Cholesterol Transport in Wild-Type NPC1 and P691S: Molecular Dynamics Simulations Reveal Changes in Dynamical Behavior.

Nadia Elghobashi-Meinhardt

doi:10.3390/ijms21082962

Nadia Elghobashi-Meinhardt

Open Access

https://doi.org/10.3390/ijms21082962

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Abstract

The Niemann–Pick C1 (NPC1) protein is the main protein involved in NPC disease, a fatal lysosomal lipid storage disease. NPC1, containing 1278 amino acids, is comprised of three lumenal domains (N-terminal, middle lumenal, C-terminal) and a transmembrane (TM) domain that contains a five helix bundle referred to as the sterol-sensing domain (SSD). The exact purpose of the SSD is not known, but it is believed that the SSD may bind cholesterol, either as a part of the lipid trafficking pathway or as part of a signaling mechanism. A recent cryo-EM structure has revealed an itraconazole binding site (IBS) in the SSD of human NPC1. Using this structural data, we constructed a model of cholesterol-bound wild-type (WT) and mutant P691S and performed molecular dynamics (MD) simulations of each cholesterol-bound protein. For WT NPC1, cholesterol migrates laterally, in the direction of the lipid bilayer. In the case of P691S, cholesterol is observed for the first time to migrate away from the SSD toward the N-terminal domain via a putative tunnel that connects the IBS with the lumenal domains. Structural features of the IBS are analyzed to identify the causes for different dynamical behavior between cholesterol-bound WT and cholesterol-bound P691S. The side chain of Ser691 in the P691S mutant introduces a hydrogen bond network that is not present in the WT protein. This change is likely responsible for the altered dynamical behavior observed in the P691S mutant and helps explain the disrupted cholesterol trafficking behavior observed in experiments.

Highlights

The Niemann–Pick C1 (NPC1) is a 140 kDa lysosomal protein (1278 amino acids) that is one of the central biochemical players in NPC disease, a fatal, autorecessive, lysosomal lipid storage disease [1]
In WT NPC1, cholesterol translocation was in the direction of the lipid bilayer, whereas in P691S, the sterol molecule moved along the putative transport tunnel in the direction of the lumenal domains
One critical structural factor responsible for these differences in dynamical behavior is the orientation of the side chain of Glu688

Summary

Introduction

The Niemann–Pick C1 (NPC1) is a 140 kDa lysosomal protein (1278 amino acids) that is one of the central biochemical players in NPC disease, a fatal, autorecessive, lysosomal lipid storage disease [1]. It is believed that after endocytosis, low-density-lipoprotein (LDL)-derived cholesterol is bound by the smaller, soluble NPC2 protein (25 kDa, 131 amino acids) in the lumen and transferred to NPC1, after which the cholesterol is further processed out of the lysosome [3,4]. The co-crystal structure (2.4 Å) of NPC1 with the smaller, soluble NPC2 protein provided insight into how NPC1 and NPC2 may form a stable protein-protein complex [5]. With the continuing improvement in cryo-electron microscopy (EM) imaging technology, high-resolution structures of full-length NPC1 have emerged that have provided the community with further insight into the architecture of this large protein and the possible significance of mutations in specific domains [6,7]. How specific mutations in NPC1 are related to disrupted cholesterol trafficking and to disease phenotype is not understood. Some mutants, e.g., homozygous I1061T, give rise to a severe disease phenotype with abolished cholesterol trafficking, while others are related to a mild disease phenotype [9,10]

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