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Regulation of the Protein-Conducting Channel by a Bound Ribosome

2009; Elsevier BV; Volume: 17; Issue: 11 Linguagem: Inglês

10.1016/j.str.2009.09.010

1878-4186

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

RNA modifications and cancer

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.