Proteopedia - User contributions [en]

Molecular Playground/RBP

2011-05-04T20:35:05Z

Jan Panteli: New page: D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria. One of the CBI Molecules being studied in the [http:...

D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.

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].

== Molecular Playground/D-Ribose Binding Protein ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP). The differnt colors signify the different subunits.' scene='Insert optional scene name here' />
In the open conformation the RBP is found as a tetramer with four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. See the figure to the right.

<Structure load='2dri' size='300' frame='true' align='bottom' caption='Closed monomeric conformation of the RBP upon binding with ligand, D-Ribose(2dri)' scene='Insert optional scene name here' />
When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers, the RBP monomer undergoes a conformational change and folds in a hinge motion locking the ligand into its <scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binding site</scene>.The ligand bound form of the RBP interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

Molecular Playground banner: A bacterial periplasmic ligand-binding protein for chemotaxis signal transduction.

User:Jan Panteli/sandbox 1

2011-05-04T20:31:51Z

Jan Panteli:

CBI Molecules

2011-05-04T20:26:58Z

Jan Panteli:

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]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.

Fall 2010: New entries are due 12/10/10. Please append the designation (new Fall 2010) to your new entries.

Spring 2011: New entries are due 5/4/11. Please append the designation (new Spring 2011) to your new entries

Bhatia Lab
: '''[[Molecular Playground/Alginate]]''', David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin (new Fall 2010)

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer (new Spring 2011)

[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 (new Fall 2010)

Forbes Lab

: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang (new Spring 2011)

: '''[[Molecular Playground/RBP]]''', Jan Panteli (new Spring 2011)

[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

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

: '''[[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/ERMan1]]''', Johan Sunryd

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

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano (new Fall 2011)

Kaltashov Lab

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

Knapp lab

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

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

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

: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia (new Fall 2010)

[http://robertsgroup.ecs.umass.edu/ 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

Schnarr Lab

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

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

Thayumanavan Lab

: '''[[Molecular Playground/Lysozime ]]''', 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/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang

[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 (NEW FALL 2010)

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! These also provide great examples to follow. Another prize for best CBI Molecules page and/or scene will be awarded in spring 2011!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]).

3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Choose a "green scene" on your Proteopedia page to suggest for display at the Molecular Playground and specify a "banner" which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too.

User:Jan Panteli/sandbox 1

2011-05-04T20:22:17Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T20:20:52Z

Jan Panteli:

D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.

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].

== Molecular Playground/D-Ribose Binding Protein ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP). The differnt colors signify the different subunits.' scene='Insert optional scene name here' />
In the open conformation the RBP is found as a tetramer with four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. See the figure to the right.

<Structure load='2dri' size='300' frame='true' align='bottom' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />
When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers, the RBP monomer undergoes a conformational change and folds in a hinge motion locking the ligand into its <scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binding site</scene>.The ligand bound form of the RBP interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

User:Jan Panteli/sandbox 1

2011-05-04T20:16:29Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T20:14:49Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T19:58:58Z

Jan Panteli:

D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />
In the open conformation the RBP is found as a tetramer with four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose.

<Structure load='2dri' size='300' frame='true' align='right' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />
When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers, the RBP monomer undergoes a conformational change and folds in a hinge motion locking the ligand into its

<scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binding site</scene>. The ligand bound form of the RBP interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

== Forbes Lab ==
The Forbes Lab have shown that a nonfunctional mutant of the Trg protein of ''Salmonella Typhimurium'' can control bacterial localization in tumor tissue. Normally facultative anaerobes will accumulate in the hypoxic and necrotic center of large solid tumors(cite). The mutant ''Salmonella Typhimuruium'' instead does not properly receive the ribose, chemoattractant, signal in the ligand bound RBP because the TRG is nonfunctional and this results in the bacteria accumulating in the border region of live and dead cells which is more therapeutically sensitive. This ability to target the living cells of a tumor greatly increases the affect of protein therapeutics that can be delivered by the bacteria.

User:Jan Panteli/sandbox 1

2011-05-04T19:57:19Z

Jan Panteli:

D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

In the open conformation the RBP is found as a tetramer with four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers, the RBP monomer undergoes a conformational change and folds in a hinge motion locking the ligand into its
<Structure load='2dri' size='500' frame='true' align='right' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />
<scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binding site</scene>. The ligand bound form of the RBP interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

== Forbes Lab ==
The Forbes Lab have shown that a nonfunctional mutant of the Trg protein of ''Salmonella Typhimurium'' can control bacterial localization in tumor tissue. Normally facultative anaerobes will accumulate in the hypoxic and necrotic center of large solid tumors(cite). The mutant ''Salmonella Typhimuruium'' instead does not properly receive the ribose, chemoattractant, signal in the ligand bound RBP because the TRG is nonfunctional and this results in the bacteria accumulating in the border region of live and dead cells which is more therapeutically sensitive. This ability to target the living cells of a tumor greatly increases the affect of protein therapeutics that can be delivered by the bacteria.

User:Jan Panteli/sandbox 1

2011-05-04T19:52:31Z

Jan Panteli:

D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

<Structure load='2dri' size='500' frame='true' align='right' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />

In the open conformation the RBP is found as a tetramer with four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers, the RBP monomer undergoes a conformational change and folds in a hinge motion locking the ligand into its <scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binding site</scene>. The ligand bound form of the RBP interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

== Forbes Lab ==
The Forbes Lab have shown that a nonfunctional mutant of the Trg protein of ''Salmonella Typhimurium'' can control bacterial localization in tumor tissue. Normally facultative anaerobes will accumulate in the hypoxic and necrotic center of large solid tumors(cite). The mutant ''Salmonella Typhimuruium'' instead does not properly receive the ribose, chemoattractant, signal in the ligand bound RBP because the TRG is nonfunctional and this results in the bacteria accumulating in the border region of live and dead cells which is more therapeutically sensitive. This ability to target the living cells of a tumor greatly increases the affect of protein therapeutics that can be delivered by the bacteria.

User:Jan Panteli/sandbox 1

2011-05-04T19:45:58Z

Jan Panteli:

D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

In the open conformation the RBP is found as a tetramer with four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers, the RBP monomer undergoes a conformational change and folds in a hinge motion locking the ligand into its <scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binding site</scene>. The ligand bound form of the RBP interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

<Structure load='2dri' size='500' frame='true' align='right' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />

== Forbes Lab ==
The Forbes Lab have shown that a nonfunctional mutant of the Trg protein of ''Salmonella Typhimurium'' can control bacterial localization in tumor tissue. Normally facultative anaerobes will accumulate in the hypoxic and necrotic center of large solid tumors(cite). The mutant ''Salmonella Typhimuruium'' instead does not properly receive the ribose, chemoattractant, signal in the ligand bound RBP because the TRG is nonfunctional and this results in the bacteria accumulating in the border region of live and dead cells which is more therapeutically sensitive. This ability to target the living cells of a tumor greatly increases the affect of protein therapeutics that can be delivered by the bacteria.

User:Jan Panteli/sandbox 1

2011-05-04T19:28:21Z

Jan Panteli:

E. Coli D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in the bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

In the open conformation the RBP is found in a tetramer four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. When d-ribose enters the periplasmic space of the gram negative bacteria and <scene name='User:Jan_Panteli/sandbox_1/Rbp_bound_to_d-ribose/1'>binds</scene> to one of the monomers, the bound form then interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

<Structure load='2dri' size='500' frame='true' align='right' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />

User:Jan Panteli/sandbox 1

2011-05-04T19:14:18Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T19:01:43Z

Jan Panteli:

E. Coli D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in the bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

In the open conformation the RBP is found in a tetramer four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers this bound form then interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

<Structure load='2dri' size='500' frame='true' align='right' caption='Closed monomeric conformation of the RBP upon binding with ligand (2dri), D-Ribose' scene='Insert optional scene name here' />
<Structure load='Insert PDB code or filename here' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

User:Jan Panteli/sandbox 1

2011-05-04T18:59:48Z

Jan Panteli:

E. Coli D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in the bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='Tetrameric open conformation of E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

In the open conformation the RBP is found in a tetramer four identical domains, A,B,C,and D. Within each of these domains lies a binding site for d-ribose. When d-ribose enters the periplasmic space of the gram negative bacteria and binds to one of the monomers this bound form then interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose. Trg then sends biochemical signals to tell the bacteria's flagella to rotate leading to bacterial migration towards the sugar food source.

<Structure load='2dri' size='500' frame='true' align='right' caption='Closed conformation of the RBP upon binding with ligand (2dri), D-Ribose in monomer' scene='Insert optional scene name here' />
<Structure load='Insert PDB code or filename here' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

User:Jan Panteli/sandbox 1

2011-05-04T16:06:05Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T16:04:39Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T14:59:55Z

Jan Panteli:

E. Coli D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in the bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />

There are four domains to RBP, A,B,C,and D. These domains form a binding site for d-ribose and the bound form of the protein then interacts with transmembrane protein Trg, the chemotaxis transducer for d-ribose.
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T14:50:57Z

Jan Panteli:

E. Coli D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in the bacteria.

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T14:47:53Z

Jan Panteli:

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].

== Exploring the Structure ==
<Structure load='1urp' size='500' frame='true' align='right' caption='E. Coli D-Ribose Binding Protein for signal transduction of Chemotaxis machinery RBP(1URP)' scene='Insert optional scene name here' />
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T12:53:52Z

Jan Panteli:

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].

== Exploring the Structure ==
<Structure load='1bxd' size='500' frame='true' align='right' caption='E. Coli Histadine Kinase Domain of the Osmosensor Envz(1BXD)' scene='Insert optional scene name here' />
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T12:52:41Z

Jan Panteli:

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].

== Exploring the Structure ==
<Structure load='1bxd' size='500' frame='true' align='right' caption='E. Coli Histadine Kinase Domain of the Osmosensor Envz' scene='Insert optional scene name here' />
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T12:45:31Z

Jan Panteli:

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].

== Exploring the Structure ==
<Structure load='1bxd' size='500' frame='true' align='right' caption='Envz' scene='Insert optional scene name here' />
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T03:58:25Z

Jan Panteli:

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].

== Exploring the Structure ==
<Structure load='1bxd' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).

User:Jan Panteli/sandbox 1

2011-05-04T03:55:55Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T03:53:44Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T03:53:06Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T03:51:57Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T03:48:51Z

Jan Panteli:

User:Jan Panteli/sandbox 1

2011-05-04T03:41:42Z

Jan Panteli: New page: Bacterial chemotaxis receptor One of the CBI Molecules being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Ch...

[[Image:intactModelLargeText.jpg|frame|Bacterial chemotaxis receptor]]

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].

Many bacteria can "smell" their surroundings and "choose" where to go. They detect molecules such as amino acids or sugars using receptors that bind these molecules and transmit a signal into the cell. This signal controls several proteins which ultimately control the direction of rotation of the motors that rotate the flagella. One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds, the receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble and try a new swimming direction."

A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

{{Clear}}
<applet load='1wat' size='[450,338]' frame='true' align='right'
caption='Aspartate receptor ligand binding domain (1wat)' scene='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'/>

=== Ligand-binding domain ===

The spinning protein (<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>Initial view</scene>) ) is the ligand binding domain of the aspartate receptor with the aspartate ligand bound (LKT).

Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.

{{Clear}}
<applet load='2ho9' size='[450,338]' frame='true' align='right'
caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>

=== Chemotaxis adaptor protein CheW ===

CheW is a chemotaxis adaptor protein, and part of the tertiary complex formed by the chemotaxis receptor, histidine kinase protein CheA, and CheW. As an adaptor protein, CheW mediates the interaction between the chemotaxis receptor and CheA, and is necessary for the formation of kinase active complexes. CheW has been found to bind to the P5 domain of CheA through crystallographic studies.

At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).