Parvin: Difference between revisions

The most diverged fragments in the C-terminal CH domain of alpha-parvin correspond to 1) an <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_Parvin//Parvin_overlap/3'>additional helix</scene> (so called N-terminal linker helix; it is labelled αN in the picture above on the right) located at the N-terminal end of the domain and not observed in any other CH domain and 2) a <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_Parvin//Parvin_overlap/5'>long loop</scene> between two helices (which are labelled αC and αE in the picture above on the right). One could ask whether the N-terminal linker helix is an integral part of the C-terminal CH domain or just a part of a linker region between the two CH domains. The fact that it interacts strongly with the core helices by means of both electrostatic (<scene name='Alpha-parvin/Parvin_overlap/1'>residues D248, D251 and D255 with K355 and R359</scene>) and hydrophobic (<scene name='Alpha-parvin/Parvin_overlap/4'>residues F250, L253 and F254 with L354, K355, L358, R359, K260 and L261</scene>) interactions suggests that it is indeed integral to the domain. The long loop mentioned above contains a <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_Parvin//Parvin_overlap/6'>3-amino acid insertion</scene> (313-315) relative to other known CH domains and differs in conformation between different structures of alpha-parvin, suggesting it is relatively flexible.<ref>PMID: 18940607</ref> Interestingly, these two regions, the N-terminal linker helix and the long loop, are involved in binding of alpha-parvin to its binding partners, paxillin and ILK respectively.

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 differently. 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^α positions.<ref>PMID: 18940607</ref>  

When you <scene name='Alpha-parvin/Parvin/5'>align</scene> 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 good overall overlap (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.

The <scene name='Alpha-parvin/Ilk_parvin/1'>scene on the left</scene> shows the complex ([[3kmw]]) of the kinase domain of integrin-linked kinase (ILK, red) bound to the C-terminal CH domain of alpha-parvin (blue). One can also see the molecule of ATP (green) and the space-fill representation of the magnesium atom (white). When we <scene name='Alpha-parvin/Ilk_parvin/2'>turn the structure</scene> so that the N-terminal helix (now orange) of the CH domain of alpha-parvin is pointing up, we can see that unlike paxillin LD motifs, ILK kinase domain does not bind to the N-terminal region of the CH domain, but rather near the <scene name='Alpha-parvin/Ilk_parvin/3'>long loop</scene> between helices αC and αE. Other parts of the CH domain are also involved in binding, leading to a high interface area (around 1900 Ų) characteristic of high-affinity complexes.<ref>PMID:20005845</ref> Interestingly, ILK, which was recently proved to lack kinase activity<ref>PMID:20005845</ref><ref>PMID: 20033063</ref>, binds alpha-parvin analogously to the way in which kinases bind their substrates, i.e. with its pseudoactive site. The binding is not dependent on the presence of ATP. On the ILK's side the binding is mediated primarily by <scene name='Alpha-parvin/Ilk_parvin/6'>one of the helices</scene> (αG) and a <scene name='Alpha-parvin/Ilk_parvin/5'>part of the activation loop</scene>. The complex formation is particularly dependent on <scene name='Alpha-parvin/Ilk_parvin/7'>methionine 402 and lysine 403</scene> in αG of ILK - if these two residues are mutated to alanines, the complex formation is completely abolished. These residues are involved in many interactions with alpha-parvin (one of them, a hydrogen bond to asparagine 280, is shown) or water molecules (one of them shown as a pink dot).

==References==

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