CBI Molecules

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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 (see also 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.

Fall 2014: CBI Molecules are due 12/3/14 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not). Follow the instructions at the bottom of this page.


** Designates CBI Molecules Featured on CBI website

Chen Lab

Molecular Playground/ClyA, Monifa Fahie, Bib Yang Revised 2014
Molecular Playground/OmpG, Christina Chisholm, Monifa Fahie, Bib Yang Revised 2014

Chien Lab

Molecular Playground/ClpP, Lisa Hernandez, Rob Vass New 2014
Molecular Playground/Homo-dimeric RcdA, Kamal K. Joshi
**Molecular Playground/Hexameric ClpX, Joanne Lau Best CBI Molecule 2011
Molecular Playground/DNA replication initiator DnaA, Jing Liu

Farkas Lab

Molecular Playground/CLOCK:BMAL1 heterodimer complex, Hui-Hsien Lin, Joseph Hardie, Michael Mingroni New 2014

Garman Lab

Molecular Playground/Human Protective Protein Cathepsin A, Yadilette Rivera-Colon
Molecular Playground/Human PPCA, Nilima Kolli

Gierasch Lab

Molecular_Playground/DnaK, Joseph Tilitsky, New 2014
Molecular Playground/CRABP I, Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy Best Overall CBI Molecule 2010
Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein), Gustavo Elberto Epalza Sanchez
**Molecular_Playground/DHFR, Karan Hingorani Best CBI Molecule 2012

Hardy Lab

Molecular Playground/Executioner Caspase-7, Derek MacPherson, Maureen E. Hill
Molecular Playground/Caspase-3 Regulatory Mechanisms, Scott Eron, Bay Serrano, Yunlong Zhao
Molecular Playground/Caspase-6 and neurodegeneration, Kevin Buadlart Dagbay
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/Hsp70-Hsp90, Jill Graham "Revised 2014"
Molecular_Playground/ERDj5, Lydia Lamriben
Molecular Playground/Saposin C, Abla Tannous
Molecular_Playground/ERMan1, Johan Sunryd

Heuck Lab

Molecular_Playground/Pcr H, Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang

Kaltashov Lab

**Molecular Playground/Hemoglobin-Haptoglobin Complex, Ololade Fatunmbi, Chibueze Egeruoh ***New Fall 2014***
Molecular Playground/Inteferon[Revised], Chengfeng Ren
Molecular Playground/Transferrin, Khaja Muneeruddin, Jake Pawlowski
Molecular Playground/Velaglucerase, Adriana Kita
Molecular Playground/Antithrombin-Heparin, Yunlong Zhao

Knapp Lab

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin, Serap Pektas Best CBI Molecule Proteopedia Page 2010 ***New Fall 2014***
Molecular Playground/FIH, Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky

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
Molecular Playground/Human mtRNA pol, Ketan Mathavan

Peyton Lab

Molecular Playground/IntegrinBeta1, Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***NEW FALL 2014'***
Molecular Playground/MMP14, Lauren Jansen
Molecular Playground/C-Raf, Thuy Nguyen
Molecular Playground/FAK, Dannielle Ryman

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

Schiffman Lab

Molecular Playground/Streptavidin, Katrina Rieger

Tew Lab

Molecular Playground/HIV Tat, Brittany deRonde, Coralie Backlund

Thayumanavan Lab

Interleukin-1 beta, Huan He
Molecular Playground/Lysozyme , 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/Gluconase, Jing Guo
Molecular Playground/Glutathione Reductase, Reuben Chacko
Molecular Playground/MMP9, Jiaming Zhuang, Mallory Gordon Revised 2014

Thayumanavan & Vachet Labs

Molecular Playground/Trypsin, Gladys Murage

Thompson Lab

Molecular Playground/Bacterial Chemotaxis Complex, Elizabeth R. Haglin, Maryam Kashefi "Revised 2014"
Molecular Playground/CheA, Elizabeth R. Haglin
Molecular Playground/Bacterial Chemotaxis Receptors, Lynmarie K. Thompson, Shiela M. Jones
Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima, Xuni Li

Vachet Lab

**Molecular Playground/Human Serum Albumin, Mahalia Serrano *Revised 2014*
Molecular playground/beta 2 microglobulin, Nick Borotto, Tyler Marcinko ***Revised Fall 2014*** Best CBI Molecule Jmol scenes 2010
Molecular Playground/Myoglobin, Yuping Zhou
Molecular Playground/ Copper-Zinc Superoxide Dismutase, Shaynah Browne
Molecular Playground/Ubiquitin salt bridge discussion, Zhe Zhang

Vierling Lab

Molecular Playground/sHSP, Keith Ballard New 2014

Other Molecules of interest

Molecular Playground/PcrA Helicase, Luis E Ramirez-Tapia, Martin Lab

Other Laboratories

Molecular Playground/UreE, Priyanka Basak, New 2014, Maroney Lab
Molecular Playground/Nickel Superoxide Dismutase, Carolyn Carr, Maroney Lab
Molecular Playground/CsoR and RcnR, Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, Revised 2014, Maroney Lab
Molecular Playground/HypA, Heidi Hu, Maroney Lab
Molecular Playground/Glutamate Receptor, Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano, Chambers Lab
Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp), Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
Molecular Playground/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab
Molecular Playground/ACP apo, Gitanjeli Prasad, Schnarr lab
Molecular Playground/CheR, Miaomin Zhang, Forbes Lab
Molecular Playground/RBP, Jan Panteli, Forbes Lab
Molecular Playground/TRAIL, Charley Swofford, Forbes Lab
Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor, Meili Yang, Weis lab
Molecular Playground/Taxol, Elizabeth Cummings, Rohan Patil, Sarah Wilson ***Revised Fall 2014***, Roberts Lab
Molecular Playground/Insulin, Whitney Stoppel, Roberts Lab
Molecular Playground/Alginate-Fall2011, Joe White, David Griffi, Bhatia Lab
Molecular Playground/Poly(ethylene glycol), Erika M. Saffer, Bhatia Lab
Molecular Playground/Tic40, Mine Canakci, Schnell Lab
Molecular Playground/Protective Antigen, Jing Huang, Holden Lab
Molecular Playground/YKL-40, Ralph A. Francescone III, Shao Lab
Molecular Playground/β-lactoglobulin, Daniel Seeman, Dubin Lab
Molecular Playground/ADAM13, Genevieve Abbruzzese, Alfandari Lab


The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.

Fall 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind.

A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. It's great if you can end with a brief statement about how it relates to your group's research goals.

1. If you don't already have one, request a Proteopedia account and log in.

2. Read through the rest of the instructions, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make.

3. Get started working in Proteopedia. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. Explore the HELP links below to learn how to make a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).

Complete the above steps before the CBI Molecule Workshop.

4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to log in as themself and create a green scene to get credit for their work and to appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2014" or "revised 2014". Minimize text; tell your story with green scenes!

6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption).

Links to HELP pages

Overview at Help:Contents

See also Help:Getting_Started_in_Proteopedia

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 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. 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 in the navigation box at the upper left of every page in Proteopedia.

Proteopedia Page Contributors and Editors (what is this?)

Lynmarie K Thompson, Carrie Morrison Penland, Lauren Jansen, Khaja Muneeruddin, Yuping Zhou, Daniel Seeman, Eric Martz, Brittany deRonde, Luis E Ramirez-Tapia, Lawrence Sheringham Borketey, Gitanjeli Prasad, Heidi Hu, Chengfeng Ren, Derek MacPherson, Carolyn Carr, Yadilette Rivera-Colon, Robert Vass, Mahalia Serrano, Bib Yang, Tsung-Yi Lin, Kamal K. Joshi, Maryam Kashefy, Vanessa Chaplin, Kevin Buadlart Dagbay, Ololade Fatunmbi, Keith Ballard, Miaomin Zhang, Elizabeth Cummings, Hsin-Ting Huang, Whitney Stoppel, Joseph Tilitsky, Nick Borotto, Yunlong Zhao, Xuni Li, Huan He, Joanne Lau, Katrina Rieger, Elizabeth R. Haglin, Rui Tang, Carolina Morell-Perez, Nilima Kolli, Jing Liu, Daniel Moyano-Marino, Thuy V. Nguyen, Jaime Prilusky, Joe White, Abla Tannous, Coralie Backlund, Ankit Vahia, Joseph Hardie, Shaynah Browne, Priyanka Basak, Mine Canakci, Banyuhay P. Serrano, Lydia Lamriben, Shiela M. Jones, Rohan Patil, Judy Ventura, Adriana Kita, Reuben Chacko, Gustavo Elberto Epalza Sanchez, David Griffin, Ketan Mathavan, Daniella C. Gonzalez-Toro, Kristine Faye Pobre, Mallory Gordon, Mariel Feliciano, Jill Graham, Tyler Marcinko, Dannielle Ryman, Diego Amado-Torres, Yuzhou Tang, Erika M. Saffer, Karan Hingorani, Genevieve Abbruzzese, Jiaming Zhuang, Krishna Reddy Ragupathi, Sarah Wilson, Zhe Zhang, Jan Panteli, Jing Huang, Christina Chisholm, Jake Pawlowski, Kristen Huber, Serap Pektas, Meili Yang, Muslum Yildiz, David Solfiell, Mangai Periasamy, Johan Sunryd, Cristina B. Martin, Bradley Duncan, Samantha B. Nicholls, Charles Swofford, Jing Guo, Gladys Wanjiku Murage, Rami Rajasekhar Reddy, John Hangasky, Ralph A. Francescone III

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