MECHANISM OF PEPTIDE BOND FORMATION IN RIBOSOME

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 核糖体是活细胞中的重要分子机器，其中蛋白质通过氨基酸单元之间的肽键形成（PBF）来合成。PBF是肽基转移RNA的酯键被氨酰基转移RNA的氨基氨解。PBF在核糖体中的详细化学机制，尽管从晶体学，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特定作用，即一些关键RNA基团和肽基转移酶中心中存在的少量沃茨如何催化PBF。由于相关核糖体环境的相当大的尺寸和直接参与需要量子化学处理的反应事件的大量原子，因此需要QM/MM技术。我们会分两步研究PBF的化学机制：（a）核心反应系统（CRS）的过渡态优化-包括最直接参与反应的原子-嵌入核糖体环境中，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/B3 LYP/6- 31 G *，周围环境由经典的琥珀力场描述。(b)QM/MM分子动力学模拟使用伞形采样在几个假设的反应坐标由上一步建议，以计算反应自由能-模拟将使用CHARMM和Q-CHEM软件，或其他一些软件包适合QM/MM模拟。

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.