Mechanism of Cholesterol Sensing in the Niemann Pick Protein (NPC1) using Molecular Dynamics Simulations

Abstract

The accumulation of cholesterol and other lipids in lysosomes and endosomes leads to the Niemann Pick type C (NPC) disease. Cholesterol accumulation results from disrupted cholesterol transport mediated by the NPC1 and NPC2 proteins. NPC1 is a large transmembrane (TM) protein which putatively receives luminal cholesterol from the soluble NPC2, and subsequently transfers it to the lysosomal membrane. The mechanism by which the luminal N-terminal domain (NTD) of NPC1 transfers cholesterol to the lysosomal membrane nearly 8 nm away remains unknown. The allosteric signalling mechanism between the cholesterol-sensing TM domain and the spatially distant luminal domains of NPC1 are equally fascinating. We implemented large-scale Molecular Dynamics (MD) simulations of NPC1 in the presence and absence of cholesterol in the lysosomal membrane, and show that cholesterol binding to the sterol sensing domain (SSD) to the TM region of NPC1 suppresses conformational changes in the luminal domains that can potentially tilt the NTD towards the lipid bilayer. Using a structural alphabet which translates structural ensembles into strings which can then be subject to statistical analysis (GSATools), we propose a mechanism of allosteric signalling from the transmembrane SSD to the luminal NTD. We provide evidence that the NTD of NPC1 is indeed remarkably flexible, and can alternate between membrane-bound and luminal conformations to transport cholesterol from the lumen to the membrane. We also show that this conformational equilibrium is influenced by the binding of membrane cholesterol to the SSD of NPC1.