Proteopedia - User contributions [en]

Molecular Playground/CheA

2014-04-22T20:01:06Z

Elizabeth R. Haglin:

In Progress: One of the [http://www.proteopedia.org/wiki/index.php/CBI_Molecules CBI Molecules] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst].
<Structure load='1b3q' size='500' frame='true' align='right' caption='Structure of histidine kinase CheA, [[1b3q]]' scene='User:Elizabeth_R._Haglin/Sandbox_1/P3p4p5/3'>

__TOC__
== Biological context ==
'''Histidine Kinase (HK) CheA''' relays signals from the transmembrane chemoreceptors (methyl-accepting chemotaxis proteins/MCPs) to regulate bacterial chemotaxis. The functional form of CheA exists as a dimer and is associated to the receptors through a coupling protein CheW. Kinase activity of CheA depends on signals received from the receptor via an ATP-dependent phosphoryl transfer the trans monomer of dimeric CheA. The phosphoryl group is subsequently transferred to the response regulator (RR) CheY and carried throughout the cell to interact with the flagellar motor and control cellular mobility and directionality.

Chemotaxis is a behavior used by most motile flagellated bacteria,like ''E. coli'' and ''T. maritima'', to modify their swimming pattern in response to environmental stimuli. Directionality is controlled by the counter-clockwise (CCW) running or clockwise (CW) tumbling motion of the flagellar motor, which in turn is regulated by large arrays of a two-component signal transduction complex responsible for sensing extracellular chemical concentration gradients. Upon binding of a chemical ligand, the MCPs regulate ATP-dependent trans-autophosphorylation activity of the histidine kinase CheA. A repellent binding event leads to increases in phosphorylated CheA (CheA-P) and a subsequent increase in phosphorylation of CheA’s binding partner and CheY. Phosphorylated CheY (CheY-P) has a high affinity for the flagellar motor switch protein FliM and at increased concentrations will change the motor rotation from CCW to CW, leading to tumbling. Likewise, attractant binding inhibits CheA phosphorylation so unphosphorylated CheY dominates, the motor switch CCW motion is unaffected, and the cell maintains smooth swimming. The CheY-P signal is additionally regulated by the phosphatase CheZ. Ultimately, the flux of phosphoryl groups governs the mobility response to external stimuli.

== Structure ==

'''CheA''' exists as a homodimer of 71-kDa subunits. Each monomer catalyzes an ATP-dependent ''trans''-phosphorylation of a histidine. A monomer contains five domains (P1-P5 from N- to C-terminus) connected by highly dynamic linkers of various lengths. Each domain has a distinct function.Due to the size of CheA, the solved structures available to date do not have all five domains. The PDB files included in this proteopedia page are <scene name='User:Elizabeth_R._Haglin/Sandbox_1/P3p4p5/3'>1B3Q</scene> with a dimer of P3P4P5 and <scene name='User:Elizabeth_R._Haglin/Sandbox_1/P1_p2_chey/2'>2LP4</scene> which contains a P1P2-CheY complex.
*P1: histidine phosphotransfer domain (HPt) mediates phosphate transfer from ATP to CheY
*P2: CheY binding domain releases CheY-P upon small conformational changes
*P3: dimerization domain
*P4: ATP-binding catalytic domain
*P5: autophosphorylation regulatory domain relays signal input to P4 from the chemoreceptor and CheW

=== P1P2: Histidine phosphotransfer domains ===

<scene name='User:Elizabeth_R._Haglin/Sandbox_1/P1p2_active_site/1'>Active site</scene>

=== P3P4P5: Kinase core domains ===

== Binding partners ==

== Additional 3D structures of CheA ==

== References ==

<references/>

CBI Molecules

2013-12-17T23:12:35Z

Elizabeth R. Haglin:

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 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 [http://http://www.umass.edu/cbi/ 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

[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]

: New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm
: New Fall 2013!! '''[[Molecular Playground/ClyA]]''', Bib Yang

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

[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]

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

: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani
:: Best CBI Molecule 2012

[http://people.chem.umass.edu/jhardy/ 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

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez

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

: New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

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

New 2013! '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]''', Chengfeng Ren

: Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

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

[http://people.chem.umass.edu/mmaroney/ 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

[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]
: New Fall 2013! '''[[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]
:New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab]

: New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

[http://www.biochem.umass.edu/faculty/danny-j-schnell 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

: '''[[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] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: New Fall 2013!! '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin

: 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

: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html 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, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

: '''[[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 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: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.

User:Elizabeth R. Haglin/Sandbox 2

2013-12-17T23:10:11Z

Elizabeth R. Haglin: User:Elizabeth R. Haglin/Sandbox 2 moved to Molecular Playground/Bacterial Chemotaxis Complex

#REDIRECT [[Molecular Playground/Bacterial Chemotaxis Complex]]

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T23:10:11Z

Elizabeth R. Haglin: User:Elizabeth R. Haglin/Sandbox 2 moved to Molecular Playground/Bacterial Chemotaxis Complex

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW ([[3UR1]])' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

[[Image:3UR1_4JPB_alignment.png|thumb|left|upright=1|alt=Alignment|Fig. 1 CheA and CheW alignment for 3UR1 and 4JPB]]A recent structure of the ternary complex has defined specific contacts between the protein interfaces. Although the receptor is 'unzipped' at the known hairpin loop, the specific residues at the protein-protein interfaces are still believed to be accurate because CheA and CheW align well with a previous crystal structure (Fig. 1). More information can be found [http://http://www.ncbi.nlm.nih.gov/pubmed/23668907 here]
• <scene name='57/571407/Receptor_chea_interface/1'>Receptor to CheA</scene>: Residues highlighted in red are (receptor) 135, 138, 142 and (CheA) 563, 566 (4JPB)

• <scene name='57/571407/Receptor_chew_interface/1'>Receptor to CheW</scene>: Residues highlighted in red are (receptor) 137, 139-143, 145, 146, 156 and (CheW) 14, 27, 30, 98, 99 (3UR1)

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T23:04:00Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T23:01:30Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW ([[3UR1]])' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

A recent structure of the ternary complex has defined specific contacts between the protein interfaces. Although the receptor is 'unzipped' at the known hairpin loop, the specific residues at the protein-protein interfaces are still believed to be accurate because CheA and CheW align well with a previous crystal structure (Fig. 1). More information can be found [http://http://www.ncbi.nlm.nih.gov/pubmed/23668907 here][[Image:3UR1_4JPB_alignment.png|thumb|left|upright=1.5|alt=Alignment|Fig. 1 CheA and CheW alignment for 3UR1 and 4JPB]]
• <scene name='57/571407/Receptor_chea_interface/1'>Receptor to CheA</scene>: Residues highlighted in red are (receptor) 135, 138, 142 and (CheA) 563, 566 (4JPB)

• <scene name='57/571407/Receptor_chew_interface/1'>Receptor to CheW</scene>: Residues highlighted in red are (receptor) 137, 139-143, 145, 146, 156 and (CheW) 14, 27, 30, 98, 99 (3UR1)

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T22:28:24Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW ([[3UR1]])' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

A recent structure of the ternary complex has defined specific contacts between the protein interfaces. Although the receptor is 'unzipped' at the known hairpin loop, the specific residues at the protein-protein interfaces are still believed to be accurate because CheA and CheW align well with a previous crystal structure (Fig. 1). More information can be found [http://http://www.ncbi.nlm.nih.gov/pubmed/23668907 here][[Image:3UR1_4JPB_alignment.png|thumb|left|upright=1.5|alt=Alignment|Fig. 1 CheA and CheW alignment for 3UR1 and 4JPB]]
• Receptor to CheA: <scene name='57/571407/Receptor_chea_interface/1'>TextToBeDisplayed</scene>

• Receptor to CheW:

• CheW to P5 of CheA:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T22:23:46Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

A recent structure of the ternary complex has defined specific contacts between the protein interfaces. Although the receptor is 'unzipped' at the known hairpin loop, the specific residues at the protein-protein interfaces are still believed to be accurate because CheA and CheW align well with a previous crystal structure. [[Image:3UR1_4JPB_alignment.png|thumb|upright=1.5|alt=Alignment|CheA/CheW alignment of 3UR1 and 4JPB|]]

• Receptor to CheA: <scene name='57/571407/Receptor_chea_interface/1'>TextToBeDisplayed</scene>

• Receptor to CheW:

• CheW to P5 of CheA:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T22:19:44Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

A recent structure of the ternary complex has defined specific contacts between the protein interfaces. Although the receptor is 'unzipped' at the known hairpin loop, the specific residues at the protein-protein interfaces are still believed to be accurate because CheA and CheW align well with a previous crystal structure. [[Image:3UR1_4JPB_alignment.png|thumb|upright=1.5|alt=Alignment|CheA/CheW alignment of 3UR1 and 4JPB]]

• Receptor to CheA: <scene name='57/571407/Receptor_chea_interface/1'>TextToBeDisplayed</scene>

• Receptor to CheW:

• CheW to P5 of CheA:

File:3UR1 4JPB alignment.png

2013-12-17T21:55:50Z

Elizabeth R. Haglin: uploaded a new version of "Image:3UR1 4JPB alignment.png": Aligned CheA from 3UR1 to 4JPB using PyMol

== Summary ==
Aligned CheA from 3UR1 to 4JPB using PyMol
== Licensing ==
{{PD-self}}

File:3UR1 4JPB alignment.png

2013-12-17T21:54:14Z

Elizabeth R. Haglin: Aligned CheA from 3UR1 to 4JPB using PyMol

== Summary ==
Aligned CheA from 3UR1 to 4JPB using PyMol
== Licensing ==
{{PD-self}}

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T20:29:38Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

• Receptor to CheA: <scene name='57/571407/Receptor_chea_interface/1'>TextToBeDisplayed</scene>

• Receptor to CheW:

• CheW to P5 of CheA:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T20:13:55Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

===Protein Interfaces===

• Receptor to CheA:

• Receptor to CheW:

• CheW to P5 of CheA:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T19:48:43Z

Elizabeth R. Haglin:

ö<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes with the receptor in gray, CheA in blue, and CheW in cyan. Recent cryo-EM data from the [http://www.pnas.org/cgi/doi/10.1073/pnas.1115719109 Crane Lab] shows evidence for extended hexagonal arrays in which the receptors exist as trimers of dimers with rings of CheA and CheW connecting them together.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T19:46:07Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T19:41:37Z

Elizabeth R. Haglin:

ö<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/4'>This scene</scene> shows a top down view of a set of three ternary complexes beginning to form a larger hexagonal-like assembly. Recent cryo-EM data shows evidence for extended hexagonal arrays.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T19:40:11Z

Elizabeth R. Haglin:

ö<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/5'>This scene</scene> shows a top down view of a set of three ternary complexes beginning to form a larger hexagonal-like assembly. Recent cryo-EM data shows evidence for extended hexagonal arrays.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-17T19:38:53Z

Elizabeth R. Haglin:

ö<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. <scene name='57/571407/Ternary_complex_side_view/5'>This scene</scene> illustrates a set of three ternary complexes beginning to form a larger hexagonal-like assembly. Recent cryo-EM data shows evidence for extended hexagonal arrays.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T21:09:14Z

Elizabeth R. Haglin:

ö<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single asymmetric unit ternary complex with the truncated receptor, CheA, and CheW [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and scaffold/adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

===Structure===

• The <scene name='57/571407/Cytoplasmic_receptor/1'>chemoreceptor</scene> (1QU7) – also called methyl-accepting protein, MCP – is a ~380Å long, alpha helical homo-dimer with many domains. The <scene name='57/571407/Cytoplasmic_receptor/2'>signaling domain</scene> at the cytosplasmic tip is where both CheW and CheA interact and bind.

• <scene name='57/571407/Chea_p3p4p5/1'>CheA</scene> is a large 5-subdomain (P1-P5) histidine kinase that auto-phosphorylates depending on it's interaction with the receptor and localized concentrations of the response regulator protein CheY. This scene is of P3-P5 as a homo-dimer (1B3Q). For more information, see [http://proteopedia.org/wiki/index.php/Molecular_Playground/CheA CheA Molecular Playground page]

• The small multi-functioning adaptor and scaffolding protein <scene name='57/571407/Chew/1'>CheW</scene> (2HO9) is not directly involved in the signaling event but is essential for CheA activity.

• When combined, these three proteins assemble into large membrane associated complex primed for relaying signals from outside the cell. This scene illustrates the beginning of a larger hexagonal-like assembly of the complexes. Recent cryo-EM data shows evidence for extended hexagonal arrays.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T20:59:32Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T20:55:23Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T20:50:54Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T20:38:47Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T20:36:00Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T17:43:22Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T17:15:00Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T16:51:35Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single ternary bacterial chemotaxis complex [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the <scene name='57/571407/Single_ternary_complex/3'>transmembrane receptor</scene>, <scene name='57/571407/Single_ternary_complex/4'> histidine kinase CheA </scene>, and <scene name='57/571407/Single_ternary_complex/5'> adaptor protein CheW</scene>. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

<scene name='57/571407/Ternary_complex_side_view/4'>Chemoreceptor complexes assemble into hexagonal arrays</scene>

===Structure===

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-16T16:22:19Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single ternary bacterial chemotaxis complex [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the <scene name='57/571407/Single_ternary_complex/3'>transmembrane receptor</scene>, <scene name='57/571407/Single_ternary_complex/4'> histidine kinase CheA </scene>, and <scene name='57/571407/Single_ternary_complex/5'> adaptor protein CheW</scene>. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

<scene name='57/571407/Ternary_complex_side_view/1'>Chemoreceptor complexes assemble into hexagonal arrays</scene>

===Structure===

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-13T19:10:31Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single ternary bacterial chemotaxis complex [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the <scene name='57/571407/Single_ternary_complex/3'>transmembrane receptor</scene>, <scene name='57/571407/Single_ternary_complex/4'> histidine kinase CheA </scene>, and <scene name='57/571407/Single_ternary_complex/5'> adaptor protein CheW</scene>. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

<scene name='57/571407/Ternary_complex_side_view/1'>Chemoreceptor complexes form extended hexagonal arrays</scene>

===Structure===

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T02:40:10Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single ternary bacterial chemotaxis complex [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the <scene name='57/571407/Single_ternary_complex/3'>transmembrane receptor</scene>, <scene name='57/571407/Single_ternary_complex/4'> histidine kinase CheA </scene>, and <scene name='57/571407/Single_ternary_complex/5'> adaptor protein CheW</scene>. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

<scene name='57/571407/Ternary_complex_side_view/1'>Chemoreceptor complexes form extended hexagonal arrays</scene>

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T02:32:00Z

Elizabeth R. Haglin:

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T02:24:53Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='A single ternary bacterial chemotaxis complex [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the <scene name='57/571407/Single_ternary_complex/2'>transmembrane receptor</scene>, histidine kinase CheA, and adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to govern CheA's kinase activity, and ultimately lead to changes in swimming behavior.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T02:17:19Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Ternary complex of the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor. The signal is then relayed within the cytoplasm to ultimately control CheA's kinase activity and subsequently the second messenger protein CheY which is responsible changing the direction of the flagellar motor and therefore the swimming direction.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T02:15:13Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Ternary complex of the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene='57/571407/Single_ternary_complex/1‹

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor which then relays the signal within the cell to ultimately control CheA's kinase activity.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T02:05:27Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Ternary complex of the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the transmembrane receptor, histidine kinase CheA, and adaptor protein CheW. Repellants and attractants bind to the periplasmic domain of the receptor which then relays the signal within the cell to ultimately control CheA's kinase activity.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-10T01:48:47Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Ternary complex of the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Bacterial chemotaxis is a method for cells to sense and adapt to chemicals in their environment. It is carried out by large arrays of membrane associated multi-protein complexes that form at the poles of the cells. The major players involved are the receptor, histidine kinase CheA, and adaptor protein CheW. Upon ligand binding to the receptor – be it attractant or repellant – a signal is relayed to CheA, which subsequently phosphorylates CheY

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:54:55Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Ternary complex with the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene='57/571407/Single_ternary_complex/1'/>

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.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:54:17Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Ternary complex with the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene=''57/571407/Single_ternary_complex/1'/>

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.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:48:57Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Thermatoga maritima chemotaxis ternary complex with the truncated receptor (gray), CheA (blue), and CheW (cyan) [[3UR1]]' scene='57/571407/Ternary_complex_side_view/3'/>

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.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:47:21Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor [[3UR1]]' scene='57/571407/Ternary_complex_side_view/3'/>

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.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:41:34Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor [[3UR1]]' scene='57/571407/Ternary_complex_side_view/3'/>

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.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:39:54Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor [[3UR1]]' scene='57/571407/Ternary_complex_side_view/1'/>

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.

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T19:35:45Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor [[3UR1]]'/>

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.

<scene name='57/571407/Ternary_complex_side_view/1'>Chemoreceptor complexes assemble in large hexagonal arrays</scene>

File:Hexameric 3UR1.pdb

2013-12-09T17:06:32Z

Elizabeth R. Haglin: Three symmetry mates of the ternary complex in 3UR1 to show the hexagonal array structure formed by chemoreceptor complexes

Three symmetry mates of the ternary complex in 3UR1 to show the hexagonal array structure formed by chemoreceptor complexes

File:3UR1 hexameric ternary complex.pdb.zip

2013-12-09T16:56:02Z

Elizabeth R. Haglin: Three copies of 3UR1 ternary complex to show hexagonal array structure

Three copies of 3UR1 ternary complex to show hexagonal array structure

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T16:42:10Z

Elizabeth R. Haglin:

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor [[3UR1]]'/>

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.

<scene name='User:Elizabeth R. Haglin/sandbox_2/Banner_1/1'>Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor</scene>

Molecular Playground/Bacterial Chemotaxis Complex

2013-12-09T16:23:30Z

Elizabeth R. Haglin: New page: <applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Chemoreceptor complex 3UR1'/> One of the CBI Molecules being studied in the [http://www.umass.edu...

<applet load='3UR1' size='400' color='white' frame='true' align='right' caption='Chemoreceptor complex [[3UR1]]'/>

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.

<scene name='User:Elizabeth R. Haglin/sandbox_2/Banner_1/1'>Thermatoga maritima chemotaxis ternary complex with CheA, CheW and truncated chemoreceptor</scene>

User:Elizabeth R. Haglin

2013-12-09T16:04:43Z

Elizabeth R. Haglin:

* Full Real Name: Libbie Haglin

* Position: Graduate student

* Institution (NO ABBREVIATIONS):University of Massachusetts, Amherst

* City, State/Province, Country: Amherst, MA, USA

* Field of Expertise or Study: Biochemistry/biophysics

*[[User:Elizabeth R. Haglin/Sandbox 1]]

*[[User:Elizabeth R. Haglin/Sandbox 2]]

Molecular Playground/CheA

2012-12-13T03:58:23Z

Elizabeth R. Haglin:

In Progress: One of the [http://www.proteopedia.org/wiki/index.php/CBI_Molecules CBI Molecules] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst].
<Structure load='1b3q' size='500' frame='true' align='right' caption='Structure of histidine kinase CheA' scene='User:Elizabeth_R._Haglin/Sandbox_1/P3p4p5/3'>
[[Image:Chemotaxis.png|300px|right|thumb|Chemotaxis overview <ref>PMID:15573139</ref>]]
__TOC__
== Biological context ==
'''Histidine Kinase (HK) CheA''' relays signals from the transmembrane chemoreceptors (methyl-accepting chemotaxis proteins/MCPs) to regulate bacterial chemotaxis. The functional form of CheA exists as a dimer and is associated to the receptors through a coupling protein CheW. Kinase activity of CheA depends on signals received from the receptor via an ATP-dependent phosphoryl transfer the trans monomer of dimeric CheA. The phosphoryl group is subsequently transferred to the response regulator (RR) CheY and carried throughout the cell to interact with the flagellar motor and control cellular mobility and directionality.

Chemotaxis is a behavior used by most motile flagellated bacteria,like ''E. coli'' and ''T. maritima'', to modify their swimming pattern in response to environmental stimuli. Directionality is controlled by the counter-clockwise (CCW) running or clockwise (CW) tumbling motion of the flagellar motor, which in turn is regulated by large arrays of a two-component signal transduction complex responsible for sensing extracellular chemical concentration gradients. Upon binding of a chemical ligand, the MCPs regulate ATP-dependent trans-autophosphorylation activity of the histidine kinase CheA. A repellent binding event leads to increases in phosphorylated CheA (CheA-P) and a subsequent increase in phosphorylation of CheA’s binding partner and CheY. Phosphorylated CheY (CheY-P) has a high affinity for the flagellar motor switch protein FliM and at increased concentrations will change the motor rotation from CCW to CW, leading to tumbling. Likewise, attractant binding inhibits CheA phosphorylation so unphosphorylated CheY dominates, the motor switch CCW motion is unaffected, and the cell maintains smooth swimming. The CheY-P signal is additionally regulated by the phosphatase CheZ. Ultimately, the flux of phosphoryl groups governs the mobility response to external stimuli.

== Structure ==
[[Image:CheA_domains.png|410px|left|thumb|CheA Domains <ref>PMID: 22494339</ref>]]
'''CheA''' exists as a homodimer of 71-kDa subunits. Each monomer catalyzes an ATP-dependent ''trans''-phosphorylation of a histidine. A monomer contains five domains (P1-P5 from N- to C-terminus) connected by highly dynamic linkers of various lengths. Each domain has a distinct function.Due to the size of CheA, the solved structures available to date do not have all five domains. The PDB files included in this proteopedia page are <scene name='User:Elizabeth_R._Haglin/Sandbox_1/P3p4p5/3'>1B3Q</scene> with a dimer of P3P4P5 and <scene name='User:Elizabeth_R._Haglin/Sandbox_1/P1_p2_chey/2'>2LP4</scene> which contains a P1P2-CheY complex.
*P1: histidine phosphotransfer domain (HPt) mediates phosphate transfer from ATP to CheY
*P2: CheY binding domain releases CheY-P upon small conformational changes
*P3: dimerization domain
*P4: ATP-binding catalytic domain
*P5: autophosphorylation regulatory domain relays signal input to P4 from the chemoreceptor and CheW

=== P1P2: Histidine phosphotransfer domains ===

<scene name='User:Elizabeth_R._Haglin/Sandbox_1/P1p2_active_site/1'>Active site</scene>

=== P3P4P5: Kinase core domains ===

== Binding partners ==

== Additional 3D structures of CheA ==

== References ==

<references/>

CBI Molecules

2012-12-13T03:57:26Z

Elizabeth R. Haglin:

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 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. 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 -- I may be able to request additions to the author list).

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

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

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

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

: **'''[[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

[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]

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

: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani
:: Best CBI Molecule 2012

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[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/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

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

: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas
:: Best CBI Molecule Proteopedia Page 2010

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

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

: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', 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

Peyton Lab
: '''[[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

[https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab ]

: '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

Tew Lab

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

Thayumanavan Lab

: '''[[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] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: '''[[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

: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

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

: '''[[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

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

: '''[[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==

'''Congratulations to the prize-winning CBI molecules noted above! The new 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 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.

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

2. 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).

3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.

You are encouraged to collaborate on this year's 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.

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.

4. 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.

==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.