期刊
STRUCTURE
卷 17, 期 11, 页码 1453-1464出版社
CELL PRESS
DOI: 10.1016/j.str.2009.09.010
关键词
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资金
- National Institutes of Health [R01-GM067887, P41-RR05969]
- National Science Foundation [PHY0822613]
- National Center for Supercomputing Applications through the National Resources Allocation Committee [MCA93S028]
- Division Of Physics
- Direct For Mathematical & Physical Scien [0822613] Funding Source: National Science Foundation
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 cryoelectron 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.
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