CBI Molecules

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; follow the instructions below the list.

Molecular Playground/Bacterial Chemotaxis Receptors, Thompson & Weis laboratories

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, Roberts Research Group (Rohan Patil)

Molecular Playground/Human Protective Protein Cathepsin A, Yadilette Rivera-Colon, Garman Research Group

Molecular Playground/YKL-40, Ralph A. Francescone III, Shao Lab

Molecular Playground/Reverse Transcriptase, Rotello lab (Daniel Moyano-Marino)

Molecular Playground/Carbonic Anhydrase, Thai lab (Krishna Reddy Raghupathi)

Molecular Playground/Avidin, Thai lab (Rami Rajasekar Reddy)

Molecular_Playground/ERMan1, Johan Sunryd

Molecular Playground/Insulin, Roberts Research Group (Whitney Stoppel)

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

Molecular Playground/Human PPCA, Nilima Kolli (Garman Lab)

Molecular Playground/Alginate, Bhatia Research Group (David Griffin)

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

Molecular Playground/Biotin binding avidin, Diego Amado (Thai Lab)

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

Molecular Playground/MMP12, Thai lab (Jiaming Zhuang)

Molecular Playground/Pancreatic Lipase, Rotello lab (Rui Tang)

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

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

Molecular Playground/Gluconase, Thai lab (Jing Guo)

Molecular playground/Chymotrypsin, Rotello lab (Brad)

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

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

Molecular Playground/Glutathione Reductase, Thai Lab (Reuben Chacko)

Molecular Playground/Velaglucerase, Adriana Kita, Kaltashov 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, Hardy Lab[1] (Samantha Nicholls)

Molecular Playground/Targeting Peptide, Rotello Lab (David Solfiell)

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.