: Best CBI Molecule 2011
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

: NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://roberts.openwetware.org/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson

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

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino

: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang

: '''[[Molecular playground/Chymotrypsin]]''', Brad

: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

Schnarr Lab

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

Thayumanavan Lab

: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez

: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura

: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi

: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy

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

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

: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo

: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

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

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang

: New Fall 2011 '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''

Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.

Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.

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. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).

5. 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.

6. Choose a "green scene" on your Proteopedia page to suggest for display at the Molecular Playground and specify a "banner" which will be projected with the molecule. 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."

7. 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.

8. 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 examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.

==Links to HELP pages==
Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

CBI Molecules

2010-04-30T21:08:31Z

Whitney Stoppel:

2010-04-29T23:41:15Z

Whitney Stoppel:

'''Insulin'''

Insulin is a hormone that controls sugar metabolism and storage in the human body. The body is able to sense the concentration of glucose in the blood and respond by secreting insulin, which is produced by beta cells in the pancreas. Synthesis of human insulin in E. coli is important to producing insulin for the treatment of type 1 diabetes. The hydrophobic portions of the insulin monomer lead to aggregation over time in hydrophilic solutions, initially causing problems in the manufacture and storage for pharmaceutical use.

Insulin is made up of two pieces called the A- and B-chain. These two chains are joined by two disulfide bonds. This single piece made up of the A- and B-chains is the active form of the insulin hormone. This is the form that binds the insulin receptor on fat or muscle cells in the body, singling them to take up glucose, or sugar, from the blood and save it for later.

Insulin is able to pair-up with itself and form a dimer by forming hydrogen bonds between the ends of two B-chains. Then, 3 dimers can come together in the presence of zinc ions and form a hexamer. Insulin is stored in the hexameric form in the body.

<scene name='User:Whitney_Stoppel/sandbox1/Insulin_hexamer/2'>Symmetric Insulin Hexamer</scene>

User:Whitney Stoppel/sandbox1

2010-04-28T18:29:13Z

Whitney Stoppel:

User:Whitney Stoppel/sandbox1

2010-04-28T18:23:57Z

Whitney Stoppel:

User:Whitney Stoppel/sandbox1

2010-04-28T18:23:37Z

Whitney Stoppel:

User:Whitney Stoppel/sandbox1

2010-04-28T18:23:04Z

Whitney Stoppel:

<math>Insert formula here</math>'''Insulin'''</n>
Insulin is a hormone that controls sugar metabolism and storage in the human body. The body is able to sense the concentration of glucose in the blood and respond by secreting insulin, which is produced by beta cells in the pancreas. Synthesis of human insulin in E. coli is important to producing insulin for the treatment of type 1 diabetes. The hydrophobic portions of the insulin monomer lead to aggregation over time in hydrophilic solutions, initially causing problems in the manufacture and storage for pharmaceutical use.

<scene name='User:Whitney_Stoppel/sandbox1/Human_insulin/1'>Insulin dimer synthesized in E. coli</scene></n>
<scene name='User:Whitney_Stoppel/sandbox1/Human_insulin/2'>Hydrophobic (gray) and polar (purple) portions of the insulin dimer</scene>

User:Whitney Stoppel/sandbox1

2010-04-28T18:21:32Z

Whitney Stoppel:

File:HumanInsulin.pdb

2010-04-28T17:28:45Z

Whitney Stoppel: uploaded a new version of "Image:HumanInsulin.pdb"

Human Insulin

File:HumanInsulin.pdb

2010-04-28T17:24:03Z

Whitney Stoppel: uploaded a new version of "Image:HumanInsulin.pdb": Human Insulin

Human Insulin

File:HumanInsulin.pdb

2010-04-28T17:21:46Z

Whitney Stoppel: Human Insulin

Human Insulin

User:Whitney Stoppel/sandbox1

2010-04-28T17:19:15Z

Whitney Stoppel: New page: '''Insulin'''

'''Insulin'''