Chenyue Xing

Interactions of Lipid Bilayers with Supports: A Coarse-Grained Molecular Simulation Study

The study of lipid structure and phase behavior at the nanoscale is of utmost importance due to implications in understanding the role of the lipids in biochemical membrane processes. Supported lipid bilayers play a key role in understanding real biological systems, but they are vastly underrepresented in computational studies. In this paper, we discuss molecular dynamics simulations of supported lipid bilayers using a coarse-grained model. We first focus on the technical implications of modeling solid supports for biomembrane simulations. We then describe noticeable influences of the support on the systems. We are able to demonstrate that the bilayer system behavior changes when supported by a hydrophilic surface. We find that the thickness of the water layer between the support and the bilayer (the inner-water region in the latter part of this paper) adapts through water permeation on the microsecond time scale. Additionally, we discuss how different surface topologies affect the bilayer. Finally, we point out the differences between the two leaflets induced by the support.

Coarse-grained modeling of lipids.

Molecular modeling of phospholipids on many scales has progressed significantly over the last years. Here we review several membrane models on intermediate to large length scales restricting ourselves to particle based coarse-grained models with implicit and explicit solvent. We explain similarities and differences as well as their connection to experiments and fine-grained models. We neglect any field descriptions on larger scales. We discuss then a few examples where we focus on studies of lipid phase behavior as well as supported lipid bilayers as these examples can only be meaningfully studied using large-scale models to date.

Density imbalances and free energy of lipid transfer in supported lipid bilayers

Supported lipid bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability and at the same time have a fundamental structure approximating cell membranes. However, in computer simulations these systems have been studied only rarely up to now. An important property, which cannot be easily determined by molecular dynamics or experiments, is the unsymmetrical density profiles of bilayer leaflets (density imbalance) inflicted on the membrane by the support. This imbalance in the leaflets composition has consequences for membrane structure and phase behavior, and therefore we need to understand it in detail. The free energy can be used to determine the equilibrium structure of a given system. We employ an umbrella sampling approach to obtain the free energy of a lipid crossing the membrane (i.e., lipid flip-flop) as a function of bilayer composition and hence the equilibrium composition of the supported bilayers. In this paper, we use a variant of the coarse-grained Martini model. The results of the free energy calculation lead to a 5% higher density in the proximal leaflet. Recent data obtained by large scale modeling using a water free model suggested that the proximal leaflet had 3.2% more lipids than the distal leaflet [Hoopes et al., J. Chem. Phys. 129, 175102 (2008)]. Our findings are in line with these results. We compare results of the free energy of transport obtained by pulling the lipid across the membrane in different ways. There are small quantitative differences, but the overall picture is consistent. We additionally characterize the intermediate states, which determine the barrier height and therefore the rate of translocation. Calculations on unsupported bilayers are used to validate the approach and to determine the barrier to flip-flop in a free membrane.

Silica xerogel/aerogel-supported lipid bilayers: consequences of surface corrugation.

The objective of this paper was to review our recent investigations of silica xerogel and aerogel-supported lipid bilayers. These systems provide a format to observe relationships between substrate curvature and supported lipid bilayer formation, lipid dynamics, and lipid mixtures phase behavior and partitioning. Sensitive surface techniques such as quartz crystal microbalance and atomic force microscopy are readily applied to these systems. To inform current and future investigations, we review the experimental literature involving the impact of curvature on lipid dynamics, lipid and phase-separated lipid domain localization, and membrane-substrate conformations and we review our molecular dynamics simulations of supported lipid bilayers with the atomistic and molecular information they provide.

Asymmetric nature of lateral pressure profiles in supported lipid membranes and its implications for membrane protein functions

The study of lipid membrane structure and phase behavior at the nano-scale is of utmost importance due to implications in understanding the interplay of lipids and membrane proteins in biochemical membrane processes. Supported lipid bilayers play a key role in providing the means to understand real biological systems. Yet, with regard to membrane protein activation and their functions, the limitations of supported membranes and the possible artifacts they may induce are weakly understood. Here, we study DPPC (dipalmitoylphosphatidylcholine) bilayers on a weakly hydrophilic substrate using coarse grained simulations and show that the lateral pressure profile of a supported bilayer is distinctly different from the corresponding pressure profile for a free-standing DPPC bilayer. The results indicate that due to the substrate, the lateral pressure profile becomes asymmetric, expressing major peaks at the proximal leaflet of the membrane, implying the membrane to be under strong tension. The results provide a new mechanism to explain malfunctions of transmembrane proteins used in supported bilayers.

Coarse-grained simulations of supported and unsupported lipid monolayers

Coarse-grained molecular simulations of various phospholipid monolayer systems are presented and compared to each other. The differences between supported and unsupported systems are discussed in terms of structure and thermodynamics. The structural information allows us to obtain a thorough understanding of such systems at the molecular level.

Multiscale Modeling of Supported Lipid Bilayers

Cell membranes consist of a multitude of lipid molecules that serve as a framework for the even greater variety of membrane associated proteins [1–4]. As this highly complex (nonequilibrium) system cannot easily be understood and studied in a controlled way, a wide variety of model systems have been devised to understand the dynamics, structure, and thermodynamics in biological membranes. One such model system is a supported lipid bilayer (SLB), a two-dimensional membrane suspended on a surface. SLBs have been realized to be manageable experimentally while reproducing many of the key features of real biological membranes [5,6]. One of the main advantages of supported bilayers is the physical stability due to the solid support that enables a wide range of surface characterization techniques not available to free or unsupported membranes. As SLBs maintain some of the crucial structural and dynamic properties of biological membranes, they provide an important bridge to natural systems. In order to mimic cell membranes reliably, certain structural and dynamic features have to be reliably reproduced in the artificially constructed lipid bilayers. SLBs should display lateral mobility as in living cells, because many membrane activities involve transport, recruitment, or assembly of specific components. It is also critical for membranes to exhibit the correct thermodynamic phase, namely, a fluid lipid bilayer, to respond to environmental stress such as temperature and pressure changes [7]. There are several ways to fabricate supported lipid bilayers (SLBs) on planar substrates. One can use vesicle fusion on solid substrates [5,8–10] as well as Langmuir-Blodgett deposition [11,12]. Proteoliposome adsorption and subsequent membrane formation on a mica surface was first demonstrated by Brian and McConnell [13]. Because of its simplicity and reproducibility, this is one of the most common approaches to prepare supported membranes. A diverse range of different solid substrates has been used as support material below the bilayer [14,15]. Silicon oxide is the material of choice for vesicle fusion [16]. Polymer cushions dampen the effect of hard surfaces and therefore have been actively investigated [17–20]. However, it is not fully understood which changes the introduction of a solid support introduces into such a biomimetic system. Experimentally it is almost impossible to address such changes, as extremely highresolution data would be required.

What Is the Difference Between a Supported and a Free Bilayer? Insights from Molecular Modeling on Different Scales

Abstract Supported lipid bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for mechanical stability and enable characterization techniques not reachable otherwise. However, in computer simulations, these systems have been studied only rarely. Here, we discuss systematically the changes that a support inflicts on a phospholipid bilayer, using molecular modeling on different length scales. We characterize density and pressure profiles as well as the density imbalance induced by the support. It turns out that the changes in pressure profile are strong enough that protein function should be impacted leading to a previously neglected mechanism of transmembrane protein malfunction in supported bilayers. We also discuss the diffusion and reorientation behavior and characterize the influence of different corrugations of the support. The free energy of transfer of phospholipids between the proximal (close to the surface) and distal leaflet of a supported membrane shows that there is at equilibrium about a 3–4% higher density in the proximal leaflet.

What is the Difference Between a Supported and a Free Lipid Bilayer

Supported Lipid Bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability and enable characterization techniques not reachable otherwise. However, in computer simulations these systems have been studied only rarely up to now. Here we present a systematic study of the changes that a support inflicts on a phospholipid bilayer using coarse-grained molecular modeling.We characterize the density and pressure profiles as well as the density imbalance induced by the support. It turns out that the changes in pressure profile are strong enough that protein function should be impacted leading to a previously neglected mechanism of transmembrane protein malfunction in supported bilayers. We also determine the diffusion coefficients and characterize the influence of different corrugations of the support. We then determine the free energy of transfer of phospholipids between the proximal (close to the surface) and distal leaflet of a supported membrane using the coarse-grained Martini model. It turns out that there is at equilibrium about a 2-3% higher density in the proximal leaflet. These results are in favorable agreement with recent data obtained by very large scale modeling using a water free model where flip-flop can be observed directly. We compare results of the free energy of transfer obtained by pulling the lipid across the membrane in different ways. There are small quantitative differences but the overall picture is consistent. We are additionally characterizing the intermediate states which determine the barrier height and therefore the rate of translocation. Simulations in atomistic detail are performed for selected systems in order to confirm the findings.