MECHANISM OF PEPTIDE BOND FORMATION IN RIBOSOME

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 核糖体是活细胞中重要的分子机器，蛋白质在核糖体中通过氨基酸单元之间的肽键形成(PBF)来合成。PBF是肽基转移核糖核酸的酯键被氨酰基转移核糖核糖核酸的氨基氨解。核糖体中PBF的详细化学机制，尽管从结晶学、动力学和计算研究中获得了许多有价值的见解，但尚未完全阐明，包括核糖体环境所起的具体作用，即一些关键的RNA基团和存在于肽转移酶中心的少数水是如何催化PBF的。由于相关核糖体环境的规模相当大，以及直接参与反应事件的大量原子需要进行量子化学处理，因此需要QM/MM技术。我们将采用两步法来研究PBF的化学机理：(A)核心反应体系(CRS)的过渡态优化-包括最直接参与反应的原子--嵌入核糖体环境，然后计算从反应物到产物的内禀反应坐标路径(IRCP)-CRS将在DFT/B3LYP/6-31G*从头开始处理，周围环境由经典的琥珀力场描述。(B)在上一步建议的几个假定反应坐标下使用伞形抽样进行QM/MM MD模拟，以计算反应自由能-模拟将使用CHARMM和Q-CHEM软件，或适用于QM/MM模拟的一些其他软件包。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The ribosome is an important molecular machine in living cells in which proteins are synthesized via peptide bond formation (PBF) between amino acid units. PBF is an aminolysis of the esteric bond of the peptidyl-transfer-RNA by the amino group of the aminoacyl-transfer-RNA. The detailed chemical mechanism of PBF in the ribosome, despite numerous and valuable insights from crystallographic, kinetic, and computational studies, has yet to be fully elucidated, including the specific roles played by the ribosomal environment, i.e. how some key RNA groups and the few waters present in the peptidyl transferase center catalyze PBF. Because of both the rather large size of the relevant ribosomal environment and the significant number of atoms directly involved in the reactive event that need to be treated quantum chemically, QM/MM technology is required. We will adopt a two-step approach to the study of the PBF chemical mechanism: (a) Transition state optimization of the core reaction system (CRS) --- comprising the atoms most directly involved in the reaction --- embedded in the ribosomal environment, followed by the calculation of the intrinsic reaction coordinate path (IRCP) from reactants to products --- the CRS will be treated ab initio at the DFT/B3LYP/6-31G* with the surrounding environment described by the classical AMBER force field. (b) QM/MM MD simulations using umbrella sampling in several assumed reaction coordinates suggested by the previous step to calculate the reaction free energy --- the simulations will use the CHARMM and Q-CHEM software, or some other packages suitable for QM/MM simulations.