CBI Molecules

From Proteopedia

Revision as of 18:17, 11 May 2010

These are molecules under study by members of the University of Massachusetts Amherst Chemistry-Biology Interface Program. Many of the molecules we study are featured at the Molecular Playground. Follow the links below to read nontechnical descriptions in Proteopedia.

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

Bhatia Lab: Molecular Playground/Alginate, David Griffin

Chambers Lab: Molecular Playground/Glutamate Receptor, Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

Forbes Lab: Molecular Playground/TRAIL, Charley Swofford

Garman Lab: Molecular Playground/Human Protective Protein Cathepsin A, Yadilette Rivera-Colon

Molecular Playground/Human PPCA, Nilima Kolli

Gierasch Lab: Molecular Playground/CRABP I, Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy

Hardy Lab

Molecular Playground/Caspase-7 Dynamics, Hardy Lab (Daniel Seeman)

Molecular Playground/Caspase-9 Regulation, Hardy Lab (Kristen Huber)

Molecular Playground/Influenza A M2 transmembrane domain, (Samantha Nicholls)

Hebert Lab

Molecular_Playground/ERMan1, (Johan Sunryd)

Kaltashov Lab

Molecular Playground/Velaglucerase, Adriana Kita,

Knapp lab

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, (Cristina Martin)

Molecular Playground/FIH, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

Martin Lab

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

Roberts Lab

Molecular Playground/Taxol, (Rohan Patil)

Molecular Playground/Insulin, (Whitney Stoppel)

Rotello Lab

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

Molecular Playground/6-Deoxyerythronolide B Synthase, (Tsung-Yi Lin)

Thayumanavan Lab

Molecular Playground/Lysozime , Daniella Gonzalez,

Molecular Playground/Beta-galactosidase, Judy Ventura,

Molecular Playground/Carbonic Anhydrase, (Krishna Reddy Raghupathi)

Molecular Playground/Avidin,Rami Rajasekar Reddy

Molecular Playground/Biotin binding avidin, Diego Amado

Molecular Playground/MMP12, (Jiaming Zhuang)

Molecular Playground/Gluconase, (Jing Guo)

Molecular Playground/Glutathione Reductase, (Reuben Chacko)

Thayumanavan & Vachet Labs

Molecular Playground/Trypsin,(Murage, Gladys)

Thompson & Weis Labs

Molecular Playground/Bacterial Chemotaxis Receptors,

Vachet Lab

Molecular playground/beta 2 microglobulin, (Nick)

Other UMass labs: Molecular Playground/YKL-40, Ralph A. Francescone III, Shao Lab

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.