Diffusion of tRNA inside the ribosome is position-dependent

Area of Science:

• Biophysics
• Molecular Biology
• Computational Chemistry

Background:

• Quantifying the energy landscape of ribosome dynamics is crucial for integrating theoretical and experimental findings.
• Understanding the diffusive properties of molecules within the ribosome is essential for this quantification.

Purpose of the Study:

• To investigate the positional dependence of tRNA diffusion coefficients within the ribosome.
• To elucidate the role of electrostatic and solvation interactions in governing tRNA diffusion during accommodation.

Main Methods:

• All-atom explicit-solvent simulations with 50 μs of aggregate sampling.
• Comparison with an energetically "smooth" model to isolate interaction effects.

Main Results:

• The diffusion coefficient of tRNA is position-dependent within the ribosome.
• A significant (order of magnitude) decrease in apparent diffusion coefficient occurs during aminoacyl-tRNA (aa-tRNA) accommodation.
• Nonuniform diffusion arises from electrostatic and solvation interactions between tRNA and the ribosome.

Conclusions:

• Ribosomal energetics exhibit a hierarchical character, with steric interactions forming large-scale barriers and short-range features dictating diffusion rates.
• Electrostatic and solvation forces play a key role in modulating tRNA diffusion within the ribosome.