Mechanistic Basis of Cholesterol Binding and Transfer in NPC2: Insights From Molecular Dynamics Simulations

The Niemann-Pick type C (NPC) disease is characterized by impaired function of the lysosomal proteins NPC1 or NPC2. The soluble NPC2 protein is believed to transport cholesterol to the larger, membrane-bound NPC1, thereby maintaining cholesterol homeostasis; disruption of this trafficking results in sterol accumulation and disease. Numerous NPC2 variants have been reported in NPC patients and cell-based assays. However, the underlying connection between mutated primary amino acid sequence and disrupted sterol trafficking is not understood. To advance our understanding of mechanistic behavior in NPC2, here we present results of extensive all-atom molecular dynamics simulations of wild-type NPC2 and prominent NPC2 variants. The behavior of cholesterol-bound (holo) and unbound (apo) NPC2 was analyzed using several descriptors, including binding-pocket volume, entrance-gating metrics, and principal component analysis. These analyses reveal that cholesterol binding in most variants restricts the protein's conformational freedom. Furthermore, we identify coordinated loop motions that modulate pocket closure, and we propose a mechanistic basis for how variation in protein sequence perturbs cholesterol trafficking.