Sandbox Reserved 824: Difference between revisions
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''Note : for a readability purpose the structures enlighten in the Jmol applet will focus only on one SRP54. The same structures are present in the second SRP54M of the dimer.'' | ''Note : for a readability purpose the structures enlighten in the Jmol applet will focus only on one SRP54. The same structures are present in the second SRP54M of the dimer.'' | ||
The secondary structure of | The secondary structure of human SRP54M is formed of <scene name='56/568022/Hsrp54m_h1_to_h7/1'>7 alpha helixes (H1 to H7)</scene>. The helices 2 to 7 form the <scene name='56/568022/Hsrp54m_core_and_h1v2/2'>Core structure</scene>, stabilized by hydrophobic, hydrogen and ionic interactions. | ||
Several residues important to maintain the Core structure were identified. Among them the <scene name='56/568022/Hsrp54m_core_and_h1/2'>Methionine 382,Glutamine 386, Arginine 402 and Arginine 405.</scene> | Several residues important to maintain the Core structure were identified. Among them the <scene name='56/568022/Hsrp54m_core_and_h1/2'>Methionine 382,Glutamine 386, Arginine 402 and Arginine 405.</scene> | ||
Met382 is invariable while Glu386, Arg402 and Arg405 are well-conserved but not systemically found in the SRP54M of different organisms. | Met382 is invariable while Glu386, Arg402 and Arg405 are well-conserved but not systemically found in the SRP54M of different organisms. | ||
The remaining helix, <scene name='56/568022/ | The remaining helix, <scene name='56/568022/Hsrp54m_core_and_h1v2/1'>H1</scene>, is not part of the Core and protrudes from it. | ||
Between the helices are loops of various importance. | Between the helices are loops of various importance. | ||
The loop including the <scene name='56/568022/Hsrp54m_loop_349-365/ | The loop including the <scene name='56/568022/Hsrp54m_loop_349-365/2'>aminoacids 349 to 365</scene>, besides having an important role in SRP54 function, has the particularity to have two phenylalanine residues, <scene name='56/568022/Hsrp54m_phe355_and_phe359/1'>Phe355 and Phe359</scene>, stacking their aromatic cycles. The function of this loop will be developed in the next part. | ||
==Fonction== | ==Fonction== | ||
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SRP54M binds the SRP RNA 7S by electrostatic interactions. | SRP54M binds the SRP RNA 7S by electrostatic interactions. | ||
The residues responsible for this interaction are localized in <scene name='56/568022/Hsrp54m_rna_bindv3/1'>helices 4, 5, 6 and 7</scene>, but most particularly in helices 5 and 6. | The residues responsible for this interaction are localized in <scene name='56/568022/Hsrp54m_rna_bindv3/1'>helices 4, 5, 6 and 7</scene>, but most particularly in helices 5 and 6. | ||
A large part of the top is therefore positively charged to bind with the negatively charged 7S RNA. | A large part of the top of SRP54M is therefore positively charged to bind with the negatively charged 7S RNA. | ||
[[Image:Proteopedia charge.png|300px|center|thumb| The helices 4, 5, 6 and 7 surfaces are colored in blue on the spacefill model of SRP54M in this picture. For more details see figure 7 of reference 1.]] | [[Image:Proteopedia charge.png|300px|center|thumb| The helices 4, 5, 6 and 7 surfaces are colored in blue on the spacefill model (left) of SRP54M in this picture. For more details see figure 7 of reference 1.]] | ||
It was also shown that the SRP54M - SRP RNA interaction is highly dependent of the structural integrity of the <scene name='56/568022/ | It was also shown that the SRP54M - SRP RNA interaction is highly dependent of the structural integrity of the <scene name='56/568022/Hsrp54m_core_and_h1v2/2'>Core structure</scene>. | ||
Experiments conducted with shorter versions of the M-domain, lacking some aminoacids of the Core, showed a loss in SRP RNA binding activity. | Experiments conducted with shorter versions of the M-domain, lacking some aminoacids of the Core, showed a loss in SRP RNA binding activity. | ||
