Makarov G I, Makarova T M, Sumbatyan N V, Bogdanov A A
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
Biochemistry (Mosc). 2016 Dec;81(13):1579-1588. doi: 10.1134/S0006297916130010.
The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.
核糖体作为一种复杂的分子机器，在合成蛋白质分子时会经历显著的构象变化。分子动力学模拟已被用作X射线晶体学、冷冻电子显微镜以及生化方法的补充手段，以回答许多现代结构方法尚未解决的问题。在本综述中，我们证明核糖体分子动力学的全原子建模在描述tRNA易位过程、新生肽在核糖体隧道中的行为原子细节、抗生素和其他小分子以及变构信号传递到核糖体功能位点的推定机制方面特别有用。
