Molecular dynamics study with mutation shows that N‐terminal domain structural re‐orientation in Niemann‐Pick type C1 is required for proper alignment of cholesterol transport

AbstractThe lysosomal membrane protein NPC1 (Niemann-Pick type C1) and NPC2 (Niemann-Pick type C2) are main players of cholesterol control in lysosome and it is known that mutation on these proteins leads to cholesterol trafficking related disease, called Niemann-Pick disease type C (NPC) disease. The mutation R518W or R518Q on NPC1 is one of such disease-related mutations, causing reduced cholesterol transport by half, resulting in accumulation of cholesterol and lipids in late endosomal/lysosomal region of the cell. Even though there has been significant progress in understanding cholesterol transport by NPC1 in combination with NPC2, especially after the structural determination of full length NPC1 in 2016, many details such as interaction of full length NPC1 with NPC2, molecular motions responsible for cholesterol transport during and after this interaction, and structure and function relations of many mutations are still not well understood.We report the extensive molecular dynamics simulations to gain insight into the structure and motions of NPC1 lumenal domain for cholesterol transport and disease behind the mutation (R518W). It is found that the mutation induces structural shift of NTD (N-terminal domain), toward the loop region in MLD (middle lumenal domain), which is believed to play central role in interaction with NPC2 protein, such that the interaction with NPC2 protein might be less favorable compare to wild NPC1. Also, the simulation indicates the possible re-orientation of the NTD, aligning to form an internal tunnel, after receiving the cholesterol from NPC2 with wild NPC1 unlike the mutated one, a possible pose for further action in cholesterol trafficking. We believe the current study can provide better understanding on the cholesterol transport by NPC1, especially the role of NTD of NPC1, in combination with NPC2 interaction.Synopsismodeling study of cholesterol binding protein NPC1

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Lysosomal cholesterol export reconstituted from fragments of Niemann-Pick C1

eLife ◽

10.7554/elife.38564 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 14

Author(s):

Michael Nguyen Trinh ◽

Michael S Brown ◽

Joachim Seemann ◽

Joseph L Goldstein ◽

Feiran Lu

Keyword(s):

Membrane Protein ◽

Lipid Bilayer ◽

Full Length ◽

Cholesterol Transport ◽

Transmembrane Helices ◽

Terminal Domain ◽

Data Support ◽

Covalently Linked ◽

Niemann Pick ◽

Polytopic Membrane Protein

Niemann-Pick C1 (NPC1) is a polytopic membrane protein with 13 transmembrane helices that exports LDL-derived cholesterol from lysosomes by carrying it through the 80 Å glycocalyx and the 40 Å lipid bilayer. Transport begins when cholesterol binds to the N-terminal domain (NTD) of NPC1, which projects to the surface of the glycocalyx. Here, we reconstitute cholesterol transport by expressing the NTD as a fragment separate from the remaining portion of NPC1. When co-expressed, the two NPC1 fragments reconstitute cholesterol transport, indicating that the NTD has the flexibility to interact with the remaining parts of NPC1 even when not covalently linked. We also show that cholesterol can be transferred from the NTD of one full-length NPC1 to another NPC1 molecule that lacks the NTD. These data support the hypothesis that cholesterol is transported through interactions between two or more NPC1 molecules.

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A new system to evaluate characteristics of Niemann-Pick C1 Like 1-mediated cholesterol transport using Xenopus laevis oocytes

Biochimica et Biophysica Acta (BBA) - Biomembranes ◽

10.1016/j.bbamem.2020.183508 ◽

2021 ◽

Vol 1863 (2) ◽

pp. 183508

Author(s):

Shunsuke Nashimoto ◽

Saori Yagi ◽

Naoki Takeda ◽

Miku Nonaka ◽

Yoh Takekuma ◽

...

Keyword(s):

Xenopus Laevis ◽

Cholesterol Transport ◽

Xenopus Laevis Oocytes ◽

Niemann Pick ◽

New System

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The Role of the N-Terminal Domain in the Regulation of the “Constitutively Active” Conformation of Protein Kinase CK2α: Insight from a Molecular Dynamics Investigation

ChemMedChem ◽

10.1002/cmdc.201100046 ◽

2011 ◽

Vol 6 (7) ◽

pp. 1207-1216 ◽

Cited By ~ 5

Author(s):

Andrea Cristiani ◽

Giorgio Costa ◽

Giorgio Cozza ◽

Flavio Meggio ◽

Leonardo Scapozza ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Kinase ◽

Active Conformation ◽

Terminal Domain ◽

Constitutively Active

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Exploring the Regulatory Function of the N ‐terminal Domain of SARS‐CoV‐2 Spike Protein through Molecular Dynamics Simulation

Advanced Theory and Simulations ◽

10.1002/adts.202100152 ◽

2021 ◽

pp. 2100152

Author(s):

Yao Li ◽

Tong Wang ◽

Juanrong Zhang ◽

Bin Shao ◽

Haipeng Gong ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Spike Protein ◽

Regulatory Function ◽

Terminal Domain

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Use of NBD-cholesterol to identify a minor but NPC1L1-independent cholesterol absorption pathway in mouse intestine

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00392.2010 ◽

2011 ◽

Vol 300 (1) ◽

pp. G164-G169 ◽

Cited By ~ 8

Author(s):

Michelle R. Adams ◽

Eddy Konaniah ◽

James G. Cash ◽

David Y. Hui

Keyword(s):

Intestinal Mucosa ◽

Cholesterol Absorption ◽

Intestinal Lumen ◽

Cholesterol Transport ◽

Cholesteryl Esters ◽

Main Function ◽

Absorption Mechanism ◽

Ezetimibe Treatment ◽

Niemann Pick ◽

A Minor

The importance of Niemann-Pick C1 Like-1 (NPC1L1) protein in intestinal absorption of dietary sterols, including both cholesterol and phytosterols, is well documented. However, the exact mechanism by which NPC1L1 facilitates cholesterol transport remains controversial. This study administered 22-( N(-7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-23,24-bisnor-5-cholen-3β-ol (NBD-cholesterol) and [3H]cholesterol to Npc1l1+/+ and Npc1l1−/− mice to determine whether NPC1L1 facilitates dietary sterol uptake by enterocytes and/or participates in intracellular sterol delivery to the endoplasmic reticulum (ER) for lipoprotein assembly before secretion into plasma circulation. Results showed that [3H]cholesterol absorption was reduced but not abolished in Npc1l1−/− mice compared with Npc1l1+/+ mice. In the presence of Pluronic L-81 to block pre-chylomicron exit from the ER, significant amounts of [3H]cholesterol were found to be associated with lipid droplets in the intestinal mucosa of both Npc1l1+/+ and Npc1l1−/− mice, and the intracellular [3H]cholesterol can be esterified to cholesteryl esters. These results provided evidence indicating that the main function of NPC1L1 is to promote cholesterol uptake from the intestinal lumen but that it is not necessary for intracellular cholesterol transport to the ER. Surprisingly, NBD-cholesterol was taken up by intestinal mucosa, esterified to NBD-cholesteryl esters, and transported to plasma circulation to similar extent between Npc1l1+/+ and Npc1l1−/− mice. Ezetimibe treatment also had no impact on NBD-cholesterol absorption by Npc1l1+/+ mice. Thus, NBD-cholesterol absorption proceeds through an NPC1L1-independent and ezetimibe-insensitive sterol absorption mechanism. Taken together, these results indicate that NBD-cholesterol can be used to trace the alternative cholesterol absorption pathway but is not suitable for tracking NPC1L1-mediated cholesterol absorption.

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A role for NPC1 and NPC2 in intestinal cholesterol absorption – the hypothesis gutted

Biochemical Journal ◽

10.1042/bj20071340 ◽

2007 ◽

Vol 408 (1) ◽

Cited By ~ 5

Author(s):

Laura Liscum

Keyword(s):

Endoplasmic Reticulum ◽

Dietary Cholesterol ◽

Cholesterol Absorption ◽

Cholesterol Transport ◽

Intestinal Epithelial ◽

Intestinal Cholesterol Absorption ◽

Biochemical Journal ◽

Good Target ◽

Type C ◽

Niemann Pick

Dietary and biliary cholesterol are taken up by intestinal epithelial cells and transported to the endoplasmic reticulum. At the endoplasmic reticulum, cholesterol is esterified, packaged into chylomicrons and secreted into the lymph for delivery to the bloodstream. NPC1L1 (Niemann–Pick C1-like 1) is a protein on the enterocyte brush-border membrane that facilitates cholesterol absorption. Cholesterol's itinerary as it moves to the endoplasmic reticulum is unknown, as is the identity of any cellular proteins that facilitate the movement. Two proteins that play an important role in intracellular cholesterol transport and could potentially influence NPC1L1-mediated cholesterol uptake are NPC1 and NPC2 (Niemann–Pick type C disease proteins 1 and 2). In this issue of the Biochemical Journal, Dixit and colleagues show that the absence or presence of NPC1 and NPC2 has no effect on intestinal cholesterol absorption in the mouse. Thus neither protein fills the gap in our knowledge of intra-enterocyte cholesterol transport. Furthermore, the NPC1/NPC2 pathway would not be a good target for limiting the uptake of dietary cholesterol.

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Analysis of the Structural and Dynamic Properties of Human N-Terminal Domain of Apolipoprotein E by Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp8002678 ◽

2008 ◽

Vol 112 (29) ◽

pp. 8730-8736 ◽

Cited By ~ 2

Author(s):

Isabelle Ortmans ◽

Martine Prévost

Keyword(s):

Molecular Dynamics ◽

Apolipoprotein E ◽

Molecular Dynamics Simulations ◽

Dynamic Properties ◽

Terminal Domain ◽

Dynamics Simulations

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Computational Modeling Explains the Multi Sterol Ligand Specificity of the N-Terminal Domain of Niemann–Pick C1-Like 1 Protein

ACS Omega ◽

10.1021/acsomega.9b01668 ◽

2019 ◽

Vol 4 (25) ◽

pp. 20894-20904

Author(s):

Vasanthanathan Poongavanam ◽

Jacob Kongsted ◽

Daniel Wüstner

Keyword(s):

Computational Modeling ◽

Ligand Specificity ◽

Terminal Domain ◽

Niemann Pick

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NPC1 regulates ER contacts with endocytic organelles to mediate cholesterol egress

Nature Communications ◽

10.1038/s41467-019-12152-2 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 40

Author(s):

D. Höglinger ◽

T. Burgoyne ◽

E. Sanchez-Heras ◽

P. Hartwig ◽

A. Colaco ◽

...

Keyword(s):

Dietary Cholesterol ◽

Cholesterol Transport ◽

Cholesterol Accumulation ◽

C Protein ◽

Membrane Contact Sites ◽

Sterol Transport ◽

Membrane Contact ◽

Mitochondrial Cholesterol ◽

Niemann Pick ◽

The Impact

Abstract Transport of dietary cholesterol from endocytic organelles to the endoplasmic reticulum (ER) is essential for cholesterol homoeostasis, but the mechanism and regulation of this transport remains poorly defined. Membrane contact sites (MCS), microdomains of close membrane apposition, are gaining attention as important platforms for non-vesicular, inter-organellar communication. Here we investigate the impact of ER-endocytic organelle MCS on cholesterol transport. We report a role for Niemann-Pick type C protein 1 (NPC1) in tethering ER-endocytic organelle MCS where it interacts with the ER-localised sterol transport protein Gramd1b to regulate cholesterol egress. We show that artificially tethering MCS rescues the cholesterol accumulation that characterises NPC1-deficient cells, consistent with direct lysosome to ER cholesterol transport across MCS. Finally, we identify an expanded population of lysosome-mitochondria MCS in cells depleted of NPC1 or Gramd1b that is dependent on the late endosomal sterol-binding protein STARD3, likely underlying the mitochondrial cholesterol accumulation in NPC1-deficient cells.

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