Gene

Function (biology)

Cell biology

Peptide bond

Biology

Messenger RNA

Transfer RNA

Protein biosynthesis

Peptide

Ribosomal protein

Biochemistry

Eukaryotic Ribosome

Translation (biology)

Stereochemistry

Ribosomal RNA

Nucleotide

23S ribosomal RNA

Peptidyl transferase

Chemistry

Chemical ligation

Ribosome

Biophysics

Nature Chemistry

During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies.

Insights into the ribosome function from the structures of non-arrested ribosome–nascent chain complexes