Sandbox Reserved 824: Difference between revisions

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SRP54M is a 120 aminoacids long polypeptide. 1QB2 is a <scene name='56/568022/Hsrp54m_dimer/1'>dimer of SRP54M</scene>, since the studied polypeptide has the interesting property to dimerize in solution.
SRP54M is a 120 aminoacids long polypeptide. 1QB2 is a <scene name='56/568022/Hsrp54m_dimer/1'>dimer of SRP54M</scene>, since the studied polypeptide has the interesting property to dimerize in solution.


Note : for lisibility purpose the structures enlighten in the Jmol applet will focuse only on one SRP54. The same structures are present in the second SRP54M of the dimer.
Note : in 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 Hsrp54M is formed of <scene name='56/568022/Hsrp54m_h1_to_h7/1'>7 alpha helixes (H1 to H7)</scene>.The helixes 2 to 7 form the <scene name='56/568022/Hsrp54m_core_and_h1/1'>Core structure</scene>, stabilized by hydrophobic, hydrogen and ionic interactions.
The secondary structure of Hsrp54M 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_h1/1'>Core structure</scene>, stabilized by hydrophobic, hydrogen and ionic interactions.


Several residues importants to maintain the Core structure where identified.
Several residues important to maintain the Core structure were identified.
Among them the Methionine 382,Glutamine 386, Arginine 402 and Arginine 405.  
Among them the Methionine 382,Glutamine 386, Arginine 402 and Arginine 405.  
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.
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The remaining helix, <scene name='56/568022/Hsrp54m_core_and_h1/1'>H1</scene>, is not part of the Core and protrudes from it.
The remaining helix, <scene name='56/568022/Hsrp54m_core_and_h1/1'>H1</scene>, is not part of the Core and protrudes from it.


Between the helixes are loops of various importance.  
Between the helices are loops of various importance.  
The loop including the aminoacids 349 to 365, 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.
The loop including the aminoacids 349 to 365, 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.


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:Signal peptide binding  
:Signal peptide binding  


The signal peptide binds SRP54M in an <scene name='56/568022/Hsrp54m_groove/1'>hydrophobic groove</scene> formed by helixes 2, 3 and 4 as well as the loop 349-365 (17 aminoacids) previously mentioned.
The signal peptide binds SRP54M in an <scene name='56/568022/Hsrp54m_groove/1'>hydrophobic groove</scene> formed by helices 2, 3 and 4 as well as the loop 349-365 (17 aminoacids) previously mentioned.
These structures circumscribe a deep elongated hydrophobic groove matching the shape and chemical properties of known signal peptides.
These structures circumscribe a deep elongated hydrophobic groove matching the shape and chemical properties of known signal peptides.


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This hypothesis has however to be confirmed since 1QB2 is only a fragment of SRP54, and that the M-domain, linked to the N and G domains, might adopt another conformation.
This hypothesis has however to be confirmed since 1QB2 is only a fragment of SRP54, and that the M-domain, linked to the N and G domains, might adopt another conformation.


: SRP RNA binding (pas encore corrigée)
: SRP RNA binding


SRP54M binds the SRP RNA 7S by electrostatic interactions  
SRP54M binds the SRP RNA 7S by electrostatic interactions  
Most of the residues involved are localized on <scene name='56/568022/Hsrp54m_rna_bind/1'>helixes 5 and 6</scene>, but a few aminoacids of <scene name='56/568022/Hsrp54m_rna_bind/1'>helixes 4 and 7</scene> also play a role. (inserer image)
Most of the residues involved are localized on <scene name='56/568022/Hsrp54m_rna_bind/1'>helices 5 and 6</scene>, but a few aminoacids of <scene name='56/568022/Hsrp54m_rna_bind/1'>helixes 4 and 7</scene> also play a role. (inserer image)


It was also shown that the SRP54M - SRP RNA interaction is highly dependant of the structural integrity of the SRP54M Core.  
It was also shown that the SRP54M - SRP RNA interaction is highly dependent of the structural integrity of the SRP54M Core.  
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.


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