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==Context / Work in Progress==
==Context / Work in Progress==
-
SRP54 is a 54kDa cytosolic protein part of the Signal Recognition Particle (SRP).
+
SRP54 is a 54kDa cytosolic protein part of the Signal Recognition Particle (SRP).
-
SRP54 homologous proteins can be referred to as Ffh (Fifty Four Homologous)*.
+
SRP54 bacterial homologous can be referred to as Ffh (Fifty Four Homologous)*.
 +
SRP is a ribonucleoprotein particle essential for the translation and integration in membranes of signal peptide-bearing proteins. SRP is composed of an RNA backbone, on which bind different proteins.
 +
For example Mammalian SRP are formed of the RNA 7S and SRN 9-14-19-54-68-72*.
 +
SRP54 and regions of RNA 7S are highly conserved in every organism and it was found that these two components are sufficient to form a minimal SRP*.
 +
The role of SRP is to :
 +
*Bind signal peptide bearing proteins at the beginning of their translation by the ribosome (at this step we call the ribosome and the protein it began to translate the Ribosome Nascent Chain – RNC)
 +
*Stop protein elongation
 +
*Dock the RNC to a SRP Receptor (SR) and insert the protein into a translocon channel. This final step is GTP-dependant.
-
SRP is a ribonucleoprotein particle essential for the translation and integration in membranes of signal peptide-bearing proteins.
+
SRP54 is responsible for the signal peptide binding and the GTP-dependant interaction with SR. This protein is therefore essential in the SRP mechanism resulting in the integration of proteins into membranes or their secretion.
-
SRP is composed of an RNA backbone, on which bind different proteins.
+
-
For example Mammalian SRP are formed of the RNA 7S and SRN 9-14-19-54-68-72*.
+
SRP54 is a 504 aminoacids protein,composed of 3 domains:
 +
- A N-terminal domain with 4 alpha-helices;
 +
- A G domain, central, with a GTPase activité
 +
- and the M domain ( for Methionin Rich).
-
SRP54 and regions of RNA 7S are highly conserved in every organism and it was found that these two components are sufficient to form a minimal SRP*.
+
The 1QB2 structure is the M-domain of the human SRP54. It includes the aminoacids 322 to 441.
 +
The following parts will treat of 1QB2 structure and its relation to the functions of SRP54M.
-
The role of SRP is to :
+
==Structure==
-
:* Bind signal peptide bearing proteins at the beginning of their translation by the ribosome (at this step we call the ribosome and the protein it began to translate the Ribosome Nascent Chain – RNC)
+
SRP54M is a 120 aminoacids long polypeptide. 1QB2 shows two of them, since the SRP54M has the interesting property to dimerize in solution.
-
:* Stop protein elongation
+
-
:* Dock the RNC to a SRP Receptor (SR) and insert the protein into a translocon channel. This final step is GTP-dependant.
+
-
SRP54 is responsible for the signal peptide binding and the GTP-dependant interaction with SR.
+
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.
-
This protein is therefore essential in the SRP mechanism resulting in the integration of proteins into membranes or their secretion.
+
-
asterisque = references aux publis, faire le lien avec les publis cites en fin d’article
+
The secondary structure of Hsrp54M is formed of 7 alpha helixes (H1 to H7).The helixes 2 to 7 form the Core structure, stabilized by hydrophobic, hydrogen and ionic interactions.
-
 
+
-
==Structure==
+
-
''(Domaines N, G, M / ''
+
Several residues importants to maintain the Core structure where identified.
-
''Interaction N-G => Domaine NG pour activité GTPase / Mention du domaine NG très similaire de SR alpha''
+
Among them the Methionine 382,Glutamine 386, Arginine 402 and Arginine 405.
-
''Domaine M avec partie rigide en c-term, partie flexible en n-term et grossièrement leurs fonctions)''
+
Met382 is invariable while Glu386, Arg402 and Arg405 are well-conserved but not systemically found in the SRP54M of different organisms.
 +
The remaining helix, H1, is not part of the Core and protrudes from it.
-
SRP54 is composed of 3 domains: N terminal domain with 4 alpha-helices; G domain, central, corresponding to a GTPase activity and the M domain (Methionin Rich). M domain corresponds to 1qb2 protein.
+
Between the helixes 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 (Phe355 and Phe359) stacking their aromatic cycles. The function of this loop will be developed in the next part.
-
SRP54M is composed by 504 Amino Acids, forming 7 alpha helices (h1 to h7). The helices 2 to 7 from the core protein, stabilized by hydrophobic residues such as Met382 (invariant) and by hydrogen and salt bonds involving conserved amino acids: Glu386, Arg402, and Arg405. The helix 1 extends from the core protein.
+
==Fonction==
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The protein was difficult to crystalize, and it appears in the crystals dimeres of 1QB2 protein.
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:Signal peptide binding
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1QB2 contains 2 binding domains:
+
-
:* Peptide signal binding domain
+
-
:* SRP RNA binding domain
+
-
+
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: Signal peptide binding domain
+
-
This domain involves h2 to h4 to generate the hydrophobic groove witch will recognise and bind the nascent protein. It also involves a highly structured loop between h2 and h3: 17 amino acids (349 to 365) with the Met-Ile-Pro-Gly motif (351 to 354) and two phenylalanins (355 and 359). In addition of the loop and the three helices, h1 is located near the hydrophobic groove and is an equivalent of the signal peptide. This similarity explains the dimerization of 1QB2 in the crystal. Each h1 take place in the groove of the opposite monomer. Because of this interaction, we are able to suppose that h1 in vivo is involved in protection of the hydrophobic groove against solvents.
+
-
: SRP RNA binding domain
+
The signal peptide binds SRP54M in an hydrophobic groove formed by helixes 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.
-
The RNA is linked to the 1QB2 protein by electrostatic potential. This interaction involves helices 5 and 6, but also some small parts of helices 4 and 7. This proposal is confirmed by experiments of directed site mutation (Gowda et al., 1998). It appears that some basics residues are required (Arg402 and Arg405) to maintain the core structure and the interaction with the RNA.
+
Interestingly enough, the dimer structure of 1QB2 shows that the groove of the first SRP54M is occupied by the H1 helix of the second SRP54M.
 +
The study of the H1 helix indicates that it shares common physical and chemical properties with alpha-helical signal peptides.
 +
Theses similarities might come from the fact that the H1 helix is near the hydrophobic groove of its own SRP54M, and that conformational changes (in a full SRP54 protein) might bring H1 into the groove in order to protect it from solvent interaction in the absence of signal peptide.
 +
It was therefore hypnotized that the binding of H1 into the groove of another SRP54M provides a possible model of the interaction between the signal peptide and SRP54M in vivo.
 +
It also explains the dimerization of SRP54M in solution.
-
==Remarks:==
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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.
-
It is important to note the linkage between M and G subunits of SRP54, GTP hydrolysis in the G subunit could provide conformational changes and modify interactions, especially for electrostatic bonds with the signal peptide (released after hydrolysis).
+
 +
: SRP RNA binding (pas encore corrigée)
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==Fonctions==
+
The RNA is linked to the 1QB2 protein by electrostatic potential. This interaction involves helices 5 and 6, but also some small parts of helices 4 and 7. This proposal is confirmed by experiments of directed site mutation (Gowda et al., 1998). It appears that some basics residues are required (Arg402 and Arg405) to maintain the core structure and the interaction with the RNA.
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''Lien avec la structure, explications des intéractions en fonction des structures etc ...
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==Scènes à intégrer==
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''
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<scene name='56/568022/Hsrp54m_dimer/1'>hSRP54M Dimer</scene>
<scene name='56/568022/Hsrp54m_dimer/1'>hSRP54M Dimer</scene>

Revision as of 02:40, 4 January 2014

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This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.
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Contents

Context / Work in Progress

SRP54 is a 54kDa cytosolic protein part of the Signal Recognition Particle (SRP). SRP54 bacterial homologous can be referred to as Ffh (Fifty Four Homologous)*. SRP is a ribonucleoprotein particle essential for the translation and integration in membranes of signal peptide-bearing proteins. SRP is composed of an RNA backbone, on which bind different proteins. For example Mammalian SRP are formed of the RNA 7S and SRN 9-14-19-54-68-72*. SRP54 and regions of RNA 7S are highly conserved in every organism and it was found that these two components are sufficient to form a minimal SRP*. The role of SRP is to :

  • Bind signal peptide bearing proteins at the beginning of their translation by the ribosome (at this step we call the ribosome and the protein it began to translate the Ribosome Nascent Chain – RNC)
  • Stop protein elongation
  • Dock the RNC to a SRP Receptor (SR) and insert the protein into a translocon channel. This final step is GTP-dependant.

SRP54 is responsible for the signal peptide binding and the GTP-dependant interaction with SR. This protein is therefore essential in the SRP mechanism resulting in the integration of proteins into membranes or their secretion.

SRP54 is a 504 aminoacids protein,composed of 3 domains: - A N-terminal domain with 4 alpha-helices; - A G domain, central, with a GTPase activité - and the M domain ( for Methionin Rich).

The 1QB2 structure is the M-domain of the human SRP54. It includes the aminoacids 322 to 441. The following parts will treat of 1QB2 structure and its relation to the functions of SRP54M.

Structure

SRP54M is a 120 aminoacids long polypeptide. 1QB2 shows two of them, since the SRP54M 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.

The secondary structure of Hsrp54M is formed of 7 alpha helixes (H1 to H7).The helixes 2 to 7 form the Core structure, stabilized by hydrophobic, hydrogen and ionic interactions.

Several residues importants to maintain the Core structure where identified. 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.

The remaining helix, H1, is not part of the Core and protrudes from it.

Between the helixes 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 (Phe355 and Phe359) stacking their aromatic cycles. The function of this loop will be developed in the next part.

Fonction

Signal peptide binding

The signal peptide binds SRP54M in an hydrophobic groove formed by helixes 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.

Interestingly enough, the dimer structure of 1QB2 shows that the groove of the first SRP54M is occupied by the H1 helix of the second SRP54M. The study of the H1 helix indicates that it shares common physical and chemical properties with alpha-helical signal peptides. Theses similarities might come from the fact that the H1 helix is near the hydrophobic groove of its own SRP54M, and that conformational changes (in a full SRP54 protein) might bring H1 into the groove in order to protect it from solvent interaction in the absence of signal peptide.

It was therefore hypnotized that the binding of H1 into the groove of another SRP54M provides a possible model of the interaction between the signal peptide and SRP54M in vivo. It also explains the dimerization of SRP54M in solution.

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)

The RNA is linked to the 1QB2 protein by electrostatic potential. This interaction involves helices 5 and 6, but also some small parts of helices 4 and 7. This proposal is confirmed by experiments of directed site mutation (Gowda et al., 1998). It appears that some basics residues are required (Arg402 and Arg405) to maintain the core structure and the interaction with the RNA.

Scènes à intégrer

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