Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Structure. 2009 Nov 11;17(11):1453-64. doi: 10.1016/j.str.2009.09.010.
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.
在蛋白质合成过程中，核糖体常常需要与膜结合通道 SecY/Sec61 复合物形成复合物，以便将新生蛋白质穿过细胞膜易位。核糖体通道复合物的结构数据目前仅限于低分辨率的冷冻电子显微镜图谱，其中一个图谱显示了一个与单体 SecY 复合物结合的细菌核糖体。我们使用该图谱以及核糖体和 SecY 的可用原子水平模型，通过分子动力学灵活拟合（MDFF），确定了核糖体通道复合物的原子分辨率模型。我们通过计算确定了复合物中核糖体与 SecY 相互作用的位点，并确定了核糖体结合对 SecY 通道的影响。我们还通过向 MDFF 衍生的模型添加第二个 SecY 副本，构建了一个与 SecY 二聚体结合的核糖体模型。该研究涉及总共近 50 ns 的 270 万个原子模拟。
