Phosphoinositide, a phosphorylated form of phosphatidylinositol (PI), plays an important role in, eg, cell signaling and membrane trafficking. Phosphatidylinositol 4, 5-bisphosphate (PI (4, 5) P2) found in, for instance, the plasma membrane and the Golgi apparatus is known to bind to a number of proteins. How the PI (4, 5) P2-binding proteins recognize their substrate and how the binding is regulated and fine-tuned remains unclear. In this work, we hypothesize that the increasing cholesterol concentration along a path from the nucleus towards the plasma membrane may be one of the key regulators in this process. To consider this hypothesis, we employed both atomistic and coarse-grained (CG) molecular dynamics simulations to study the binding of PI (4, 5) P2 with phospholipase C delta 1 (PLC) that is an important signaling enzyme known to bind PI (4, 5) P2. Unbiased CG MARTINI simulations in POPC/PI (4, 5) P2 and POPC/PI (4, 5) P2/cholesterol mixtures were complemented by umbrella sampling simulations to measure the free energy of PI (4, 5) P2 binding to PLC. The final structures of the PLC-PI (4, 5) P2 complexes were fine-grained to atomistic detail and simulated over microseconds to explore the details of the binding process.

In essence, we observed deeper free energy minima for the binding of PI (4, 5) P2 to PLC in the cholesterol-rich membrane system, compared to cholesterol-free membranes, thus supporting the underlying hypothesis that PI (4, 5) P2 binding to PLC and possibly also other PI (4, 5) P2-binding proteins is strengthened by increasing cholesterol concentration. The atom-scale features such as hydrogen bonding patterns and lipid-specific interactions that dictate the binding preference are discussed in detail in the presented work.