Composition dependence of cholesterol flip-flop rates in physiological mixtures

https://doi.org/10.1016/j.chemphyslip.2020.104967Get rights and content

Highlights

  • Spontaneous cholesterol flip-flop is observed in unbiased all-atom simulations of physiological lipid mixtures.

  • Models of a synaptic vesicle membrane and the inner and outer leaflet of a mammalian plasma membrane are simulated.

  • Cholesterol flip-flop rates in the range 103 to 104 sec−1 are observed.

  • Rates are higher in mixtures containing more tail unsaturation.

Abstract

Unbiased, all-atom simulations of mixtures representative of the inner and outer leaflets of a mammalian red blood cell and a synaptic vesicle reveal many cholesterol flip-flop events over the 5 μsec duration of the simulations. Enough events are observed for a direct estimate of the flip-flop rate. Slower rates are found in more ordered membranes, and faster rates in more disordered membranes, consistent with earlier reports in the literature. However, the rates found here are neither as fast as the fastest nor as slow as the slowest rates obtained by previous simulations. The difference likely stems from the compositions studied here, which unlike previous work include exclusively lipids with differing acyl chains, as observed in mammalian lipidomes.

Introduction

Cholesterol in the human body is taken up from the diet or synthesized in the liver, trafficked to cells by lipoprotein particles, and stored in cellular membranes, especially the plasma membrane, (Lange et al., 1989) endosomes, and the trans Golgi (Van Meer et al., 2008; Ikonen, 2008) Within the cell, the concentration of cholesterol in different membranes varies widely and is tightly controlled. For example, cholesterol varies from only a few mole percent (<5 %) in the endoplasmic reticulum (ER) to 30–40 mole percent in the plasma membrane (PM) — an observation made all the more remarkable by the fact that the two membranes are physically connected at the PM-ER junction (Mesmin et al., 2013). Because of its abundance and critical role in regulating membrane physical properties, cholesterol trafficking and homeostasis are critical to a wide range of cellular and physiological processes.

Cholesterol homeostasis requires interleaflet flip-flop, since cholesterol is either synthesized exclusively on the inner leaflet of the ER or delivered to the lumenal leaflet in endosomes after digestion of cholesterol esters from lipoprotein particles (Ikonen, 2008). Following the delivery of cholesterol to the plasma membrane by either mechanism, the ratio of cholesterol in each leaflet will be equilibrated by flip-flop, on a timescale set by the typical time for a spontaneous flip-flop event (Lange et al., 1981). If the lipid composition in each leaflet were identical, then the abundance of cholesterol (Allender et al., 2019; Ayuyan and Cohen, 2018) in each leaflet would be equal, but this need not be the case. It is well established that the lipid composition of the plasma membrane is asymmetric and maintained by active processes, (Lorent et al., 2020) which may well lead to an asymmetric distribution of cholesterol between the leaflets, even when cholesterol flip-flop is fast enough for tyhe two populations to be in equilibrium. Cho and coworkers, for example, recently reported a 12-fold higher concentration of cholesterol in the outer leaflet as compared to the inner leaflet (Liu et al., 2017; Steck and Lange, 2018).

The rate of cholesterol and lipid flip flop between leaflets of biological membranes is therefore important both to understanding cholesterol trafficking processes, and for establishing bounds on the rate at which energy must be consumed to maintain asymmetry. In this context, it is noteworthy that the range reported for the rate of cholesterol flip-flop varies over six orders of magnitude, from μsec−1 to sec−1 (Bennett et al., 2009; Bennett and Tieleman, 2012; Bruckner et al., 2009; Filipe et al., 2018; Garg et al., 2011; Gu et al., 2019; Javanainen and Martinez-Seara, 2019; Jo et al., 2010; Steck et al., 2002). This range includes both experimental measurements and various types of simulations.

An extensive prior literature reports cholesterol flip-flop rates and translocation free energies via a variety of simulation techniques including unbiased all-atom simulation, (Filipe et al., 2018; Gu et al., 2019; Javanainen and Martinez-Seara, 2019) umbrella sampling methods, (Bennett et al., 2009; Jo et al., 2010) and replica molecular dynamics, (Choubey et al., 2013) obtaining a range of flip-flop rates that depend strongly (over 3–4 orders of magnitude) on composition — highly saturated, ordered membranes reduce flip-flop rates relative to unsaturated, disordered membranes. However, all previous publications have simulated very simple membranes, usually comprised of at most a few lipid types most often with two identical acyl chains, representative of neither the complexity nor the typical lipid structure of mammalian lipidomes.

In this work, cholesterol flip-flop rates from 1.6(103) to 1.9(104) sec−1 are observed by unbiased, all-atom molecular dynamics simulation. The simulated compositions are based on lipidomic data for synaptic vesicles (Takamori et al., 2006) and an asymmetric lipidome (inner and outer leaflet obtained separately) of the human red blood cell (Lorent et al., 2020). These compositions contain between 4 and 11 different lipids, carefully selected to capture the headgroup, chain, and backbone chemistry of natural lipidomes. The high melting temperature lipids in these lipidomes are almost entirely sphingolipids, and the lower melting temperature lipids have a variety of hydrophobic chains at the sn-1 and sn-2 position. The present work therefore adds important new insights into cholesterol dynamics across physiologically relevant variations in composition, across leaflets, and among different membranes.

Section snippets

Methods

The four membrane systems were built using packmol (Martínez et al., 2009) to assemble the numbers of lipids indicated in Table 1. Each system was hydrated with at least 50 TIP3P waters per lipid and the salt concentration set to 150 mM NaCl. Lipids and ions were modeled with the CHARMM36 parameters for the lipids (Klauda et al., 2010; Venable et al., 2014; Leonard et al., 2018) and ions with NBFixes applied as described in (Venable et al., 2013). A recent analysis of small angle scattering

Results

Fig. 1 shows the number of cholesterols in each leaflet of all four systems over the course of the simulations, with the location of each cholesterol defined by whether its hydroxyl is above or below the midplane. Cholesterol movement along the bilayer normal appears as discrete steps, with each step having a mirror image in the other leaflet. (These are not flip-flop events, as discussed below.) It is clear that cholesterol is much more dynamic in the less ordered membranes (the synaptic

Discussion and conclusions

Cholesterol flip-flop rates were obtained by unbiased all-atom simulations of physiologically complex lipid mixtures. The compositions of each system were based on lipidomics of representative mammalian membranes: the inner and outer leaflet of the human red blood cell, and the overall lipidome of a synaptic vesicle (with no distinction between inner and outer leaflet, so this system effectively represents a scrambled synaptic vesicle membrane.) An essential difference to previous work on

Acknowledgements

Funding for IL was provided by the NIH/National Institute of General Medical Sciences (GM114282, GM124072, GM120351, GM134949), the Volkswagen Foundation (grant 93091), and the Human Frontiers Science Program (RGP0059/2019). EL and SB were supported by NIH/National Institute of General Medical Sciences GM120351. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by US National Science Foundation grant number ACI-1548562. Anton 2 computer time

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