Stress testing the ELBA water model

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles

The ELBA coarse-grained force field was originally developed for lipids, and its water model is described as a single-site Lennard-Jones particle with electrostatics modeled by an embedded point-dipole, while other molecules in this force field have a three (or four)-to-one mapping scheme. Here, ELBA was applied to investigate the self-assembly processes of dodecyl-phosphocholine (DPC) micelle, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dihexaoyl-sn-glycero-3-phosphocholine (DPPC/DHPC) bicelles, and DPPC/cyclohexane/water reverse micelles through coarse-grained molecular dynamics (MD) simulations. New parameters were obtained using a simplex algorithm-based calibration procedure to determine the Lennard-Jones parameters for cyclohexane, dodecane, and cyclohexane-dodecane cross-interactions. Density, self-diffusion coefficient, surface tension, and mixture excess volume were found to be in fair agreement with experimental data. These new parameters were used in the simulations, and the obtained structures were analyzed for shape, size, volume, and surface area. Except for the shape of DPC micelles, all other properties match well with available experimental data and all-atom simulations. Remarkably, in agreement with experiments the rodlike shape of the DPPC reverse micelle is well described by ELBA, while all-atom data in the literature predicts a disclike shape. To further check the consistency of the force field in reproducing the correct shapes of reverse micelles, additional simulations were performed doubling the system size. Two distinct reverse micelles were obtained both presenting the rodlike shape and correct aggregation number.

Molecular simulations of water adsorption and transport in mesopores with varying hydrophilicity arrangements

The adsorption and transport of water in an open cylindrical mesopore with two different inner surface arrangements of hydrophilicities were examined by molecular simulations. The first model has a weak hydrophilic surface at both entrances of the pore and a stronger hydrophilic surface in the mid-section. The second pore has stronger hydrophilic surfaces at the entrances and weaker in the middle region. The simulation results show that the water adsorption isotherms obtained from Grand Canonical Monte Carlo simulations and pore filling curves acquired from Grand Canonical Molecular Dynamics simulations change depending on the arrangement of the strong and weak hydrophilic surfaces. In the first model, water condensation focuses on the mid-section forming a liquid bridge or a film, which creates a concave meniscus accelerating subsequent adsorption within the pore. Two bridges form in the entrance regions, where a cavity naturally occurs in between the films, in the second model. The different filling and emptying mechanisms clearly change the adsorption-desorption characteristics for the two pore types, but the second type generally showed faster transitions overall. Flux and meniscus analysis also reveals a circulating flow at the menisci of the interfaces within the pore. The results are expected to be valuable in understanding the effects of interior surface modification of nanopores in future applications.

Atomistic and Coarse-Grained Modeling of the Adsorption of Graphene Nanoflakes at the Oil-Water Interface

The high interfacial tension between two immiscible liquids can provide the necessary driving force for the self-assembly of nanoparticles at the interface. Particularly, the interface between water and oily liquids (hydrocarbon chains) has been exploited to prepare networks of highly interconnected graphene sheets of only a few layers thickness, which are well suited for industrial applications. Studying such complex systems through particle-based simulations could greatly enhance the understanding of the various driving forces in action and could possibly give more control over the self-assembly process. However, the interaction potentials used in particle-based simulations are typically derived by reproducing bulk properties and are therefore not suitable for describing systems dominated by interfaces. To address this issue, we introduce a methodology to derive solid-liquid interaction potentials that yield an accurate representation of the balance between interfacial interactions at atomistic and coarse-grained resolutions. Our approach is validated through its ability to lead to the adsorption of graphene nanoflakes at the interface between water and n-hexane. The development of accurate coarse-grained potentials that our approach enables will allow us to perform large-scale simulations to study the assembly of graphene nanoparticles at the interface between immiscible liquids. Our methodology is illustrated through a simulation of many graphene nanoflakes adsorbing at the interface.

Effects of High Pressure on Phospholipid Bilayers

The response of lipid membranes to changes in external pressure is important for many biological processes, and it can also be exploited for technological applications. In this work, we employ all-atom molecular dynamics simulations to characterize the changes in the physical properties of phospholipid bilayers brought about by high pressure (1000 bar). In particular, we study how the response differs, in relation to different chain unsaturation levels, by comparing monounsaturated 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and biunsaturated dioleoyl-phosphatidylcholine (DOPC) bilayers. Various structural, mechanical, and dynamical features are found to be altered by the pressure increase in both bilayers. Notably, for most properties, including bilayer area and thickness, lipid order parameters, lateral pressure profile, and curvature frustration energy, we observe significantly more pronounced effects for monounsaturated POPC than biunsaturated DOPC. Possible biological implications of the results obtained are discussed, especially in relation to how different lipids can control the structure and function of membrane proteins.

An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations

Biological membranes and model lipid systems containing high amounts of unsaturated lipids and sterols are subject to chemical and/or photo-induced lipid oxidation, which leads to the creation of exotic oxidized lipid products (OxPLs). OxPLs are known to have significant physiological impact in cellular systems and also affect physical properties of both biological and model lipid bilayers. In this paper we (i) provide a perspective on the existing literature on simulations of lipid bilayer systems containing oxidized lipid species as well as the main related experimental results, (ii) describe our new data of all-atom and coarse-grained simulations of hydroperoxidized lipid monolayer and bilayer systems and (iii) provide a comparison of the MARTINI and ELBA coarse grained force fields for lipid bilayer systems. We show that the better electrostatic treatment of interactions in ELBA is able to resolve previous conflicts between experiments and simulations. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics

Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their tendency to form the lamellar phase, ubiquitous in biology. Nonlamellar lipids, such as dioleoylphosphatidylethanolamine (DOPE), prefer instead to form nonlamellar phases, which are mostly nonbiological. However, nonlamellar lipids mix with lamellar lipids in biomembrane structures that remain overall lamellar. Importantly, changes in the lamellar vs nonlamellar lipid composition are believed to affect membrane function and modulate membrane proteins. In this work, we employ atomistic molecular dynamics simulations to quantify how a range of bilayer properties are altered by variations in the lamellar vs nonlamellar lipid composition. Specifically, we simulate five DOPC/DOPE bilayers at mixing ratios of 1/0, 3/1, 1/1, 1/3, and 0/1. We examine properties including lipid area and bilayer thickness, as well as the transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. While the bilayer structure is only marginally altered by lipid composition changes, dramatic effects are observed for the lateral pressure, electric field, and dipole potential profiles. Possible implications for membrane function are discussed.