Regulation of the protein-conducting channel by a bound ribosome.
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.
Gumbart
James
J
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Trabuco
Leonardo G
LG
Schreiner
Eduard
E
Villa
Elizabeth
E
Schulten
Klaus
K
D003198:Computer Simulation; D020285:Cryoelectron Microscopy; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D017017:Methanococcus / Q000737:chemistry*; D008958:Models, Molecular; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D000069816:SEC Translocation Channels
D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D000069816:SEC Translocation Channels