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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding.

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    Summary
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    Poly(ADP-ribose) (PAR), a key regulator in cells, is stiffer than DNA or RNA. Its unique switch-like compaction in response to cations and proteins may explain its specific molecular recognition functions.

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    Area of Science:

    • Biochemistry and Molecular Biology
    • Biophysics

    Background:

    • Poly(ADP-ribose) (PAR) is an RNA-like homopolymer crucial for DNA repair, RNA metabolism, and biomolecular condensate formation.
    • Dysregulation of PAR is linked to cancer and neurodegeneration, yet its fundamental biophysical properties remain largely unknown.
    • Previous studies faced challenges in characterizing PAR due to its dynamic and repetitive nature.

    Approach:

    • Employed single-molecule fluorescence resonance energy transfer (smFRET) for the first time to characterize PAR's biophysical properties.
    • Investigated PAR flexibility and compaction under varying cation (Na+, Mg2+, Ca2+, spermine) concentrations and conditions.
    • Assessed the role of the intrinsically disordered protein FUS as a macromolecular cation in compacting PAR.

    Key Points:

    • PAR exhibits a significantly longer persistence length and greater stiffness compared to DNA and RNA.
    • PAR undergoes a sharp, switch-like transition from an extended to a compact state, unlike the gradual compaction of DNA/RNA.
    • The degree of PAR compaction is dependent on cation concentration and valency, as well as protein binding.

    Conclusions:

    • PAR possesses inherent stiffness and undergoes abrupt compaction triggered by cationic environments and protein interactions.
    • These unique physical properties suggest a mechanism for PAR's specific molecular recognition in cellular processes.
    • Understanding PAR's biophysics provides insights into its regulatory roles and potential therapeutic targeting.