Design principles of PI(4,5)P(2) clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

Phosphatidylinositol 4,5-bisphosphate (PIP(2)) clustering is a key component in cell signaling, yet little is known about the atomic-level features of this phenomenon. Network-theoretic analysis of multimicrosecond atomistic simulations of PIP(2) containing asymmetric bilayers under protein-free conditions, presented here, reveals how design principles of PIP(2) clustering are determined by the specific cation effects. Ca(2+) generates large clusters (6% are pentamer or larger) by adding existing PIP(2) dimers formed by strong O‒Ca(2+)‒O bridging interactions of unprotonated P4/P5 phosphates. In contrast, monovalent cations (Na(+) and K(+)) form smaller and less-stable clusters by preferentially adding PIP(2) monomers. Despite having the same net charge, the affinity to P4/P5 is higher for Na(+), while affinity toward glycerol P1 is higher for K(+). Consequently, a mixture of K(+) and Ca(2+) (as would be produced by Ca(2+) influx) synergistically yields larger and more stable clusters than Ca(2+) alone due to the different binding preferences of these cations.