Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain

Abstract

Lysosomal accumulation of cholesterol is a hallmark of Niemann Pick type C (NPC) disease caused by mutations primarily in the lysosomal membrane protein NPC1. NPC1 contains a transmembrane sterol-sensing domain (SSD), which is supposed to regulate protein activity upon cholesterol binding, but the mechanisms underlying this process are poorly understood. Using atomistic simulations, we show that in the absence of cholesterol in the SSD, the luminal domains of NPC1 are highly dynamic, resulting in the disengagement of the NTD from the rest of the protein. The disengaged NPC1 adopts a flexed conformation that approaches the lipid bilayer, and could represent a conformational state primed to receive a sterol molecule from the soluble lysosomal cholesterol carrier NPC2. The binding of cholesterol to the SSD of NPC1 allosterically suppresses the conformational dynamics of the luminal domains resulting in an upright NTD conformation. The presence of an additional 20% cholesterol in the membrane has negligible impact on this process. The additional presence of an NTD-bound cholesterol suppresses the flexing of the NTD. We propose that cholesterol acts as an allosteric effector, and the modulation of NTD dynamics by the SSD-bound cholesterol constitutes an allosteric feedback mechanism in NPC1 that controls cholesterol abundance in the lysosomal membrane.

An intracellular pathway controlled by the N-terminus of the pump subunit inhibits the bacterial KdpFABC ion pump in high K+conditions

“…These clouds are likely to represent free energy minima in the protein conformational landscape which are clearly different for PHOS (blue) and SER (orange) simulations. The analysis is similar to what we performed earlier in the context of a different membrane protein [14]. More specifically, this analysis reveals novel conformations, labeled C and D, that are sampled in the PHOS simulations, whereas the SER simulations remain within the larger cloud of conformations labeled B.…”

Physics-based inverse design of cholesterol attracting transmembrane helices reveals a paradoxical role of hydrophobic length

“…The overall fraction of cholesterol in the plasma membrane relative to total plasma membrane lipids is about 30 to 40 % in leukocytes, epithelial cells, neurons, and mesenchymal cells (1). The localization, trafficking, and functionality of membrane proteins involved in cholesteroldependent pathways and cholesterol homeostasis may critically rely on their ability to attract and bind cholesterol molecules (2)(3)(4)(5)(6)(7)(8)(9)(10). Prediction of cholesterol binding affinity could therefore illuminate their role in diseases that are characterized by loss of cholesterol homeostasis (e.g.…”

Lipid Transporters Beam Signals from Cell Membranes

“…Allosteric binding sites are common in proteins, allowing substrates to bind in areas other than the active binding site to produce changes in the overall protein conformation. Exemplified by sterol sensing in proteins like Niemann Pick C1 (NPC1), cholesterol binding allosterically affects the protein morphology and then regulates the protein function [ 134 ]. SSD is believed to bind accessible cholesterol as their substrates, this being a minority group of sterols found in the membrane representing an unsequestered, unbound and active version of cholesterol [ 135 , 136 ].…”