Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures

Area of Science:

• Structural Biology
• Molecular Biology
• Biochemistry

Background:

• Numerous 3D density maps of the 70S ribosome in various functional states are publicly available.
• Understanding ribosome conformational dynamics is crucial for elucidating protein synthesis mechanisms.

Purpose of the Study:

• To systematically analyze available 70S ribosome EM structures using a novel flexible-fitting approach.
• To reveal global conformational differences and dynamics between different functional states of the 70S ribosome.

Main Methods:

• Utilized a new flexible-fitting approach for analyzing existing 3D electron microscopy (EM) density maps of the 70S ribosome.
• Systematic comparison of conformational states across multiple available EM structures.

Main Results:

• Observed large-scale, ratchet-like deformations in initiation complexes and structures bound with elongation factor G (EFG), ribosome recycling factor (RRF), and release factor 3 (RF3).
• The L1 stalk was frequently in a 'blocking state' for E-site tRNA, potentially hindering tRNA release.
• EM structures bound with EFG or RRF showed aligned conformational spaces, indicating a concerted pathway for large-scale ribosome changes.

Conclusions:

• The 70S ribosome undergoes significant conformational changes during key steps of protein synthesis.
• The L1 stalk's position plays a critical role in regulating tRNA interaction and release.
• Factor-mediated ribosome conformational changes likely follow specific, concerted pathways.