James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and
Klaus Schulten.
Regulation of the protein-conducting channel by a bound ribosome.
Structure, 17:1453-1464, 2009.
(PMC: 2778611)
GUMB2009
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 most recently one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with molecular dynamics flexible fitting, we have modeled and simulated an atomic-resolution structure of the ribosome-channel complex. We characterized the sites of interaction within the complex and determined the effects of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer, finding that in simulation the dimer enhances ribosome binding and destabilizes a channel-blocking plug, preparing the channel to receive the nascent polypeptide. The study involved 2.7-million-atom simulations over altogether nearly 50 ns.
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