Trobro Stefan, Aqvist Johan
Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
Biochemistry. 2006 Jun 13;45(23):7049-56. doi: 10.1021/bi0605383.
The reaction mechanism of peptide bond formation on the ribosome is now becoming established by results from both experiments and computer simulations. Here, we analyze predictions from molecular dynamics simulations, as well as from new crystal structures, and examine their implications for the mechanisms of peptidyl transfer and peptidyl-tRNA hydrolysis. A number of computational predictions for the peptidyl transfer reaction, including quantitative energetics, stereochemistry, hydrogen bonding network, and role of solvent molecules, are found to be supported and confirmed by kinetic and structural data. The results show that this type of reaction calculations can provide important links between structure and function that cannot be obtained by experimental means.
核糖体上肽键形成的反应机制如今正通过实验和计算机模拟的结果得以确立。在此，我们分析了分子动力学模拟以及新晶体结构的预测结果，并研究了它们对肽基转移和肽基 - tRNA水解机制的影响。肽基转移反应的多项计算预测，包括定量能量学、立体化学、氢键网络以及溶剂分子的作用，均得到了动力学和结构数据的支持与证实。结果表明，这类反应计算能够提供结构与功能之间重要的联系，而这是通过实验手段无法获得的。
