Proteopedia - User contributions [en]

CBI Molecules

2014-12-02T22:09:34Z

Hsin-Ting Huang:

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.

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.

==Molecules==
'''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]'''

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

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

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

: '''[[Molecular Playground/ClyA]]''', Bib Yang
: '''[[Molecular Playground/OmpG]]''', Christina Chisholm

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

: '''[[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

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]

: '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|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'''

[http://people.chem.umass.edu/jhardy/ 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
: '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[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, Carolina Morell-Pérez

[http://people.chem.umass.edu/mholden/ Holden Lab]

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

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

: '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]''', Chengfeng Ren
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao

Knapp lab

: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010'''

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014'''
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''
: '''[[Molecular Playground/HypA]]''', Heidi Hu

[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
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ 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

[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

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
: '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde

Thayumanavan Lab
: '''[[Interleukin-1 beta]]''', Huan He
: '''[[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 Lab]

: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi
: '''[[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

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

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

Other Laboratories

:'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|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/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab

: '''[[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==

'''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: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

2014-12-02T22:08:55Z

Hsin-Ting Huang:

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.

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.

==Molecules==
'''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]'''

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

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

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

: '''[[Molecular Playground/ClyA]]''', Bib Yang
: '''[[Molecular Playground/OmpG]]''', Christina Chisholm

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

: '''[[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

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]

: '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|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'''

[http://people.chem.umass.edu/jhardy/ 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
: '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[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, Carolina Morell-Pérez

[http://people.chem.umass.edu/mholden/ Holden Lab]

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

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

: '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]''', Chengfeng Ren
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao

Knapp lab

: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010'''

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: '''[[Molecular Playground/UreE]]''', Priyanka Basak, New 2014
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''
: '''[[Molecular Playground/HypA]]''', Heidi Hu

[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
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ 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

[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

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
: '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde

Thayumanavan Lab
: '''[[Interleukin-1 beta]]''', Huan He
: '''[[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 Lab]

: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi
: '''[[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

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

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

Other Laboratories

:'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|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/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab

: '''[[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==

'''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: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.

Molecular Playground/CsoR and RcnR

2014-12-02T22:03:31Z

Hsin-Ting Huang:

Molecular Playground/CsoR and RcnR

2014-12-02T22:02:36Z

Hsin-Ting Huang:

Molecular Playground/CsoR and RcnR

2014-12-02T22:01:58Z

Hsin-Ting Huang:

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<applet load='2hh7' size='[400,388]' frame='true' align='right'
caption='Cu(I)-bound CsoR (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2HH7 2HH7])' />

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

== Introduction ==

Heavy metals such as iron, nickel, copper, and zinc are important cofactors for the functions of many different metalloenzymes. High levels of these heavy metals can also cause damage to cellular components, therefore intracellular levels of metals are tightly regulated within the cell. One of the ways that bacteria can regulate intracellular metal levels is by increasing the amount of metal efflux proteins. CsoR and RcnR are members of a large family of metal-responsive DNA-binding proteins, both of which regulate the transcription of metal-specific efflux proteins. CsoR is only responsive to the binding of Cu(I); whereas RcnR is only responsive to the binding of Ni(II) or Co(II).<ref>PMID:21511390</ref>

== RcnR and CsoR ==

In [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] apo-RcnR blocks the transcription of nickel and cobalt efflux proteins RcnA and RcnB by binding to its promoter region. Although no crystal structure of RcnR is available on the PDB, the Cu(I)-bound CsoR crystal structure from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] is available and RcnR is predicted to share a similar fold to CsoR. Upon Ni(II)- or Co(II)-binding, RcnR is released from DNA allowing the transcription of RcnA and RcnB, facilitating the efflux of Ni(II) and Co(II).<ref>PMID:20442957</ref> CsoR has been characterized in [http://en.wikipedia.org/wiki/Bacillus_subtilis ''Bacillus subtilis'']<ref>PMID:18048925</ref> and [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''M. tuberculosis'']<ref>PMID:17143269</ref> to release from the promoter regions of copper-efflux operons upon binding of Cu(I). The analogous functions of CsoR and RcnR in addition to local sequence similarity (25% identical, 56% similar) suggests a conserved mode of function in this family of metal-responsive DNA-binding proteins.<ref>PMID:18505253</ref>

== Structure of CsoR and RcnR ==

<scene name='Heidi_Hu/Sandbox_1/Tetrameric_csor/1'>Tetrameric CsoR</scene> binds one Cu(I) per monomer. The protein forms a dimer of dimers with a
<scene name='Heidi_Hu/Sandbox_1/Tetrameric_csor/5'>pore</scene> in the tetrameric interface. Each <scene name='Heidi_Hu/Sandbox_1/Tetrameric_csor/10'>Cu(I) coordinated by two different monomers</scene> of a dimer unit. Where one monomer is bound to Cu(I) by His61 and Cys65, the other monomer is bound to the metal by Cys35.<ref>PMID:17143269</ref> [http://en.wikipedia.org/wiki/Escherichia_coli ''E. coli'']
[[Image:Ni-and-Co-Site.jpg|500px|left|thumb|Fig. 1: Schematic of known Ni(II) and Co(II) binding residues in the metal sites of RcnR. Figure made with ChemDraw.]]
RcnR is also tetrameric and has the same protein-to-metal stoichiometry. Through a combination of site-directed mutagenesis, lacZ activity assays and X-ray absorption spectroscopy (XAS) structural studies it is now known that RcnR uses a different ligand set to bind Ni(II) than it does Co(II).

The Ni(II) site is bound by the N-terminal amine, Cys35, and His64.<ref>PMID: 23215580</ref><ref>PMID: 22471551</ref> Because the Ni(II) site has an octahedral geometry, there are three metal binding residues whose identity is unknown. However, using XAS and lacZ activity assays it is known that the remaining ligands bind to the Ni(II) using N/O atoms and that there are a total of two histidine ligand bound to the Ni(II), leaving the identity of one unaccounted for. Studies have shown that this histidine is not His3, His60, or His67.

The Co(II) site is bound by the the N-terminal amine, His3, Cys35, His64 and possibly His60. The Co(II) site of RcnR also has an octahedral geometry, leaving 1-2 residues whose identity is unknown. XAS reveals that these ligands are bound to Co(II) using N/O atoms and that there are a total of three histidine ligands bound to the Co(II). Studies have shown that His67 is not a Co(II) ligand.

== Research Interests ==

The mechanism of DNA binding of the CsoR/RcnR family of metal-responsive transcriptional regulators is still unknown. Additionally, RcnR has an added level of complexity because it is reponsive to both Ni(II) and Co(II) binding. The [http://people.chem.umass.edu/mmaroney/ Maroney Lab] at the University of Massachusetts Amherst is interested in the conformational changes of RcnR induced by DNA-, Ni(II)-, and Co(II)-binding. Identification of the remaining metal binding residues in RcnR is ongoing, in addition to identification of the DNA-binding residues in RcnR, as there is no crystal structure of any member of this family of proteins binding to DNA.

==3D structures of copper homeostasis protein==

[[Copper homeostasis protein]]

== References ==

<references/>

== Also See ==

[[2hh7]]

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<applet load='2hh7' size='[400,388]' frame='true' align='right'
caption='Cu(I)-bound CsoR (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2HH7 2HH7])' />

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

== Introduction ==

Heavy metals such as iron, nickel, copper, and zinc are important cofactors for the functions of many different metalloenzymes. High levels of these heavy metals can also cause damage to cellular components, therefore intracellular levels of metals are tightly regulated within the cell. One of the ways that bacteria can regulate intracellular metal levels is by increasing the amount of metal efflux proteins. CsoR, RcnR and InrS are members of a large family of metal-responsive DNA-binding proteins, all of which regulate the transcription of metal-specific efflux proteins. CsoR is only responsive to the binding of Cu(I); RcnR is responsive to the binding of Ni(II) or Co(II); whereas InrS is only responsive to the binding of Ni(II).<ref>PMID:21511390</ref><ref>PMID:22356910</ref>

== CsoR/RcnR Family ==

In [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''], apo-RcnR blocks the transcription of nickel and cobalt efflux proteins RcnA and RcnB by binding to its promoter region. Although no crystal structure of RcnR is available on the PDB, the Cu(I)-bound CsoR crystal structure from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] is available and RcnR is predicted to share a similar fold to CsoR. Upon Ni(II)- or Co(II)-binding, RcnR is released from DNA allowing the transcription of RcnA and RcnB, facilitating the efflux of Ni(II) and Co(II).<ref>PMID:20442957</ref> CsoR has been characterized in [http://en.wikipedia.org/wiki/Bacillus_subtilis ''Bacillus subtilis'']<ref>PMID:18048925</ref> and [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''M. tuberculosis'']<ref>PMID:17143269</ref> to release from the promoter regions of copper-efflux operons upon binding of Cu(I). InrS is another member of this metal-responsive transcriptional family recently found in [http://en.wikipedia.org/wiki/Synechocystis ''Synechocystis'']. InrS regulates cytosolic nickel level by releasing from the promoter regions of nickel-efflux operons upon Ni(II) binding.<ref>PMID:22356910</ref> The analogous functions of CsoR, RcnR and InrS in addition to local sequence similarity (RcnR has 24% identity, 67% similarity, and InrS has 36% idendity and 72% similarity with [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''M. tuberculosis''] CsoR.) suggests a conserved mode of function in this family of metal-responsive DNA-binding proteins.<ref>PMID:18505253</ref>

== Structure of CsoR/RcnR Family ==

<scene name='Heidi_Hu/Sandbox_1/Tetrameric_csor/1'>Tetrameric CsoR</scene> binds one Cu(I) per monomer. The protein forms a dimer of dimers with a
<scene name='Heidi_Hu/Sandbox_1/Tetrameric_csor/5'>pore</scene> in the tetrameric interface. Each <scene name='60/607938/Tetramer_metal_csor/3'>Cu(I) coordinated by two different monomers</scene> of a dimer unit. Where one monomer is <scene name='60/607938/Tetramer_metal_csor/4'>bound to Cu(I)</scene> by His61 and Cys65, the other monomer is bound to the metal by Cys35. <scene name='60/607938/Tetramer_hb_csor/1'>Hydrogen bonds</scene> in the second coordination sphere residues, Tyr35 and Glu81, with non-coordinating face of His61 stabilize the Cu(I) complex of CsoR. <ref>PMID:17143269</ref>

RcnR is also tetrameric and has the same protein-to-metal stoichiometry. Through a combination of site-directed mutagenesis, lacZ activity assays and X-ray absorption spectroscopy (XAS) structural studies it is now known that RcnR uses a different ligand set to bind Ni(II) than it does Co(II). The Ni(II) site is bound by the N-terminal amine, Cys35, and His64.<ref>PMID: 23215580</ref><ref>PMID: 22471551</ref> Because the Ni(II) site has an octahedral geometry, there are three metal binding residues whose identity is unknown. However, using XAS and lacZ activity assays it is known that the remaining ligands bind to the Ni(II) using N/O atoms and that there are a total of two histidine ligand bound to the Ni(II), leaving the identity of one unaccounted for. Studies have shown that this histidine is not His3, His60, or His67.The Co(II) site is bound by the the N-terminal amine, His3, Cys35, His64 and possibly His60. The Co(II) site of RcnR also has an octahedral geometry, leaving 1-2 residues whose identity is unknown. XAS reveals that these ligands are bound to Co(II) using N/O atoms and that there are a total of three histidine ligands bound to the Co(II). Studies have shown that His67 is not a Co(II) ligand. In addition, RcnR does not conserved the second coordination sphere hydrogen bond network, implying that there is a distance allosteric mechanism relative to CsoR.

InrS conserves all the Cu(I) binding residues identified in [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''M. tuberculosis''] CsoR, Cys53, Cys82 and His78, which have been shown as Ni(II) ligands. His21 is also important for metal binding, while it remains unclear whether or not His21 is a ligand involved in this square planar metal site. Added to this, InrS also lacks the second coordination sphere hydrogen bond network.<ref>PMID: 24666373</ref>

[[Image:CBI metal site.png|500px|left|thumb|Fig. 1: Schematic of known Ni(II) and Co(II) binding residues in the metal sites of RcnR, Cu(I) binding residues in CsoR and Ni(II) binding site in InrS. Figure made with ChemDraw.]]

== Research Interests ==

The mechanism of DNA binding of the CsoR/RcnR family of metal-responsive transcriptional regulators is still unknown. Additionally, RcnR has an added level of complexity because it is reponsive to both Ni(II) and Co(II) binding. The [http://people.chem.umass.edu/mmaroney/ Maroney Lab] at the University of Massachusetts Amherst is interested in the conformational changes of RcnR induced by DNA-, Ni(II)-, and Co(II)-binding. Identification of the remaining metal binding residues in RcnR is ongoing, in addition to identification of the DNA-binding residues in RcnR, as there is no crystal structure of any member of this family of proteins binding to DNA.

==3D structures of copper homeostasis protein==

[[Copper homeostasis protein]]

== References ==

<references/>

== Also See ==

[[2hh7]]

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RcnR tetramer

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Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.

Exploring the Structure

GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.

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Hsin-Ting Huang: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Hsin-Ting Huang/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>