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TitleAtomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates.
Journal, issue, pagesNat Chem, Vol. 15, Issue 7, Page 913-921, Year 2023
Publish dateJun 12, 2023
AuthorsZoe L Watson / Isaac J Knudson / Fred R Ward / Scott J Miller / Jamie H D Cate / Alanna Schepartz / Ara M Abramyan /
PubMed AbstractAs 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.
External linksNat Chem / PubMed:37308707 / PubMed Central
MethodsEM (single particle)
Resolution2.1 - 2.3 Å
Structure data

28254

8emm

EMDB-28254, PDB-8emm:
Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates
Method: EM (single particle) / Resolution: 2.1 Å

EMDB-28255: 70S map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates"
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-28256: 30S-focused map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates"
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-28257: 50S-focused map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates"
Method: EM (single particle) / Resolution: 2.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-SPM:
SPERMINE / Spermine

ChemComp-K:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-MET:
METHIONINE / Methionine

ChemComp-PAR:
PAROMOMYCIN / Antimicrobial, medication*YM / Paromomycin

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / tRNA / e. coli

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