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-Structure paper
タイトル | Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates. |
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ジャーナル・号・ページ | Nat Chem, Vol. 15, Issue 7, Page 913-921, Year 2023 |
掲載日 | 2023年6月12日 |
![]() | Zoe L Watson / Isaac J Knudson / Fred R Ward / Scott J Miller / Jamie H D Cate / Alanna Schepartz / Ara M Abramyan / ![]() |
PubMed 要旨 | 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. ...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. |
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手法 | EM (単粒子) |
解像度 | 2.1 - 2.3 Å |
構造データ | EMDB-28254, PDB-8emm: ![]() EMDB-28255: 70S map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates" ![]() EMDB-28256: 30S-focused map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates" ![]() EMDB-28257: 50S-focused map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates" |
化合物 | ![]() ChemComp-MG: ![]() ChemComp-SPD: ![]() ChemComp-SPM: ![]() ChemComp-K: ![]() ChemComp-ZN: ![]() ChemComp-MET: ![]() ChemComp-PAR: ![]() ChemComp-HOH: |
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![]() | RIBOSOME / tRNA / e. coli |