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Early encounters of a nascent membrane protein: specificity and timing of contacts inside and outside the ribosome.

Houben EN, Zarivach R, Oudega B, Luirink J - J. Cell Biol. (2005)

Bottom Line: The signal recognition particle (SRP) started to interact with the nascent IMP and to target the ribosome-nascent chain complex to the Sec-YidC complex in the inner membrane when maximally half of the transmembrane domain (TM) was exposed from the ribosomal exit.The combined data suggest a flexible tunnel that may accommodate partially folded nascent proteins and parts of the SRP and SecY.Intraribosomal contacts of the nascent chain were not influenced by the presence of a functional TM in the ribosome.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Microbiology, Institute of Molecular Cell Biology, Vrije Universiteit, 1081 HV Amsterdam, Netherlands.

ABSTRACT
An unbiased photo-cross-linking approach was used to probe the "molecular path" of a growing nascent Escherichia coli inner membrane protein (IMP) from the peptidyl transferase center to the surface of the ribosome. The nascent chain was initially in proximity to the ribosomal proteins L4 and L22 and subsequently contacted L23, which is indicative of progression through the ribosome via the main ribosomal tunnel. The signal recognition particle (SRP) started to interact with the nascent IMP and to target the ribosome-nascent chain complex to the Sec-YidC complex in the inner membrane when maximally half of the transmembrane domain (TM) was exposed from the ribosomal exit. The combined data suggest a flexible tunnel that may accommodate partially folded nascent proteins and parts of the SRP and SecY. Intraribosomal contacts of the nascent chain were not influenced by the presence of a functional TM in the ribosome.

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Tunnel view of the large ribosomal subunit from Deinococcus radiodurans. The 40–amino acid nascent Lep (blue) and TM (red) is stretched from P-site tRNA (salmon pink) to the ribosomal exit tunnel and makes contacts with ribosomal proteins L22 (yellow), L4 (green), and L23 (orange).
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fig5: Tunnel view of the large ribosomal subunit from Deinococcus radiodurans. The 40–amino acid nascent Lep (blue) and TM (red) is stretched from P-site tRNA (salmon pink) to the ribosomal exit tunnel and makes contacts with ribosomal proteins L22 (yellow), L4 (green), and L23 (orange).

Mentions: In conclusion, these cross-linking data show that Lep progresses through the ribosome via the main ribosomal tunnel, where it contacts or is adjacent to successively L4, L23, and Ffh during nascent chain elongation, whereas L22 is near all tested nascent chain lengths (Fig. 1 C). L4, L22, and L23 decorate, together with the 23S RNA, the main ribosomal tunnel wall (Harms et al., 2001). L4 is only exposed at the most constricted part of the tunnel, not far from the PTC, whereas a long β-hairpin of L22 lies more or less parallel to the tunnel axis. L23 penetrates with a tail into the lower part of the tunnel wall, whereas its globular domain is located at the surface of the ribosome near the ribosomal exit site and functions in the docking of SRP (see Fig. 5).


Early encounters of a nascent membrane protein: specificity and timing of contacts inside and outside the ribosome.

Houben EN, Zarivach R, Oudega B, Luirink J - J. Cell Biol. (2005)

Tunnel view of the large ribosomal subunit from Deinococcus radiodurans. The 40–amino acid nascent Lep (blue) and TM (red) is stretched from P-site tRNA (salmon pink) to the ribosomal exit tunnel and makes contacts with ribosomal proteins L22 (yellow), L4 (green), and L23 (orange).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2171371&req=5

fig5: Tunnel view of the large ribosomal subunit from Deinococcus radiodurans. The 40–amino acid nascent Lep (blue) and TM (red) is stretched from P-site tRNA (salmon pink) to the ribosomal exit tunnel and makes contacts with ribosomal proteins L22 (yellow), L4 (green), and L23 (orange).
Mentions: In conclusion, these cross-linking data show that Lep progresses through the ribosome via the main ribosomal tunnel, where it contacts or is adjacent to successively L4, L23, and Ffh during nascent chain elongation, whereas L22 is near all tested nascent chain lengths (Fig. 1 C). L4, L22, and L23 decorate, together with the 23S RNA, the main ribosomal tunnel wall (Harms et al., 2001). L4 is only exposed at the most constricted part of the tunnel, not far from the PTC, whereas a long β-hairpin of L22 lies more or less parallel to the tunnel axis. L23 penetrates with a tail into the lower part of the tunnel wall, whereas its globular domain is located at the surface of the ribosome near the ribosomal exit site and functions in the docking of SRP (see Fig. 5).

Bottom Line: The signal recognition particle (SRP) started to interact with the nascent IMP and to target the ribosome-nascent chain complex to the Sec-YidC complex in the inner membrane when maximally half of the transmembrane domain (TM) was exposed from the ribosomal exit.The combined data suggest a flexible tunnel that may accommodate partially folded nascent proteins and parts of the SRP and SecY.Intraribosomal contacts of the nascent chain were not influenced by the presence of a functional TM in the ribosome.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Microbiology, Institute of Molecular Cell Biology, Vrije Universiteit, 1081 HV Amsterdam, Netherlands.

ABSTRACT
An unbiased photo-cross-linking approach was used to probe the "molecular path" of a growing nascent Escherichia coli inner membrane protein (IMP) from the peptidyl transferase center to the surface of the ribosome. The nascent chain was initially in proximity to the ribosomal proteins L4 and L22 and subsequently contacted L23, which is indicative of progression through the ribosome via the main ribosomal tunnel. The signal recognition particle (SRP) started to interact with the nascent IMP and to target the ribosome-nascent chain complex to the Sec-YidC complex in the inner membrane when maximally half of the transmembrane domain (TM) was exposed from the ribosomal exit. The combined data suggest a flexible tunnel that may accommodate partially folded nascent proteins and parts of the SRP and SecY. Intraribosomal contacts of the nascent chain were not influenced by the presence of a functional TM in the ribosome.

Show MeSH
Related in: MedlinePlus