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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 2013: CBI Molecules are due 12/4/13 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 2013" or "Revised 2013". For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).


Molecules

** Designates CBI Molecules Featured on CBI website

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


Chambers Lab

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


Chen Lab

New Fall 2013!! Molecular Playground/ClyA, Bib Yang
Updated Fall 2013!! Molecular Playground/OmpG, Christina Chisholm

Chien Lab

New Fall 2013! : **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


Forbes Lab

Molecular Playground/CheR, Miaomin Zhang
Molecular Playground/RBP, Jan Panteli
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
Best Overall CBI Molecule 2010
Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein), Gustavo Elberto Epalza Sanchez

(compare this to the previous version above to see what's new)

**Molecular_Playground/DHFR, Karan Hingorani
Best CBI Molecule 2012


Hardy Lab

New Fall 2013!! 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

New Fall 2013!! Molecular_Playground/Hsp70-Hsp90, Jill Graham
New Fall 2012!! Molecular_Playground/ERDj5, Lydia Lamriben
Molecular Playground/Saposin C, Abla Tannous
Molecular_Playground/ERMan1, Johan Sunryd


Heuck Lab

Updated Fall 2012!! Molecular_Playground/Pcr H, Fabian Romano, Carolina Morell-Pérez


Holden Lab

New Fall 2012!! Molecular Playground/Protective Antigen, Jing Huang


Kaltashov Lab

New 2013! Molecular Playground/Inteferon, Chengfeng Ren
Updated Fall 2012!! Molecular Playground/Transferrin, Khaja Muneeruddin, Jake Pawlowski
Molecular Playground/Velaglucerase, Adriana Kita
New Summer 2014!! Molecular Playground/Antithrombin-Heparin, Yunlong Zhao



Knapp lab

Updated Fall 2013!! Molecular Playground/FIH, Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky
Updated Fall 2012!! Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme, Cristina Martin, Serap Pektas
Best CBI Molecule Proteopedia Page 2010



Maroney Lab

Molecular Playground/Nickel Superoxide Dismutase, Carolyn Carr
Updated Fall 2013!! Molecular Playground/CsoR and RcnR, Heidi Hu, Carolyn Carr
Molecular Playground/HypA, Heidi Hu


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

New Fall 2013! Molecular Playground/MMP14, Lauren Jansen
Molecular Playground/C-Raf, Thuy Nguyen
Molecular Playground/FAK, Dannielle Ryman

Roberts Lab

Molecular Playground/Taxol, Rohan Patil, Sarah Wilson
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

Schiffman Lab

New Fall 2013! Molecular Playground/Streptavidin, Katrina Rieger

Schnarr Lab

New Fall 2012!! Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp), Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey
Molecular Playground/6-Deoxyerythronolide B Synthase, Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey
Molecular Playground/ACP apo, Gitanjeli Prasad


Schnell Lab

New Fall 2012!! Molecular Playground/Tic40, Mine Canakci



Tew Lab

Updated Fall 2013!! Molecular Playground/HIV Tat, Brittany deRonde


Thayumanavan Lab

New Fall 2013!! 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/MMP12, Jiaming Zhuang
Molecular Playground/Gluconase, Jing Guo
Molecular Playground/Glutathione Reductase, Reuben Chacko

Thayumanavan & Vachet Labs

Molecular Playground/Trypsin, Gladys Murage


Thompson & Weis Labs

New Fall 2013!! Molecular Playground/Bacterial Chemotaxis Complex, Elizabeth R. Haglin, Maryam Kashefi
New Fall 2012!! Molecular Playground/CheA, Elizabeth R. Haglin
Molecular Playground/Bacterial Chemotaxis Receptors, Lynmarie K. Thompson, Shiela M. Jones
Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor, Meili Yang
Updated 2013!! Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima, Xuni Li


Vachet Lab

New Fall 2013!! Molecular Playground/Human Serum Albumin, Mahalia Serrano
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
Molecular Playground/Ubiquitin salt bridge discussion, Zhe Zhang


Other Molecules of interest

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


Other Laboratories

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

Instructions

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 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321.

A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). 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 and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop.

3. Get started working in Proteopedia by using the links at Help:Contents. 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. 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).

4. For those editing an existing CBI Molecule, start from that entry 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 do some editing of the molecule so that they each 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 2013" or "revised 2013".

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, Khaja Muneeruddin, Yuping Zhou, Daniel Seeman, Eric Martz, Brittany deRonde, Luis E Ramirez-Tapia, Lawrence Sheringham Borketey, Gitanjeli Prasad, Heidi Hu, Derek MacPherson, Carolyn Carr, Yadilette Rivera-Colon, Tsung-Yi Lin, Lauren Jansen, Chengfeng Ren, Kamal K. Joshi, Kevin Buadlart Dagbay, Miaomin Zhang, Whitney Stoppel, Nick Borotto, Yunlong Zhao, Bib Yang, 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, Joe White, Abla Tannous, Ankit Vahia, Shaynah Browne, Mahalia Serrano, 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, Mariel Feliciano, Dannielle Ryman, Diego Amado-Torres, Jaime Prilusky, Maryam Kashefy, Erika M. Saffer, Vanessa Chaplin, 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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