Modeling of the triglyceride-rich core in lipoprotein particles

Molecular dynamics simulations of intracellular lipid droplets: a new tool in the toolbox

Lipid droplets (LDs) are ubiquitous intracellular organelles with a central role in multiple lipid metabolic pathways. However, identifying correlations between their structural properties and their biological activity has proved challenging, owing to their unique physicochemical properties as compared with other cellular membranes. In recent years, molecular dynamics (MD) simulations, a computational methodology allowing the accurate description of molecular assemblies down to their individual components, have been demonstrated to be a useful and powerful approach for studying LD structural and dynamical properties. In this short review, we attempt to highlight, as comprehensively as possible, how MD simulations have contributed to our current understanding of multiple molecular mechanisms involved in LD biology.

Isotropic liquid state of cocoa butter

The complex crystal structure of coca butter (CB) is responsible for the unique melting behavior, surface gloss, and mechanical properties of chocolate. While most studies concentrated on the crystalline state of CB, few studied the isotropic liquid state, which has a major impact on the crystallization process and the characteristics of the resulting crystals. In this study, the molecular organizations of the main CB triacylglycerols (TAGs; 1,3-dipalmitoyl-2-oleoylglycerol, palmitoyl-oleoyl-stearoylglycerol, POS, and 1,3-distearoyl-2-oleoylglycerol) were studied. The findings revealed the tunning-fork (Tf) conformation, commonly found in the crystalline state, is the least abundant in the isotropic liquid state of CB and pure TAGs. Notably, POS was found to interact with itself in CB, while its molecules with Tf conformation, although in small amounts in the mixture, tend to pair with each other at lower temperatures. These results highlight the significance of POS in CB crystallization and provide insights for developing CB alternatives.

Structural insights on the deformations induced by various mutations on cholesteryl ester transfer protein

Cholesteryl Ester Transfer Protein (CETP) is a plasma glycoprotein that intervenes the reverse cholesterol transport (RCT) by equimolar exchange of Cholesteryl esters (CE) and Triglycerides (TGs) between anti-atherogenic High-Density Lipoproteins (HDLs) and pro-atherogenic Low-Density Lipoproteins (LDLs) resulting in the increased concentration of CEs in LDL. This is a potential cause for the formation of atherosclerotic plaques in blood vessels leading to fatality. Therefore, blocking the function of CETP has emerged as a novel strategy for suppressing atherosclerotic plaques. The crystal structure of CETP revealed two Cholesteryl esters (CEs) in the hydrophobic tunnel and two phospholipids (PLs) plugged on the concave surface. Previous lipid transfer assay experimental studies have shown a substantial reduction in the neutral lipid transfer in [R201S] and [I443W, V198W] mutants. However, the protein conformational arrangements due to the mutations present in the CETP system leading to a decrease in the transfer rate of neutral lipids is not explored. Thus, I explored the reason behind the decreased transfer rate in mutants using molecular dynamics (MD) simulations and free energy calculations. Resulting evidences show that R201S mutant induces unfavorable bending angle to CETP with a decreased binding efficiency between N-terminal phospholipid of CETP with S201. Also, an unfavorable conformation state of TGs is formed which makes them difficult to transfer across CETP. Likewise, [I443W, V198W] mutant induces unfavorable CE, TG, and bending angle conformation to CETP impeding neutral lipid transfer. Thus, my results provide sufficient insights on the causation for a decreased transfer rate as reported earlier. The detailed understanding obtained here could help in developing a new strategy in preventing the function of CETP by blocking the role of potential hot spot residues.

Recharging your fats: CHARMM36 parameters for neutral lipids triacylglycerol and diacylglycerol

Neutral lipids (NLs) are an abundant class of cellular lipids. They are characterized by the total lack of charged chemical groups in their structure, and, as a consequence, they play a major role in intracellular lipid storage. NLs that carry a glycerol backbone, such as triacylglycerols (TGs) and diacylglycerols (DGs), are also involved in the biosynthetic pathway of cellular phospholipids, and they have recently been the subject of numerous structural investigations by means of atomistic molecular dynamics simulations. However, conflicting results on the physicochemical behavior of NLs were observed depending on the nature of the atomistic force field used. Here, we show that current phospholipid-derived CHARMM36 parameters for DGs and TGs cannot adequately reproduce interfacial properties of these NLs because of excessive hydrophilicity at the glycerol-ester region. By following a CHARMM36-consistent parameterization strategy, we develop improved parameters for both TGs and DGs that are compatible with both cutoff-based and particle mesh Ewald schemes for the treatment of Lennard-Jones interactions. We show that our improved parameters can reproduce interfacial properties of NLs and their behavior in more complex lipid assemblies. We discuss the implications of our findings in the context of intracellular lipid storage and NLs’ cellular activity.

Crystal Memory near Discontinuous Triacylglycerol Phase Transitions: Models, Metastable Regimes, and Critical Points

It is proposed that "crystal memory", observed in a discontinuous solid-liquid phase transition of saturated triacylglycerol (TAG) molecules, is due to the coexistence of solid TAG crystalline phases and a liquid TAG phase, in a superheated metastable regime. Such a coexistence has been detected. Solid crystals can act as heterogeneous nuclei onto which molecules can condense as the temperature is lowered. We outlined a mathematical model, with a single phase transition, that shows how the time-temperature observations can be explained, makes predictions, and relates them to recent experimental data. A modified Vogel-Fulcher-Tammann (VFT) equation is used to predict time-temperature relations for the observation of "crystal memory" and to show boundaries beyond which "crystal memory" is not observed. A plot of the lifetime of a metastable state versus temperature, using the modified VFT equation, agrees with recent time-temperature data. The model can be falsified through its predictions: the model possesses a critical point and we outline a procedure describing how it could be observed by changing the hydrocarbon chain length. We make predictions about how thermodynamic functions will change as the critical point is reached and as the system enters a crossover regime. The model predicts that the phenomenon of "crystal memory" will not be observed unless the system is cooled from a superheated metastable regime associated with a discontinuous phase transition.

Effect of Protein Flexibility from Coarse-Grained Elastic Network Parameterizations on the Calculation of Free Energy Profiles of Ligand Binding

The characterization of the affinity and binding mechanism of specific molecules to a protein active site is scientifically and industrially relevant for many applications. In principle, this information can be obtained using molecular dynamics (MD) simulations by calculating the free energy profile of the process. However, this is a computationally demanding calculation. Currently, coarse-grained (CG) force fields are very well implemented for MD simulations of biomolecular systems. These computationally efficient force fields are a major advantage to the study of large model systems and/or those requiring long simulation times. The Martini model is currently one of the most popular CG force fields for these systems. For the specific case of protein simulations, to correctly maintain the macromolecular three-dimensional structure, the Martini model needs to include an elastic network (EN). In this work, the effect of protein flexibility, as induced by three EN models compatible with the Martini force field, was tested on the calculation of free energy profiles for protein-ligand binding. The EN models used were ElNeDyn, GoMartini, and GEN. The binding of triolein (TOG) and triacetin (TAG) to a lipase protein (thermomyces lanuginosa lipase-TLL) was used as a case study. The results show that inclusion of greater flexibility in the CG parameterization of proteins is of high importance in the calculation of the free energy profiles of protein-ligand systems. However, care must be taken in order to avoid unjustified large protein deformations. In addition, due to molecular flexibility there may be no absolute need for the center of the ligand to reach the center of the protein-binding site. The calculation of the energy profile to a distance of about 0.5 nm from the active site center can be sufficient to differentiate the affinity of different ligands to a protein.

On the Structure of Solid Lipid Nanoparticles

Solid lipid nanoparticles (SLNs) have a crystalline lipid core which is stabilized by interfacial surfactants. SLNs are considered favorable candidates for drug delivery vehicles since their ability to store and release organic molecules can be tailored through the identity of the lipids and surfactants used. When stored, polymorphic transitions in the core of drug-loaded SLNs lead to the premature release of drug molecules. Significant experimental studies have been conducted with the aim of investigating the physicochemical properties of SLNs, however, no molecular scale investigations have been reported on the behaviors that drive SLN formation and their polymorphic transitions. A combination of small angle neutron scattering and all-atom molecular dynamics simulations is therefore used to yield a detailed atomistic description of the internal structure of an SLN comprising triglyceride, tripalmitin, and the nonionic surfactant, Brij O10 (C_18:1 E₁₀ ). The molecular scale mechanisms by which the surfactants stabilize the crystalline structure of the SLN lipid core are uncovered. By comparing these results to simulated liquid and solid aggregates of tripalmitin lipids, how the morphology of the lipids vary between these systems is demonstrated providing further insight into the mechanisms that control drug encapsulation and release from SLNs.

Interfacial ordering of tristearin induced by glycerol monooleate and PGPR: A coarse-grained molecular dynamics study

We use coarse-grained molecular dynamics simulations to study the effect of surfactant structure on the ordering of bulk tristearin at an oil-water interface. In the absence of surfactant, tristearin acyl chains are marginally aligned normal to the interface. The surfactant glycerol monooleate (GMO), a common small-molecule monoacylglycerol (MW: 357 g/mol), preferentially adsorbs to the oil-water interface, displacing more of the tristearin as its concentration increases. The tristearin that remains at the interface is closely aligned normal to the interface. Adjacent to the interface, bulk tristearin increasingly aligns with its acyl chains entwined with the GMO acyl chain, which also preferentially aligns normal to the interface. In contrast, polyglycerol polyricinoleate (PGPR), a bulkier, polymeric surfactant (MW: 1398 g/mol for a molecule with five monomers), both displaces tristearin from the interface and reduces the alignment of the molecules that remain. We suggest that the similar fatty acid moieties of GMO (oleic acid) and tristearin (stearic acid) lead to liquid-state association and alignment, the latter of which can then serve as a template onto which tristearin crystals can nucleate. Conversely, by both displacing tristearin from the interface and reducing alignment below that of the surfactant-free system, PGPR eliminates the possibility of tristearin interfacial crystallisation.

Mechanisms of lipid extraction from skin lipid bilayers by sebum triglycerides

Microsecond computations identify the pathways leading to the extraction of skin lipids by sebum triglycerides and the associated energetic costs.

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

Understanding the interactions between sebum triglycerides and water: a molecular dynamics simulation study

Sebum triglycerides actively contribute to the water transport across the sebum layerviathe percolating network of triglyceride head groups.

The triolein/aqueous interface and lipase activity studied by spectroscopic ellipsometry and coarse grained simulations

In spite of the importance of the triglyceride aqueous interface for processes like emulsification, surfactant interactions and lipase activity, relatively little is known about this interface compared to that between alkanes and water. Here, the contact between triolein and water was investigated in terms of water inclusion in the oil phase and orientation of the molecules at the interface. Coarse grained models of triglycerides in contact with water were constructed and correlated with experimental results of the changes in thickness and refractive index, obtained using spectroscopic ellipsometry of spin-coated triolein films. The topography of the layer was revealed by atomic force microscopy. Dry triolein and a triolein sample after equilibration with water were also compared structurally using small-angle X-ray scattering. Additionally, the kinetics of adsorption/activity of three different variants of the Thermomyces lanuginosus lipase (TLL) were investigated. The results show that uptake of water in the triolein phase leads to increase in thickness of the layer. The observed increase of thickness was further enhanced by an active lipase but reduced when an inactive mutant of the enzyme was applied.

How cholesteryl ester transfer protein can also be a potential triglyceride transporter

CETP transfers cholesteryl esters (CEs) and triglycerides (TGs) between different lipoproteins and came in limelight as a drug-target against CVD. In the search for detailed mechanism of lipid transfer through CETP, enormous effort is devoted employing crystallographic, cryo-EM, and Molecular Dynamics (MD) studies. However, these studies primarily focused on CE-bound CETP structure and CE transfer mechanism. With the reported correlation that CETP looses significant CE transfer activity upon inhibiting TG transfer, it is of tremendous importance to understand the structure and dynamics of TG-bound CETP. Our results from large-scale all-atom and coarse-grained MD simulations show that CETP can accommodate two TG molecules in parallel N-N orientation with TG oleate chains majorly attaining the tuning-fork conformation. In TG-bound form, CETP not only maintained its secondary structures but also exhibited similar bending-twisting motions as reported for CE-CETP crystal structure. Obtained structural information are further validated by correlating to available functional data of 2-8 fold slower transfer rate of TG through CETP, where we show that TGs make 20% additional contacts with CETP compared to CEs. Identified CETP residues facilitating TG binding also match very well with reported mutagenesis data. The study could accelerate the drug-designing processes to combat CETP functionality and CVD.

Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets

Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids.

Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid

The removal or structural disruption of crystallised lipid is a pivotal but energy-intensive step in a wide range of industrial and biological processes. Strategies to disrupt the structure of crystallised lipid in aqueous solution at lower temperatures are much needed, where nanoparticle-based strategies show enormous promise. Using the aqueous tristearin bilayer as a model for crystallised lipid, we demonstrate that the synergistic use of surfactant and detonation nanodiamonds can depress the onset temperature at which disruption of the crystallised lipid structure occurs. Our simulations reveal the molecular-scale mechanisms by which this disruption takes place, indicating that the nanodiamonds serve a dual purpose. First, the nanodiamonds are predicted to facilitate delivery of surfactant to the lipid/water interface, and second, nanodiamond adsorption acts to roughen the lipid/water interface, enhancing ingress of surfactant into the bilayer. We find the balance of the hydrophobic surface area of the nanodiamond and the nanodiamond surface charge density to be a key determinant of the effectiveness of using nanodiamonds to facilitate lipid disruption. For the nanodiamond size considered here, we identify a moderate surface charge density, that ensures the nanodiamonds are neither too hydrophobic nor too hydrophilic, to be optimal.

Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations

Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.

Computational studies of plasma lipoprotein lipids

Plasma lipoproteins are macromolecular assemblies of proteins and lipids found in the blood. The lipid components of lipoproteins are amphipathic lipids such as phospholipids (PLs), and unesterified cholesterols (UCs) and hydrophobic lipids such as cholesteryl esters (CEs) and triglycerides (TGs). Since lipoproteins are soft matter supramolecular assemblies easily deformable by thermal fluctuations and they also exist in varying densities and protein/lipid components, a detailed understanding of their structure/function is experimentally difficult. Molecular dynamics (MD) simulation has emerged as a particularly promising way to explore the structure and dynamics of lipoproteins. The purpose of this review is to survey the current status of computational studies of the lipid components of the lipoproteins. Computational studies aim to explore three levels of complexity for the 3-dimensional structural dynamics of lipoproteins at various metabolic stages: (i) lipoprotein particles consist of protein with minimal lipid; (ii) lipoprotein particles consist of PL-rich discoidal bilayer-like lipid particles; (iii) mature circulating lipoprotein particles consist of CE-rich or TG-rich spheroidal lipid-droplet-like particles. Due to energy barriers involved in conversion between these species, other biomolecules also participate in lipoprotein biological assembly. For example: (i) lipid-poor apolipoprotein A-I (apoA-I) interacts with ATP-binding cassette transporter A1 (ABCA1) to produce nascent discoidal high density lipoprotein (dHDL) particles; (ii) lecithin-cholesterol acyltransferase (LCAT) mediates the conversion of UC to CE in dHDL, driving spheroidal HDL (sHDL) formation; (iii) transfer proteins, cholesterol ester transfer protein (CETP) and phospholipid transfer protein (PLTP), transfer both CE and TG and PL, respectively, between lipoprotein particles. Computational studies have the potential to explore different lipoprotein particles at each metabolic stage in atomistic detail. This review discusses the current status of computational methods including all-atom MD (AAMD), coarse-grain MD (CGMD), and MD-simulated annealing (MDSA) and their applications in lipoprotein structural dynamics and biological assemblies. Results from MD simulations are discussed and compared across studies in order to identify key findings, controversies, issues and future directions. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants

Molecular dynamics simulations predict that sodium dodecylbenzene sulphonate surfactant molecules embed themselves in a tristearin bilayer, packing commensurate with the hexagonally packed lattice formed by the acyl tails of tristearin.

Oil binding capacities of triacylglycerol crystalline nanoplatelets: nanoscale models of tristearin solids in liquid triolein

Polycrystalline particles composed of triacylglycerol (TAG) molecules, and their networks, in anhydrous TAG oils find extensive use as edible oils in the food industry.

Temperature- and pressure-dependent densities, self-diffusion coefficients, and phase behavior of monoacid saturated triacylglycerides: toward molecular-level insights into processing

Using molecular-dynamics (MD) simulations the densities and self-diffusion coefficients of a range of liquid monoacid triacylglycerides (TAGs) have been studied as a function of temperature and, for the first time, pressure. While offset by their ambient properties, the response of the TAGs to temperature and pressure is qualitatively similar. Application of pressure was found to significantly increase densities and reduce diffusion of the TAG molecules, suggesting that it may have as much a role in processing and crystallizing TAGs as supercooling does. A solution of glycerol tripalmitate and glycerol trihexanoate was also studied, showing that application of pressure should lead to a significant decrease in the saturation point of the solution, which is an important consideration for processing TAGs. Different solid/liquid interfaces of glycerol tripalmitate have also been investigated. Although crystal growth could not be observed, dissolution of one interface was seen in the MD simulations. The results suggest that over moderate distances the melting of TAGs may be cooperative in nature, rather than involving dissolution of individual TAG molecules.

Development of a coarse-grained model for simulations of tridecanoin liquid-solid phase transitions

Novel coarse-grained models for molecular dynamics of tridecanoin melts are here proposed as results of a coarse-graining step procedure. The procedure is implemented to develop three coarse-grained models of increasing number of particle types from two to four. Force fields are computed by minimization of the deviations of appropriate distribution functions of the coarse-grained models from those of a reference atomistic one. Density, diffusivity and shear viscosity are computed by numerical simulation and compared with experimental values. The ability of each model to describe liquid-solid transitions is also analyzed. In particular, the model with four types of coarse-grained beads shows a transition from a liquid to a crystal phase.

Lipid simulations: a perspective on lipids in action

In this article, we provide an overview of lipid simulations, describing how a computer can be used as a laboratory for lipid research. We briefly discuss the methodology of lipid simulations followed by a number of topical applications that show the benefit of computer modeling for complementing experiments. In particular, we show examples of cases in which simulations have made predictions of novel phenomena that have later been confirmed by experimental studies. Overall, the applications discussed in this article focus on the most recent state of the art and aim to provide a perspective of where the field of lipid simulations stands at the moment.

Role of lipids in spheroidal high density lipoproteins

We study the structure and dynamics of spherical high density lipoprotein (HDL) particles through coarse-grained multi-microsecond molecular dynamics simulations. We simulate both a lipid droplet without the apolipoprotein A-I (apoA-I) and the full HDL particle including two apoA-I molecules surrounding the lipid compartment. The present models are the first ones among computational studies where the size and lipid composition of HDL are realistic, corresponding to human serum HDL. We focus on the role of lipids in HDL structure and dynamics. Particular attention is paid to the assembly of lipids and the influence of lipid-protein interactions on HDL properties. We find that the properties of lipids depend significantly on their location in the particle (core, intermediate region, surface). Unlike the hydrophobic core, the intermediate and surface regions are characterized by prominent conformational lipid order. Yet, not only the conformations but also the dynamics of lipids are found to be distinctly different in the different regions of HDL, highlighting the importance of dynamics in considering the functionalization of HDL. The structure of the lipid droplet close to the HDL-water interface is altered by the presence of apoA-Is, with most prominent changes being observed for cholesterol and polar lipids. For cholesterol, slow trafficking between the surface layer and the regimes underneath is observed. The lipid-protein interactions are strongest for cholesterol, in particular its interaction with hydrophobic residues of apoA-I. Our results reveal that not only hydrophobicity but also conformational entropy of the molecules are the driving forces in the formation of HDL structure. The results provide the first detailed structural model for HDL and its dynamics with and without apoA-I, and indicate how the interplay and competition between entropy and detailed interactions may be used in nanoparticle and drug design through self-assembly.

Triglyceride blisters in lipid bilayers: implications for lipid droplet biogenesis and the mobile lipid signal in cancer cell membranes

Triglycerides have a limited solubility, around 3%, in phosphatidylcholine lipid bilayers. Using millisecond-scale course grained molecular dynamics simulations, we show that the model lipid bilayer can accommodate a higher concentration of triolein (TO) than earlier anticipated, by sequestering triolein molecules to the bilayer center in the form of a disordered, isotropic, mobile neutral lipid aggregate, at least 17 nm in diameter, which forms spontaneously, and remains stable on at least the microsecond time scale. The results give credence to the hotly debated existence of mobile neutral lipid aggregates of unknown function present in malignant cells, and to the early biogenesis of lipid droplets accommodated between the two leaflets of the endoplasmic reticulum membrane. The TO aggregates give the bilayer a blister-like appearance, and will hinder the formation of multi-lamellar phases in model, and possibly living membranes. The blisters will result in anomalous membrane probe partitioning, which should be accounted for in the interpretation of probe-related measurements.