Department of Chemistry, University of California, Berkeley, CA, USA.
Center for Genetically Encoded Materials, University of California, Berkeley, CA, USA.
Nat Chem. 2023 Jul;15(7):913-921. doi: 10.1038/s41557-023-01226-w. Epub 2023 Jun 12.
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 Å 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.
随着遗传密码的扩展超出 L-α-氨基酸，进入到主链修饰和新的聚合化学领域，确定核糖体能够容纳的底物仍然是一个挑战。大肠杆菌核糖体在体外可以容忍非 L-α-氨基酸，但目前可用的解释其如何做到这一点的结构见解很少，并且有效键形成的边界条件尚不清楚。在这里，我们确定了含有 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理解掺入效率。来自不同结构类别具有反应性的单体有利于一种构象空间，其中氨酰-tRNA 亲核试剂距离肽酰-tRNA 羰基的距离<4Å，Bürgi-Dunitz 角为 76-115°。具有落在该构象空间之外的最小自由能的单体不会有效地反应。这一见解应该加速体内和体外核糖体对序列定义的非肽杂寡聚物的合成。
