Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome

Area of Science:

• Molecular Biology
• Biophysics
• Computational Chemistry

Background:

• Protein synthesis relies on intricate ribosome conformational changes.
• Experimental methods capture intermediate states, while computational approaches elucidate energy barriers.
• Previous studies focused on early aa-tRNA accommodation; this study examines the late stage.

Purpose of the Study:

• To computationally investigate the final stage of aminoacyl-tRNA (aa-tRNA) accommodation into the peptidyl transferase center (PTC).
• To identify key interactions and steric barriers governing the 3'-CCA tail entry into the PTC.
• To explore the functional implications of these barriers for ribosome-mediated tRNA proofreading.

Main Methods:

• Simplified energetic model and molecular dynamics (MD) simulations.
• Focus on the late phase of aa-tRNA accommodation, specifically the 3'-CCA tail.
• Quantitative analysis of distinct accommodation pathways and free-energy contributions.

Main Results:

• A distinct intermediate state is observed, induced by steric confinement of the aa-tRNA 3'-CCA tail.
• Two primary pathways for tail entry into the PTC were identified, involving different ribosomal RNA helices.
• Residue C2573 within Helix 90 significantly contributes to the late-accommodation steric barrier, impacting accommodation rates.

Conclusions:

• The late-stage accommodation of the aa-tRNA 3'-CCA tail is sterically regulated, forming a crucial intermediate.
• Ribosomal structural elements, particularly C2573, create a significant barrier that influences accommodation kinetics.
• This sterically induced barrier likely contributes to the ribosome's intrinsic tRNA proofreading mechanisms, ensuring translational fidelity.