Exit strategies for charged tRNA from GluRS.

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• The dissociation of charged tRNA from aminoacyl-tRNA synthetases (aaRSs) is a critical, rate-limiting step in protein synthesis.
• Understanding the molecular mechanisms governing this release is essential for comprehending translation fidelity and regulation.

Purpose of the Study:

• To computationally investigate factors influencing charged tRNA release from class I aaRSs.
• To elucidate the roles of active site protonation states, AMP, and elongation factor Tu in the dissociation process.

Main Methods:

• Employed molecular modeling, pK(a) calculations, and molecular dynamics simulations.
• Analyzed post-transfer states of glutamyl-tRNA synthetase (Glu-tRNA(Glu)) bound to charged tRNA.
• Utilized dynamical network analysis, local energetics, and free energy calculations.

Main Results:

• Confirmed that tRNA release is influenced by protonation states and elongation factor Tu.
• Identified a proton relay system involving conserved residue Glu41 that destabilizes the amino acid-tRNA complex.
• Showed that AMP protonation (to H-AMP) and subsequent proton migration to water facilitate complex destabilization and tRNA undocking.
• Demonstrated that elongation factor Tu accelerates tRNA core and acceptor stem dissociation.

Conclusions:

• The study proposes a detailed mechanism for charged tRNA release from class I aaRSs, involving proton transfers and conserved residues.
• Glu41 is identified as a crucial catalytic residue for destabilizing the amino acid-tRNA interaction.
• Elongation factor Tu plays a significant role in promoting efficient tRNA dissociation, impacting the overall translation process.