Parvin: Difference between revisions
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===Paxillin binding=== | ===Paxillin binding=== | ||
<Structure load='Complex_parvin.pdb' size='360' scene='Alpha-parvin/Parvin/2' frame='true' align='right' caption='C-terminal CH domain of alpha-parvin bound to paxillin LD motif'/> | <Structure load='Complex_parvin.pdb' size='360' scene='Alpha-parvin/Parvin/2' frame='true' align='right' caption='C-terminal CH domain of alpha-parvin bound to paxillin LD motif'/> | ||
The <scene name='Alpha-parvin/Parvin/2'>scene on the right</scene> shows the superimposition of the three conformations that alpha-parvin adopts when bound to paxillin LD motifs, LD1 ([[2vzd]]), LD2 ([[2vzg]]) and LD4 ([[2vzi]]) respectively. These three LD motifs differ in sequence, but they are all helical. Surprisingly, the orientation of LD1 binding is reversed compared to that of LD2 and LD4. One of the LD motifs (LD1) is shown in the scene, represented by a blue helix. LD2 and LD4 are not shown, but they bind in the same location. As you can see, all three peptides, despite different sequences and different binding orientations, induce a very similar conformation of alpha-parvin, as represented by a very good alignment of the three alpha-parvin structures coloured <font color='red'>red</font>, <font color=DarkGoldenRod'>yellow</font> and <font color='DarkMagenta'>dark magenta</font>. In particular, residues 248 to 264, which experience conformational change upon binding, are similar in all complexes with RMSD values of 0.28 Å (LD1 versus LD2), 0.23 Å (LD1 versus LD4), and 0.15 Å (LD2 versus LD4) in 16 equivalent C<sup>α</sup> positions.<ref>PMID: 18940607</ref> | The <scene name='Alpha-parvin/Parvin/2'>scene on the right</scene> shows the superimposition of the three conformations that alpha-parvin adopts when bound to paxillin LD motifs, LD1 ([[2vzd]]), LD2 ([[2vzg]]) and LD4 ([[2vzi]]) respectively. These three LD motifs differ in sequence, but they are all helical. Surprisingly, the orientation of LD1 binding is reversed compared to that of LD2 and LD4. One of the LD motifs (LD1) is shown in the scene, represented by a blue helix. LD2 and LD4 are not shown, but they bind in the same location. As you can see, all three peptides, despite different sequences and different binding orientations, induce a very similar conformation of alpha-parvin, as represented by a very good alignment of the three alpha-parvin structures coloured <font color='red'>red</font>, <font color='DarkGoldenRod'>yellow</font> and <font color='DarkMagenta'>dark magenta</font>. In particular, residues 248 to 264, which experience conformational change upon binding, are similar in all complexes with RMSD values of 0.28 Å (LD1 versus LD2), 0.23 Å (LD1 versus LD4), and 0.15 Å (LD2 versus LD4) in 16 equivalent C<sup>α</sup> positions.<ref>PMID: 18940607</ref> | ||
When you align the structure of one of the <font color='DimGrey'>alpha-parvin-LD</font> complexes, say the one with LD1 peptide bound, and the structure of <font color='brown'>alpha-parvin on its own (apo)</font>, you also get a <scene name='Alpha-parvin/Parvin/5'>good overall overlap</scene> (disregarding the long loop between helices αC and αE which, as was said before, is relatively flexible), but you can see that the <scene name='Alpha-parvin/Parvin/6'>vicinity of the binding site</scene> has slightly altered conformation. In particular, the angle between the N-linker helix and αA widens by around 15° and the N-linker helix rotates.<ref>PMID: 18940607</ref> In this paragraph the binding of paxillin to the isolated C-terminal CH domain was described. However, the NMR measurements in solution confirmed that the rest of alpha-parvin molecule makes little energetic contribution to the binding. The pictue is not complete, though, since it is possible that the conformational alterations induced by LD binding in the N-terminal part of the C-terminal CH domain are somehow propagated to the nearby linker region and thus the rest of the molecule, possible affecting the behaviour of alpha-parvin towards other binding partners. | When you align the structure of one of the <font color='DimGrey'>alpha-parvin-LD</font> complexes, say the one with LD1 peptide bound, and the structure of <font color='brown'>alpha-parvin on its own (apo)</font>, you also get a <scene name='Alpha-parvin/Parvin/5'>good overall overlap</scene> (disregarding the long loop between helices αC and αE which, as was said before, is relatively flexible), but you can see that the <scene name='Alpha-parvin/Parvin/6'>vicinity of the binding site</scene> has slightly altered conformation. In particular, the angle between the N-linker helix and αA widens by around 15° and the N-linker helix rotates.<ref>PMID: 18940607</ref> In this paragraph the binding of paxillin to the isolated C-terminal CH domain was described. However, the NMR measurements in solution confirmed that the rest of alpha-parvin molecule makes little energetic contribution to the binding. The pictue is not complete, though, since it is possible that the conformational alterations induced by LD binding in the N-terminal part of the C-terminal CH domain are somehow propagated to the nearby linker region and thus the rest of the molecule, possible affecting the behaviour of alpha-parvin towards other binding partners. | ||
==References== | ==References== | ||
<references /> | <references /> | ||