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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Protein synthesis accuracy depends on correct messenger RNA (mRNA) decoding by transfer RNA (tRNA).
  • Elongation factor-Tu (EF-Tu) is crucial for guiding this decoding process.
  • Conserved residues in EF-Tu play vital roles in its function.

Purpose of the Study:

  • To investigate the functional impact of mutations at aspartate 81 (D81), a conserved residue in EF-Tu.
  • To elucidate the molecular mechanisms by which D81 mutations affect EF-Tu function and translation fidelity.

Main Methods:

  • GTPase activity assays to measure enzymatic function.
  • AlphaFold modeling (AlphaFold2 and AlphaFold3) for structural predictions.
  • Quantum-sensing-based super-resolution force spectroscopy (SURFS) to probe ribosome dynamics.
  • Sub-nucleotide ribosome footprinting to assess tRNA release.

Main Results:

  • All D81 mutations retained GTPase activity but impaired tRNA release from the ribosome.
  • AlphaFold3 modeling indicated that D81 mutations disrupt magnesium ion coordination and interaction with the sarcin-ricin loop in the GTP-bound state.
  • AlphaFold2 analysis revealed D81 anchors coevolutionary constraints, and its mutation allows for cryptic structural variation.

Conclusions:

  • A single conserved residue, D81, links catalytic coordination, allosteric communication, and evolutionary constraint in EF-Tu.
  • Mutations at D81 provide mechanistic insights into translation fidelity.
  • Super-resolution force spectroscopy (SURFS) is a valuable tool for studying ribosome dynamics.