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 the binding of cholesterol to the SSD of NPC1 suppresses conformational dynamics of the luminal domains which otherwise bring the luminal N-terminal domain (NTD) closer to the lipid bilayer. The presence of an additional 20% membrane cholesterol has negligible impact on this process. 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 which controls cholesterol abundance in the lysosomal membrane.

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

“…Before the transfer of cholesterol from NPC2 to NTD, the NTD has to have proper pose for favorable interaction with NPC2 as indicated by titling of NTD from current simulation and previous simulation. [23] The structure of full length NPC1 + NPC2 (with cholesterol) is not observed and it would be interesting to model this complex starting from putative structure presented in this work. The Texas model is based on NTD and NPC2 interaction and there is possibility that their interaction structure might be very different under the presence of full length NPC1.…”

“…In fact, this observation is in agreement with the simulation of full length NPC1 including the membrane with no cholesterol in NTD when the cholesterol was not present within the membrane. [23] The detailed structural information on the interaction or complex formation of NPC2 with NTD in the presence of full length NPC1 could significantly enhance our understanding on cholesterol transfer from NPC2 to NTD. We note that the overlap of putative NTD-NPC2 complex when there is cholesterol in NPC2 side, [19,21] which is called Texas model and it was suggested based on NTD domain only, generates significant structural crash when superimposed on the cryo-EM structure, indicating that possible involvement of some structural re-orientation or displacement of NTD to adapt the NPC2.…”

“…[10,11,22] Eventually, it is believed that once the cholesterol has been transferred to NTD from NPC2 it should be delivered to the sterol sensing domain (SSD), which is in between the helix bundle within the membrane region, possibly triggering a sequence of events once transferred there. [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.…”

“…unfolding of transmembrane 3(TM3), break of contact between MLD and CTD, and disengagement of NTD, suggesting that cholesterol on SSD can serve as either positive or negative feedback. [23] The mutational study, both theoretically and experimentally, may provide opportunities to gain insight into the mechanism of NPC1 cholesterol transfer process directly or indirectly.…”