User:Jan Panteli/sandbox 1

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D- Ribose Binding Protein (RBP) is involved in signal transduction of the chemokine D-ribose to stimulate chemotaxis in bacteria.
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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].
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].
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== Exploring the Structure ==
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== Molecular Playground/D-Ribose Binding Protein ==
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<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' />
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<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' />
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=== Ligand-binding domain ===
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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.
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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).
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Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment.
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{{Clear}}
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<applet load='2ho9' size='[450,338]' frame='true' align='right'
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caption='E. coli chemotaxis adaptor protein CheW (2ho9)' scene='User:Shiela_M._Jones/Sandbox_1/Chew_suppressionmutants/1'/>
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=== Chemotaxis adaptor protein CheW ===
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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.
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<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' />
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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.
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At right, CheW is shown with suppression mutants (blue)that have been measured to decrease receptor binding and chemotaxis (SMJ).
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Molecular Playground banner: A bacterial periplasmic ligand-binding protein for chemotaxis signal transduction.

Current revision

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 University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.


Molecular Playground/D-Ribose Binding Protein

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.

Drag the structure with the mouse to rotate

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.

Closed monomeric conformation of the RBP upon binding with ligand, D-Ribose(2dri)

Drag the structure with the mouse to rotate

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 .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.

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Jan Panteli

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