User:Jan Panteli/sandbox 1

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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='Tetrameric open conformation of 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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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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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.
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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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<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' />
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Molecular Playground banner: A bacterial periplasmic ligand-binding protein for chemotaxis signal transduction.
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== Forbes Lab ==
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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.
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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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