Regulation of the Protein-Conducting Channel by a Bound Ribosome

James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, through molecular dynamics flexible fitting (MDFF), an atomic-resolution model of the ribosome-channel complex. We characterized computationally the sites of ribosome-SecY interaction within the complex and determined the effect of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer by adding a second copy of SecY to the MDFF-derived model. The study involved 2.7-million-atom simulations over altogether nearly 50 ns.

Original languageEnglish (US)
Pages (from-to)1453-1464
Number of pages12
JournalStructure
Volume17
Issue number11
DOIs
StatePublished - Nov 11 2009

Keywords

  • DNA
  • PROTEINS
  • RNA

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

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