美国加州大学Abramyan, Ara M.团队报道了大肠杆菌核糖体的原子模拟为翻译活性底物的选择提供了标准。相关研究成果发表在2023年6月12日出版的《自然—化学》。

随着遗传密码的扩展从L-α-氨基酸扩展到主链修饰和新的聚合化学，确定核糖体可以容纳哪些底物仍然是一个挑战。大肠杆菌核糖体在体外耐受非L-α-氨基酸，但迄今为止，很少有结构见解可以解释其作用，有效键形成的边界条件也未知。

该文中，研究人员确定了含有α-氨基酸单体的大肠杆菌核糖体的高分辨率低温电子显微镜结构，并使用元动力学模拟来定义能量表面最小值并了解掺入效率。不同结构类别的反应性单体有利于构象空间，其中氨酰基tRNA亲核试剂与Bürgi–Dunitz角为76–115°的肽基tRNA羰基的距离小于4。落在该构象空间之外的具有自由能最小值的单体不能有效地反应。这一见解应加速体内和体外核糖体合成序列定义的非肽异寡聚物。

附：英文原文

Title: Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

Author: Watson, Zoe L., Knudson, Isaac J., Ward, Fred R., Miller, Scott J., Cate, Jamie H. D., Schepartz, Alanna, Abramyan, Ara M.

Issue&Volume: 2023-06-12

Abstract: As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

DOI: 10.1038/s41557-023-01226-w

Source: https://www.nature.com/articles/s41557-023-01226-w