Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin.

Giray Enkavi,Heikki Mikkolainen,Burçin Güngör,Elina Ikonen,Ilpo Vattulainen,Alexander Mackerell

doi:10.1371/journal.pcbi.1005831

Giray Enkavi, Heikki Mikkolainen + Show 4 more

Open Access

https://doi.org/10.1371/journal.pcbi.1005831

Copy DOI

Abstract

Niemann-Pick Protein C2 (npc2) is a small soluble protein critical for cholesterol transport within and from the lysosome and the late endosome. Intriguingly, npc2-mediated cholesterol transport has been shown to be modulated by lipids, yet the molecular mechanism of npc2-membrane interactions has remained elusive. Here, based on an extensive set of atomistic simulations and free energy calculations, we clarify the mechanism and energetics of npc2-membrane binding and characterize the roles of physiologically relevant key lipids associated with the binding process. Our results capture in atomistic detail two competitively favorable membrane binding orientations of npc2 with a low interconversion barrier. The first binding mode (Prone) places the cholesterol binding pocket in direct contact with the membrane and is characterized by membrane insertion of a loop (V59-M60-G61-I62-P63-V64-P65). This mode is associated with cholesterol uptake and release. On the other hand, the second mode (Supine) places the cholesterol binding pocket away from the membrane surface, but has overall higher membrane binding affinity. We determined that bis(monoacylglycero)phosphate (bmp) is specifically required for strong membrane binding in Prone mode, and that it cannot be substituted by other anionic lipids. Meanwhile, sphingomyelin counteracts bmp by hindering Prone mode without affecting Supine mode. Our results provide concrete evidence that lipids modulate npc2-mediated cholesterol transport either by favoring or disfavoring Prone mode and that they impose this by modulating the accessibility of bmp for interacting with npc2. Overall, we provide a mechanism by which npc2-mediated cholesterol transport is controlled by the membrane composition and how npc2-lipid interactions can regulate the transport rate.

Highlights

Cholesterol, ubiquitously present in all vertebrate cells, regulates the structure and permeability of cellular membranes [1, 2]
Mutations in Niemann-Pick Protein C2 (NPC2) result in the fatal genetic disease, called Niemann-Pick C disease, characterized by neuronal degeneration resulting in early death
We performed an extensive set of atomistic molecular dynamics simulations employing enhanced sampling approaches to investigate how NPC2 mediates cholesterol transport and the roles of membrane lipids in the process

Summary

Introduction

Cholesterol, ubiquitously present in all vertebrate cells, regulates the structure and permeability of cellular membranes [1, 2]. It comprises typically 20–25 mol % of all lipids in the plasma membrane [1] and acts as a precursor for many bioactive molecules such as steroid hormones, bile acids, oxysterols, and vitamin D [2]. Mutations in NPC2 or its transmembrane partner NPC1 result in accumulation of lipids such as unesterified cholesterol and sphingolipids [4, 5] This fatal genetic lysosomal storage condition called Niemann-Pick C disease results in progressive neuronal degeneration in the brain and early death [6, 7]

Methods

Results

Discussion

Conclusion