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Cooperativity in low-affinity Mg2+ binding to tRNA.

D Labuda, K Nicoghosian, R Cedergren

    The Journal of Biological Chemistry
    |January 25, 1985
    PubMed
    Summary
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    Sodium (Na+) and magnesium (Mg2+) ions noncompetitively inhibit lead (Pb2+)-catalyzed cleavage of phenylalanine tRNA (tRNAPhe). Mg2+ binding involves cooperative interactions at multiple sites, influencing tRNA structure and response to environmental signals.

    Area of Science:

    • Biochemistry
    • Molecular Biology
    • Structural Biology

    Background:

    • Transfer RNA (tRNA) is crucial for protein synthesis, undergoing structural changes upon ion binding.
    • Lead (Pb2+)-catalyzed cleavage is a method to probe tRNA structure and dynamics.
    • Understanding ion binding (Na+, Mg2+) is essential for elucidating tRNA function.

    Purpose of the Study:

    • To investigate the effects of Na+ and Mg2+ on Pb2+-catalyzed cleavage of tRNAPhe.
    • To characterize the binding sites and cooperativity of Mg2+ on tRNA.
    • To explore how low-affinity Mg2+ binding influences tRNA structure and environmental response.

    Main Methods:

    • Pb2+-catalyzed cleavage assays using tRNAPhe.
    • Inhibition kinetics analysis for Na+ and Mg2+.

    Related Experiment Videos

  • Data analysis to determine binding site number and cooperativity for Mg2+.

    • Main Results:

    • Na+ acts as a noncompetitive inhibitor of Pb2+-catalyzed tRNAPhe cleavage.
    • Millimolar concentrations of Mg2+ also noncompetitively inhibit the cleavage.
    • Mg2+ binding data suggest at least two cooperative binding sites, distinct from previously characterized weak/strong binding.

    Conclusions:

    • Low-affinity Mg2+ binding induces conformational changes in tRNA.
    • These changes may mimic protein-induced alterations, enabling concerted structural responses.
    • tRNA's overall structure can respond cooperatively to environmental cues like aminoacylation or codon binding at specific Mg2+ concentrations.