High‐content imaging and structure‐based predictions reveal functional differences between Niemann‐Pick C1 variants

Abstract

www.traf c.dkCover legend: Structure of full-length Niemann-Pick C1 (NPC1) protein embedded in a bilayer composed of a binary mixture of POPC and cholesterol. The protein is shown in ribbon representation. Each lysosomal luminal domain is indicated with a different color and the transmembrane region is shown in white. The amino acids that differ in WT-V variant of NPC1 are highlighted with red space-filling representation. The POPC and cholesterol molecules are colored by element (oxygen in red and carbon in blue) and hydrogen atoms are not shown. See Vanharanta et al., Traffic 2020; 21(5):386-397. Aim and ScopeTraffic encourages and facilitates the publication of papers covering the cell biology of intracellular transport in health and disease. Areas of interest include protein, nucleic acid and lipid traffic, molecular motors, intracellular pathogens, intracellular proteolysis, nuclear import and export, cytokinesis and the cell cycle, protein translocation, antigen processing and presentation, organelle biogenesis, metabolism, cell polarity and organization, and organelle movement.All aspects of the structural, molecular biology, biochemistry, genetics, morphology, intracellular signaling and relationship to hereditary or infectious diseases will be covered. Manuscripts must provide a clear conceptual or mechanistic advance. The editors will reject papers that require major changes, including addition of significant experimental data or other significant revision.

Signature of N-terminal domain (NTD) structural re-orientation in NPC1 for proper alignment of cholesterol transport: Molecular dynamics study with mutation

“…not much structural change starting from initial structure with Cα RMSD below 2 Å, unlike the lumenal exposed three domains. [27] Also, one of the current simulation result is in agreement with the very recent full length NPC1 simulation, which will be addressed in Results section. Therefore, the model presented here might capture the qualitative structural/dynamic features of lumenal domains within simplified framework.…”

“…[23,24] The transfer of cholesterol to SSD could proceed from NTD possibly through a conduit like channel that was observed in Patched protein by proton driven network [25,26]. Note that the modeling study with disease causing L472P mutation indicate break down of this tunnel in NPC1, [27] emphasizing importance of this tunnel in cholesterol transport. Recent structure of NPC1 with NPC1 blocker itraconazole obtained from cryo-EM indicated the blocker is located in this tunnel, supporting this scheme.…”

“…[36] In combination with experiment, the molecular dynamics simulation of L472P mutation indicates disruption of the tunnel between MLD and CTD that is believed to play essential role for cholesterol transport as mentioned earlier. [27] Since it was pointed that the R518W mutation decrease cholesterol transfer activity not because of misfolding of NPC1 but because of the functional defection of NPC1, [12] the atomic level detailed mechanism behind this defective functionality could provide insights on the structure and functional relationship of NPC1, especially its interaction with NPC2.…”

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

“…Later, a cryo-EM structure of NPC1 [ 40 ] showed the inhibitor itraconazole blocking the putative tunnel leading to the SSD, lending further support to the tunnel transfer mechanism. Simulations of a wild-type variant of NPC1 containing the mutation L472P postulated that the cholesterol transport functionality of the mutant is compromised because the tunnel is disrupted [ 85 ]. Similarly, constraining the dynamics of the NTD does not interfere with cholesterol transport activity, while locking the MLD and CTD domains does [ 79 ], lending further support to the transfer through a tunnel.…”

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

“…The transfer of the cholesterol from NTD to SSD could proceed possibly through a conduit‐like channel that was observed in the Patched protein by the proton‐driven network (Winkler et al., 2019; Zhang et al., 2018). Note that the modeling study with the disease‐causing L472P mutation indicates a breakdown of this tunnel in NPC1 (Vanharanta et al., 2020), which emphasizes the importance of this tunnel with the cholesterol transport. The recent cryo‐EM structure of NPC1 with NPC1‐blocker itraconazole shows the blocker is located in this tunnel, which supports this scheme (Long et al., 2020).…”