Structural insights into pre-translocation ribosome motions

Area of Science:

• Structural biology
• Molecular biology
• Biochemistry

Background:

• The ribosome undergoes conformational changes during translation elongation.
• Understanding the rotated ribosome conformation (R(F)) is key for novel antibiotic development.
• Previous studies lacked a complete 3D atomic structure of R(F) and its transition dynamics.

Purpose of the Study:

• To build an almost complete atomic model of the Thermus thermophilus ribosome in the R(F) conformation.
• To generate a structural model of an intermediate state (R(2)) in the R(1) to R(F) transition.
• To provide atomic insights into tRNA movement during ribosome translocation.

Main Methods:

• Fitting of Thermus thermophilus ribosomal RNA and proteins into cryo-EM reconstructions of E. coli ribosomes.
• Utilizing a cryo-EM structure of an intermediate state (R(2)) to guide model generation.
• Developing a multiresolution method for morphing large macromolecular complexes.

Main Results:

• An almost complete atomic model of the T. thermophilus ribosome in R(F) was constructed.
• The model validated known intersubunit bridges and predicted new R(F)-specific bridges.
• Structural models of R(F) and R(2) states were generated, revealing tRNA movement from P/P to P/E configuration.

Conclusions:

• The study provides detailed atomic models crucial for understanding ribosome translocation dynamics.
• The findings offer insights into the functional significance of the R(2) state.
• The developed methods are extensible to other aspects of protein synthesis and larger molecular systems.