Sandbox Reserved 822: Difference between revisions
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In the PDK1 Ins(1,3,4,5)P<sub>4</sub>-binding pocket a layer of five-ordered water molecules (B-factors) seperate Ins(1,3,4,5)P<sub>4</sub> from the protein (see Fig.2). The water molecules mediate a number of hydrogen bonds from Ins(1,3,4,5)P<sub>4</sub> to the protein. For example binding of the D2-hydroxyl group takes place via an ordered water molecule. But only one of these five water molecules is also conserved in the PH domains of other proteins contacting the D3-phosphate (see Fig.2, coloured yellow).<ref name="Structural" /> | In the PDK1 Ins(1,3,4,5)P<sub>4</sub>-binding pocket a layer of five-ordered water molecules (B-factors) seperate Ins(1,3,4,5)P<sub>4</sub> from the protein (see Fig.2). The water molecules mediate a number of hydrogen bonds from Ins(1,3,4,5)P<sub>4</sub> to the protein. For example binding of the D2-hydroxyl group takes place via an ordered water molecule. But only one of these five water molecules is also conserved in the PH domains of other proteins contacting the D3-phosphate (see Fig.2, coloured yellow).<ref name="Structural" /> | ||
Additionally, it was shown that the binding affinity for D1-phophorylated inositol phosphates is about five-fold higher than for inositol phosphates without a phosphate group at this position. This is caused by interactions of <scene name='56/568020/Arg472/1'>Arg472</scene> with the delocalised negative charge on the D1 phosphate. The formed hydrogen bonds to the D1-phosphate appear to play a crucial role in mediating binding of inositol phosphates to PDK1 (see ''''Interactions with Phosphatidylinositol Phosphates ''''). <ref name="Structural" /> | |||
=== Interactions with Phosphatidylinositol Phosphates === | === Interactions with Phosphatidylinositol Phosphates === | ||
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The interations of the PDK1 PH domain with phosphatidylinositol phosphates were investigated by co-crystallising the PH domain with a PtdIns(3,4,5)P<sub>3</sub> analogue which contains two C4 acyl chains (diC4-PtdIns(3,4,5)P<sub>3</sub>). It was found that <scene name='56/568020/Arg472/1'>Arg472</scene> coordinates the free oxygen atoms on the D1-phosphate whereas the oxygen atom involved in the ester bond to the glycerol does not make any significant contact with the protein. The glycerol backbone itself projects away from the surface of the protein and does not display any other interactions (see Fig.3). <ref name="Structural" /> | The interations of the PDK1 PH domain with phosphatidylinositol phosphates were investigated by co-crystallising the PH domain with a PtdIns(3,4,5)P<sub>3</sub> analogue which contains two C4 acyl chains (diC4-PtdIns(3,4,5)P<sub>3</sub>). It was found that <scene name='56/568020/Arg472/1'>Arg472</scene> coordinates the free oxygen atoms on the D1-phosphate whereas the oxygen atom involved in the ester bond to the glycerol does not make any significant contact with the protein. The glycerol backbone itself projects away from the surface of the protein and does not display any other interactions (see Fig.3). <ref name="Structural" /> | ||
The binding arrangement of the interaction with the D1-phophodiester appears in a characteristic way, which also explains the significantly higher affinity for D1-phosphorylated inositol phosphates (see ''''Interactions with Inositol Phosphates''''). The two oxygen atoms, which are not involved in the two phophoester linkages, carry most of the negative charge and interact with the guanidinium group of <scene name='56/568020/Arg472/1'>Arg472</scene> by forming one hydrogen bond each (see Fig.3). These interactions of Arg472 with the delocalised negative charge on the D1 phosphate is a crucial factor for the binding affinity of the PDK1 PH domain for its | The binding arrangement of the interaction with the D1-phophodiester appears in a characteristic way, which also explains the significantly higher affinity for D1-phosphorylated inositol phosphates (see ''''Interactions with Inositol Phosphates''''). The two oxygen atoms, which are not involved in the two phophoester linkages, carry most of the negative charge and interact with the guanidinium group of <scene name='56/568020/Arg472/1'>Arg472</scene> by forming one hydrogen bond each (see Fig.3). These interactions of Arg472 with the delocalised negative charge on the D1 phosphate is a crucial factor for the binding affinity of the PDK1 PH domain for its ligands. <ref name="Structural" /> | ||
For binding of PtdIns(3,4,5)P<sub>3</sub> no significant conformational changes could be observed. Only <scene name='56/568020/Lys467/1'>Lys467</scene> occupies the position of the inositol ring in the absence of ligand and rotates to a position to contact the D5-phophate upon ligand binding. <ref name="Structural" /> | For binding of PtdIns(3,4,5)P<sub>3</sub> no significant conformational changes could be observed. Only <scene name='56/568020/Lys467/1'>Lys467</scene> occupies the position of the inositol ring in the absence of ligand and rotates to a position to contact the D5-phophate upon ligand binding. <ref name="Structural" /> | ||