Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding

Abstract

Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.

Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations

“…Previously, we have shown that PAR possesses a larger persistence length than RNA, thereby being stiffer, a characteristic attributed to the greater electrostatic repulsion imposed by two phosphates instead of one in RNA per monomer. 23 Both PAR and RNA assume more compact states with increasing salt concentration—a compaction that occurs with 100x fewer divalent than monovalent ions. 23 Building on this polymeric characterization, we set out to explore the 3D structure of PAR.…”

“…23 Both PAR and RNA assume more compact states with increasing salt concentration—a compaction that occurs with 100x fewer divalent than monovalent ions. 23 Building on this polymeric characterization, we set out to explore the 3D structure of PAR. Our studies reveal that the structure of PAR markedly diverges from that of poly-A RNA.…”

“…Our MD simulations showed PAR 22 undergoes steady compaction as cation concentration increases, with Mg 2+ inducing greater compaction compared to Na + , corroborating recent findings. 23 Next, we selected conditions close to physiological ionic strength and applied MD-SAXS to extract structural ensembles for two different PAR lengths, PAR 15 and PAR 22 . These lengths are not only commonly observed in mammalian cells but are also within the bacterial PARP-produced range.…”

Regulation of Biomolecular Condensates by Poly(ADP-ribose)

“…PAR chains are also stiffer than RNA or DNA chains. 30 This section is a primer on the enzymatic cycle underlying PAR synthesis and catabolism, and the catalytic activity of PARPs.…”

“…Therefore, the structure of an ADP-ribose unit resembles NAD + without the nicotinamide group. , Target proteins can be mono- or poly­(ADP-ribosylated), and PAR chains can be up to ∼200 units long. , Because PAR chains are covalently attached to proteins, long PAR modifications significantly impact the structure and biochemical properties of the target protein. PAR chains are also stiffer than RNA or DNA chains . This section is a primer on the enzymatic cycle underlying PAR synthesis and catabolism, and the catalytic activity of PARPs.…”