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

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.

SUBMITTER: Elghobashi-Meinhardt N

PROVIDER: S-EPMC7215871 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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

Elghobashi-Meinhardt Nadia N

International journal of molecular sciences 20200422 8

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 a ...[more]

PMID: 32331453

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Project description:Polyethylene glycol (PEG) is the most prominent clinically administered synthetic polymer. For example, over 300 million people have been administered PEGylated liposome vaccines for SARS-CoV-2. PEG is used in mammals because it has low affinity for most proteins and vice versa. However, this makes it difficult to study the few interactions with proteins that PEG has. On the atomistic level, there are two PEG-protein structures: (1) PEG-LIMP-2 and (2) PEG-αPEG. In the first structure, two monomers of a 1.5 kDa PEG polymer (PEG2) had electron density deep in the postulated cholesterol transport tunnel of LIMP-2, a lysosomal cholesterol transport protein and member of the CD36 super family of proteins. It is unclear how PEG entered this tunnel. In the second structure, PEG wrapped around a surface-exposed tryptophan on its antibody. Since tryptophan is a rare residue, it is unclear if this PEG-Trp interaction is ubiquitous. To gain deeper mechanistic insight into PEG-protein interactions, we surrounded the LIMP-2 apo structure with 13 PEG chains of 10 monomers each (PEG10), water, and KCl and simulated the system using NAMD. One of the 13 chains penetrated LIMP-2 and came within 3 Å of PEG2. This was possible because of the strong hydrogen bonding between multiple oxygens along PEG10 and Arg192 but, most importantly, the clamping of the tertiary structure on PEG10. Clamping stabilized the movements of PEG10, and the leading oxygen of PEG10 was able to penetrate LIMP-2 and head toward to the position occupied by PEG2. Phe383 appears to act as a gate for objects to move through this cavity, which continues to the basal/membrane side of LIMP-2. Of all residues, PEG10 molecules had the most sustained interactions with lysine and arginine because of their strong hydrogen-bonding capabilities. These results show that the oxygens of PEG bind residues with high hydrogen bonding capabilities. However, the PEG-protein interaction is likely to be transient unless groups of resides can clamp down on PEG or a cavity that at least part of the PEG chain can enter is in close proximity to lower PEG's entropy.

Dataset Information

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

Publications

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

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