Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field

Dynamic framework for large-scale modeling of membranes and peripheral proteins

In this chapter, we present a novel computational framework to study the dynamic behavior of extensive membrane systems, potentially in interaction with peripheral proteins, as an alternative to conventional simulation methods. The framework effectively describes the complex dynamics in protein-membrane systems in a mesoscopic particle-based setup. Furthermore, leveraging the hydrodynamic coupling between the membrane and its surrounding solvent, the coarse-grained model grounds its dynamics in macroscopic kinetic properties such as viscosity and diffusion coefficients, marrying the advantages of continuum- and particle-based approaches. We introduce the theoretical background and the parameter-space optimization method in a step-by-step fashion, present the hydrodynamic coupling method in detail, and demonstrate the application of the model at each stage through illuminating examples. We believe this modeling framework to hold great potential for simulating membrane and protein systems at biological spatiotemporal scales, and offer substantial flexibility for further development and parametrization.

Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations

Lipid nanoparticles (LNPs) are essential carrier particles in drug delivery systems, particularly in ribonucleic acid delivery. In preparing lipid-based nanoparticles, microfluidic-based ethanol injection may produce precisely size-controlled nanoparticles. Ethanol is critical in LNP formation and post-treatment processes and affects liposome size, structure, lamellarity, and drug-loading efficiency. However, the effects of time-dependent changes in the ethanol concentration on the structural dynamics of liposomes are not clearly understood. Herein, we investigated ethanol-induced lipid bilayer changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations. The time-resolved SAXS measurement system revealed that single unilamellar liposomes were converted to multilamellar liposomes within 0.8 s of contact with ethanol, and the d-spacing was decreased from 6.1 (w/o ethanol) to 4.4 nm (80% ethanol) with increasing ethanol concentration. We conducted 1 μs MD simulations to understand the molecular-level structural changes in the liposomes. The MD simulations revealed that the changes in the lamellar structure caused by ethanol at the molecular level could explain the structural changes in the liposomes observed via time-resolved SAXS. Therefore, the post-treatment process to remove residual ethanol is critical in liposome formation.

Stability of Cytoplasmic Membrane of Escherichia coli Bacteria in Aqueous and Ethanolic Environment

The mechanism of action of any antibacterial agent or disinfectant depends largely on their interaction with the bacterial membrane. Herein, we use the SPICA (surface property fitting coarse graining) force-field and develop a coarse-grained (CG) model for the structure of the cytoplasmic membrane of Escherichia coli (E. coli) and its interaction with water and ethanol. We elucidate the impact of different concentrations of ethanol on the cytoplasmic membrane bilayers and vesicles of E. coli using the CG molecular dynamics (CG MD) simulations. Our modeling approach first focuses on the parametrization of the required force-field for POPG lipid and its interaction with water, ethanol, and POPE lipid. Subsequently, the structural stability of the E. coli bacterial membrane in the presence of high and low concentrations of ethanol is delineated. Both flat bilayers as well as vesicles of E. coli membrane were considered for the CG MD. Our results reveal that, at low ethanol concentrations (<30 mol %), the size of the E. coli vesicles increases with discernible deformations in their shapes. Because of ethanol-induced interdigitation, thinning of the E. coli vesicular membrane is also observed. However, at higher ethanol concentrations (>30 mol %), the integrity of the vesicles is lost because of deteriorating invasion of ethanol molecules into the vesicle bilayer and significant weakening of lipid-lipid interactions. At higher ethanol concentrations (40 and 70 mol %), both the multivesicle and single-vesicle bacterial membranes exhibit a similar rupturing pattern wherein the extraction of lipids from the membrane and formation of aggregates of the component lipids are observed. These aggregates consist of polar head groups of 3-5 POPE/POPG lipids with intertwined nonpolar tails.

Energy renormalization for temperature transferable coarse-graining of silicone polymer

The bottom-up prediction of thermodynamic and mechanical behaviors of polymeric materials based on molecular dynamics (MD) simulation is of critical importance in polymer physics. Although the atomistically informed coarse-grained (CG) model can access greater spatiotemporal scales and retain essential chemical specificity, the temperature-transferable CG model is still a big challenge and hinders widespread application of this technique. Herein, we use a silicone polymer, i.e., polydimethylsiloxane (PDMS), having an incredibly low chain rigidity as a model system, combined with an energy-renormalization (ER) approach, to systematically develop a temperature-transferable CG model. Specifically, by introducing temperature-dependent ER factors to renormalize the effective distance and cohesive energy parameters, the developed CG model faithfully preserved the dynamics, mechanical and conformational behaviors compared with the target all-atomistic (AA) model from glassy to melt regimes, which was further validated by experimental data. With the developed CG model featuring tremendously improved computational efficiency, we systematically explored the influences of cohesive interaction strength and temperature on the dynamical heterogeneity and mechanical response of polymers, where we observed consistent trends with other linear polymers with varying chain rigidity and monomeric structures. This study serves as an extension of our proposed ER approach of developing temperature transferable CG models with diverse segmental structures, highlighting the critical role of cohesive interaction strength on CG modeling of polymer dynamics and thermomechanical behaviors.

pSPICA Force Field Extended for Proteins and Peptides

Many coarse-grained (CG) molecular dynamics (MD) studies have been performed to investigate biological processes involving proteins and lipids. CG force fields (FFs) in these MD studies often use implicit or nonpolar water models to reduce computational costs. CG-MD using water models cannot properly describe electrostatic screening effects owing to the hydration of ionic segments and thus cannot appropriately describe molecular events involving water channels and pores through lipid membranes. To overcome this issue, we developed a protein model in the pSPICA FF, in which a polar CG water model showing the proper dielectric response was adopted. The developed CG model greatly improved the transfer free energy profiles of charged side chain analogues across the lipid membrane. Application studies on melittin-induced membrane pores and mechanosensitive channels in lipid membranes demonstrated that CG-MDs using the pSPICA FF correctly reproduced the structure and stability of the pores and channels. Furthermore, the adsorption behavior of the highly charged nona-arginine peptides on lipid membranes changed with salt concentration, indicating the pSPICA FF is also useful for simulating protein adsorption on membrane surfaces.

Improved Protein Model in SPICA Force Field

The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and the stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was overstabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study, we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and reoptimize almost all nonbonded parameters for amino acids. The improved FF proposed here successfully reproduces the radii of gyration of various IDPs, the binding sensitivity of several peripheral membrane proteins, and the dimerization free energies of several transmembrane helices. The new model also shows improved agreement with experiments on the free energy of peptide association in water. In addition, an extensive library of nonbonded interactions between proteins and lipids, including various glycerophospholipids, sphingolipids, and cholesterol, allows the study of specific interactions between lipids and peripheral and transmembrane proteins. Hence, the new SPICA FF (version 2) proposed herein is applicable with high accuracy for simulating a wide range of protein systems.

Pragmatic Coarse-Graining of Proteins: Models and Applications

The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.

Effects of lipid saturation on bicelle to vesicle transition of a binary phospholipid mixture: a molecular dynamics simulation study

Controlling the transition from lipid bicelles to vesicles is essential for producing engineered vesicles. We perform coarse-grained molecular dynamics (CGMD) simulations of unsaturated/saturated lipid mixtures to clarify the effects of lipid unsaturation on vesiculation at the molecular scale. The results demonstrate that vesiculation depends on the concentration of unsaturated lipids and the degree of unsaturation. The probability of vesiculation increases linearly with the apparent unsaturated lipid concentration at a low degree of unsaturation. Higher degrees of unsaturation lead to phase segregation within the binary bicelles, reducing the probability of vesiculation. A comparison between CGMD simulations and the conventional theory of vesiculation shows that the theoretical predictions of binary lipid systems must explicitly include phase segregation effects. Furthermore, simulations with biased lipid distributions reveal that vesiculation is facilitated by the preconcentration of unsaturated lipids in the core region of the bicelle but is then temporally limited as the unsaturated lipids move to the bicelle edges. These findings advance theoretical and experimental studies on binary lipid systems and promote the development of tailor-made vesicles.

Structural and thermodynamic properties of bulk triglycerides and triglyceride/water mixtures reproduced using a polarizable coarse-grained model

Triglycerides (TGs) play important roles in renewable energies, food production, medicine, and metabolism in organisms. Here, we developed a novel coarse-grained (CG) force field (FF) for triglycerides to reproduce both the structural and thermodynamic properties of bulk TGs, TG/air interfaces, and TG/water mixtures using molecular dynamics (MD) simulations. We rigorously optimized the bonded and nonbonded force parameters between the CG beads of TGs and nonbonded force parameters between TG beads and polarizable CG water beads by employing an efficient meta-multilinear interpolation parameterization algorithm recently developed by us. This CG FF performs very well in reproducing the percolating network of the TG bulk phase self-assembled in water and a variety of molecular conformations predicted by all-atom MD simulations. More importantly, it also correctly reproduces multiple experimentally measurable macroscopic thermodynamic properties, including the density and surface tensions of both the TG/air and TG/water interfaces. This paves the way for studying more complicated systems involving TGs on a large scale.

An in silico osmotic pressure approach allows characterization of pressure-area isotherms of lipid monolayers at low molecular areas

Surface pressure-area isotherms of lipid monolayers at the air-water interface provide essential information about the structure and mechanical behaviour of lipid membranes. These curves can be readily obtained through Langmuir trough measurements and, as such, have been collected for decades in the field of membrane biochemistry. However, it is still challenging to directly observe and understand nanoscopic features of monolayers through such experiments, and molecular dynamics (MD) simulations are generally used to provide a molecular view of such interfaces. In MD simulations, the surface pressure-area (Π-A) isotherms are generally computed using the Kirkwood-Irving formula, that relies on the evaluation of the pressure tensor. This approach, however, has intrinsic limitations when the molecular area in the monolayer is low (typically < 60 Ų per lipid). Recently, an alternative method to compute Π-A isotherms of surfactants, based on the calculation of the three-dimensional osmotic pressure via the implementation of semipermeable barriers was proposed. In this work, we investigate the feasibility of this approach for long-chain surfactants such as phospholipids. We identify some discrepancies between the computed values and experimental results, and we propose a semi-empirical correction based on the molecular structure of the surfactants at the monolayer interface. To validate the potential of this new approach, we simulate several phosphatidylcholine and phosphatidylethanolamine lipids at various temperatures using all-atom and coarse-grained force fields, and we compute the corresponding Π-A isotherms. Our results show that the Π-A isotherms obtained using the new method are in very good agreement with experiments and far superior to the canonical pressure tensor-based method at low molecular areas. This corrected osmotic pressure method allows for accurate characterization of the molecular packing in monolayers in various physical phases.

Application of molecular dynamics simulation in self-assembled cancer nanomedicine

Self-assembled nanomedicine holds great potential in cancer theragnostic. The structures and dynamics of nanomedicine can be affected by a variety of non-covalent interactions, so it is essential to ensure the self-assembly process at atomic level. Molecular dynamics (MD) simulation is a key technology to link microcosm and macroscale. Along with the rapid development of computational power and simulation methods, scientists could simulate the specific process of intermolecular interactions. Thus, some experimental observations could be explained at microscopic level and the nanomedicine synthesis process would have traces to follow. This review not only outlines the concept, basic principle, and the parameter setting of MD simulation, but also highlights the recent progress in MD simulation for self-assembled cancer nanomedicine. In addition, the physicochemical parameters of self-assembly structure and interaction between various assembled molecules under MD simulation are also discussed. Therefore, this review will help advanced and novice researchers to quickly zoom in on fundamental information and gather some thought-provoking ideas to advance this subfield of self-assembled cancer nanomedicine.

HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter

We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics. The methodology is based on a tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating nonphysical force aliasing. Separating the time integration of fast modes associated with internal molecular motion from slow modes associated with their density fields, we enable the first time-reversible, energy-conserving hybrid particle-field simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in particle-mesh Ewald. We demonstrate the ability of HyMD to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse-grain length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multimicrosecond regime observed with comparable coarse-grained models.

Development of a coarse-grained model for surface-functionalized gold nanoparticles: towards an accurate description of their aggregation behavior

Understanding the dispersion stability and aggregation propensity of self-assembled monolayer gold NPs at a molecular level is crucial to guide their rational design and to inform about the optimal surface functionalization for specific applications. To reach this goal, in silico modeling via coarse-grained (CG) molecular dynamics (MD) simulations is a fundamental tool to complement the information acquired from experimental studies since CG modeling allows to get a deep knowledge of the molecular interactions that take place at the nanoscale in this kind of systems. Unfortunately, current CG models of monolayer-protected AuNPs present several drawbacks that limit their accuracy in certain scenarios. We here develop a CG model that is fully compatible and extends the SPICA/SDK (Shinoda-DeVane-Klein) force field. Our model allows reproducing the behavior of AuNPs functionalized with hydrophobic as well as charged and more hydrophilic ligands. This model improves upon results obtained with previously derived CG force fields and successfully describes NPs aggregation and self-assembly in aqueous solution.

Dynamic Processes and Mechanical Properties of Lipid-Nanoparticle Mixtures

In this study, we investigate the dynamic processes and mechanical properties of lipid nanoparticle mixtures in a melt via dissipation particle dynamic simulation. By investigating the distribution of nanoparticles in lamellar and hexagonal lipid matrices in equilibrium state and dynamic processes, we observe that the morphology of such composites depends not only on the geometric features of the lipid matrix but also on the concentration of nanoparticles. The dynamic processes are also demonstrated by calculating the average radius of gyration, which indicates the isotropic conformation of lipid molecules in the x-y plane and that the lipid chains are stretched in the z direction with the addition of nanoparticles. Meanwhile, we predict the mechanical properties of lipid-nanoparticle mixtures in lamellar structures by analyzing the interfacial tensions. Results show that the interfacial tension decreased with the increase in nanoparticle concentration. These results provide molecular-level information for the rational and a priori design of new lipid nanocomposites with ad hoc tailored properties.

A top-down and bottom-up combined strategy for parameterization of coarse-grained force fields for phospholipids

Coarse-graining (CG) molecular dynamics (MD) simulations are widely used in interpreting experimental observations and predicting assembly morphology as well as collective behaviour but also face the problem of poor accuracy. A main issue is that cross-termed interactions between different CG beads are inadequately parameterized. This work proposes a novel top-down and bottom-up combined strategy to parameterize both self- and cross-termed interactions of zwitterionic phospholipids in water solution based on a piecewise Morse potential describing nonbonded van der Waals interactions. The self-interacting force parameters were optimized by matching experimental density, heat vapourization, and surface tension in a top-down manner, while the cross-termed interactions were optimized by fitting pseudo properties obtained from atomistic simulations in a bottom-up way, including mixing density, intermolecular energy, and radial mixing coefficient. The transferability of the CG force field (FF) was confirmed by reproducing a variety of structural and thermodynamic properties of lipid membranes in both liquid and gel phases. This FF can well depict vesicle self-assembly and vesicle fusion processes. Matching pseudo properties opens a new way to develop CG FF with increased accuracy and transferability.

Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes

The principles for the selection of the stereochemistry of phospholipids of biological membranes remain unclear and continue to be debated. Therefore, any new experiments on this topic may help progress in this field. To address this question, three libraries of constitutional isomeric glycerol-amphiphilic Janus dendrimers (JDs) with nonsymmetric homochiral, racemic, and symmetric achiral branching points were synthesized by an orthogonal-modular-convergent methodology. These JDs amplify self-assembly, and therefore, monodisperse vesicles known as dendrimersomes (DSs) with predictable dimensions programmed by JD concentration were assembled by rapid injection of their ethanol solution into water. DSs of homochiral JD enantiomers, racemic, including mixtures of different enantiomers, and achiral exhibited similar DS size-concentration dependence. However, the number of bilayers of DSs assembled from homochiral, achiral, and racemic JDs determined by cryo-TEM were different. Statistical analysis of the number of bilayers and coarse-grained molecular dynamics simulations demonstrated that homochiral JDs formed predominantly unilamellar DSs. Symmetric achiral JDs assembled only unilamellar DSs while racemic JDs favored multilamellar DSs. Since cell membranes are unilamellar, these results indicate a new rationale for nonsymmetric homochiral vs racemic selection. Simultaneously, these experiments imply that the symmetric achiral lipids forming more stable membrane, probably had been the preferable assemblies of prebiotic cell membranes.

Triglyceride lipolysis triggers liquid crystalline phases in lipid droplets and alters the LD proteome

Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs), but how these lipids are organized within LDs and influence their proteome remain unclear. Using in situ cryo-electron tomography, we show that glucose restriction triggers lipid phase transitions within LDs generating liquid crystalline lattices inside them. Mechanistically this requires TG lipolysis, which decreases the LD's TG:SE ratio, promoting SE transition to a liquid crystalline phase. Molecular dynamics simulations reveal TG depletion promotes spontaneous TG and SE demixing in LDs, additionally altering the lipid packing of the PL monolayer surface. Fluorescence imaging and proteomics further reveal that liquid crystalline phases are associated with selective remodeling of the LD proteome. Some canonical LD proteins, including Erg6, relocalize to the ER network, whereas others remain LD-associated. Model peptide LiveDrop also redistributes from LDs to the ER, suggesting liquid crystalline phases influence ER-LD interorganelle transport. Our data suggests glucose restriction drives TG mobilization, which alters the phase properties of LD lipids and selectively remodels the LD proteome.

Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.

Using molecular simulation to understand the skin barrier

Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.

Modeling Polyzwitterion-Based Drug Delivery Platforms: A Perspective of the Current State-of-the-Art and Beyond

Drug delivery platforms are anticipated to have biocompatible and bioinert surfaces. PEGylation of drug carriers is the most approved method since it improves water solubility and colloid stability and decreases the drug vehicles’ interactions with blood components. Although this approach extends their biocompatibility, biorecognition mechanisms prevent them from biodistribution and thus efficient drug transfer. Recent studies have shown (poly)zwitterions to be alternatives for PEG with superior biocompatibility. (Poly)zwitterions are super hydrophilic, mainly stimuli-responsive, easy to functionalize and they display an extremely low protein adsorption and long biodistribution time. These unique characteristics make them already promising candidates as drug delivery carriers. Furthermore, since they have highly dense charged groups with opposite signs, (poly)zwitterions are intensely hydrated under physiological conditions. This exceptional hydration potential makes them ideal for the design of therapeutic vehicles with antifouling capability, i.e., preventing undesired sorption of biologics from the human body in the drug delivery vehicle. Therefore, (poly)zwitterionic materials have been broadly applied in stimuli-responsive “intelligent” drug delivery systems as well as tumor-targeting carriers because of their excellent biocompatibility, low cytotoxicity, insignificant immunogenicity, high stability, and long circulation time. To tailor (poly)zwitterionic drug vehicles, an interpretation of the structural and stimuli-responsive behavior of this type of polymer is essential. To this end, a direct study of molecular-level interactions, orientations, configurations, and physicochemical properties of (poly)zwitterions is required, which can be achieved via molecular modeling, which has become an influential tool for discovering new materials and understanding diverse material phenomena. As the essential bridge between science and engineering, molecular simulations enable the fundamental understanding of the encapsulation and release behavior of intelligent drug-loaded (poly)zwitterion nanoparticles and can help us to systematically design their next generations. When combined with experiments, modeling can make quantitative predictions. This perspective article aims to illustrate key recent developments in (poly)zwitterion-based drug delivery systems. We summarize how to use predictive multiscale molecular modeling techniques to successfully boost the development of intelligent multifunctional (poly)zwitterions-based systems.

Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains

The fusion pore controls the release of exocytotic vesicle contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore (membrane fusion, nucleation, and expansion) that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve toward full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events.

The lung surfactant activity probed with molecular dynamics simulations

The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.

Nonane and Hexanol Adsorption in the Lamellar Phase of a Nonionic Surfactant: Molecular Simulations and Comparison to Ideal Adsorbed Solution Theory

Adsorption of n-nonane/1-hexanol (C9/C6OH) mixtures into the lamellar phase formed by a 50/50 w/w triethylene glycol mono-n-decyl ether (C10E3)/water system was studied using configurational-bias Monte Carlo simulations in the osmotic Gibbs ensemble. The interactions were described by the Shinoda-Devane-Klein coarse-grained force field. Prior simulations probing single-component adsorption indicated that C9 molecules preferentially load near the center of the bilayer, increasing the bilayer thickness, whereas C6OH molecules are more likely to be found near the interface of the polar and nonpolar moieties, swelling the bilayer in the lateral dimension. Here, we extend this work to binary C9/C6OH adsorption to probe whether the difference in the spatial preferences may lead to a synergistic effect and enhanced loadings for the mixture. Comparing loading trends and the thermodynamics of binary adsorption to unary adsorption reveals that C9-C9 interactions lead to the largest enhancement, whereas C9-C6OH and C6OH-C6OH interactions are less favorable for this bilayer system. Ideal adsorbed solution theory yields satisfactory predictions of the binary loading.

SPICA Force Field for Proteins and Peptides

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulations with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. An elastic network model was adopted to maintain the secondary structure within a single chain. The side-chain analogues reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable association free energy (potential of mean force) in water compared to those from AA MD. A series of peptides/proteins adsorbed onto or penetrated into the membrane simulated by the CG MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins as comparable to those in the orientations of proteins in membranes (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated the good performance of the SPICA FF.

Vesicle-based artificial cells: materials, construction methods and applications

The construction of artificial cells with specific cell-mimicking functions helps to explore complex biological processes and cell functions in natural cell systems and provides an insight into the origins of life. Bottom-up methods are widely used for engineering artificial cells based on vesicles by the in vitro assembly of biomimetic materials. In this review, the design of artificial cells with a specific function is discussed, by considering the selection of synthetic materials and construction technologies. First, a range of biomimetic materials for artificial cells is reviewed, including lipid, polymeric and hybrid lipid/copolymer materials. Biomaterials extracted from natural cells are also covered in this part. Then, the formation of microscale, giant unilamellar vesicles (GUVs) is reviewed based on different technologies, including gentle hydration, electro-formation, phase transfer and microfluidic methods. Subsequently, applications of artificial cells based on single vesicles or vesicle networks are addressed for mimicking cell behaviors and signaling processes. Microreactors for synthetic biology and cell-cell communication are highlighted here as well. Finally, current challenges and future trends for the development and applications of artificial cells are described.

Deciphering Ethanol-Driven Swelling, Rupturing, Aggregation, and Fusion of Lipid Vesicles Using Coarse-Grained Molecular Dynamics Simulations

Traditionally, liquid ethanol is known to enhance the permeability of lipid membranes and causes vesicle aggregation and fusion. However, how the amphiphilic ethanol molecules perturb the lipid vesicles to facilitate their aggregation or fusion has not been addressed at any level of molecular simulations. Herein, not only have we developed a coarse-grained (CG) model for liquid ethanol, its aqueous mixture, and hydrated lipid membranes for molecular dynamics (MD) simulations, but also utilized it to delineate the aggregation and fusion of lipid vesicles using CG-MD simulations with multimillion particles. We have systematically parametrized the force-field for pure ethanol and its interactions with hydrated POPC and POPE model lipid membranes. In this process, we have successfully reproduced the bulk ethanol structure and concentration-dependent density of aqueous ethanol. To quantify the interaction of ethanol with lipid membranes, we have reproduced the transfer free energy of the ethanol molecule across the hydrated bilayers, and the concentration-dependent distribution of ethanol molecules across the lipid bilayers. After having acceptable force-field parameters for ethanol-membrane interactions, we have checked the effect of ethanol toward the vesicles comprising POPC lipids. We observe a rapid increase in the size of the POPC lipid vesicles with increasing amounts of ethanol up to 30 mol %. We unambiguously observe swelling and decrease in the thickness of the POPC vesicles with increasing amounts of ethanol up to 30 mol %, beyond which the vesicles begin to lose their integrity and rupture at higher mol % of ethanol. The fusion study of two vesicles demonstrates that fused vesicles can be obtained from 20 to 30 mol % of ethanol provided that they are brought closer than a critical distance at a particular mol %. The multivesicle simulations show that along with the increase in the sizes of vesicles the propensity of vesicle aggregation increases as the mol % of ethanol increases.

The Dietary Nutrient Trimethylamine N-Oxide Affects the Phospholipid Vesicle Membrane: Probable Route to Adverse Intake

Trimethylamine N-oxide (TMAO), a choline-containing dietary supplement obtained from red meat, egg, and other animal resources, on excess accumulation is known to cause cardiovascular diseases (CVDs) like atherosclerosis. To understand the molecular mechanism of the pathogenesis of TMAO-induced CVDs, we have set up 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane in water that mimicked the endothelial cell membrane-blood interface of the artery wall and investigated the effect of an elevated concentration of TMAO on the membrane. We found that TMAO exerts an "action at a distance" mechanism through electrostatic force of attraction that significantly alters various properties of the membrane, like hydrophobicity, lateral organization, and interfacial water dynamics, which elevates the rigidity of the membrane. Such an effect was found to be further amplified in the presence of known causes of CVDs, i.e., high content of cholesterol (Chol). Therefore, TMAO-induced membrane rigidity may restrict the intrinsic elasticity of an artery membrane, expected to be introducing "hardening of the arteries", which makes the membrane atherosclerotic.

Rheology of sliding leaflets in coarse-grained DSPC lipid bilayers

Amphiphilic lipid bilayers modify the friction properties of the surfaces on top of which they are deposited. In particular, the measured sliding friction coefficient can be significantly reduced compared with the native surface. We investigate in this work the friction properties of a numerical coarse-grained model of DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine) lipid bilayer subject to longitudinal shear. The interleaflet friction coefficient is obtained from out-of-equilibrium pulling or from relaxation simulations. In particular, we gain access to the transient viscoelastic response of a sheared bilayer. The bilayer mechanical response is found to depend significantly on the membrane physical state, with evidence in favor of a linear response regime in the fluid but not in the gel region. The linear response validity domain is established, and the timescales appearing in the membrane response discussed.

Interfacial behavior of phospholipid monolayers revealed by mesoscopic simulation

A mesoscopic model with molecular resolution is presented for dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl oleoyl phosphatidylcholine (POPC) monolayer simulations at the air-water interface using many-body dissipative particle dynamics (MDPD). The parameterization scheme is rigorously based on reproducing the physical properties of water and alkane and the interfacial property of the phospholipid monolayer by comparison with experimental results. Using much less computing cost, these MDPD simulations yield a similar surface pressure-area isotherm as well as similar pressure-related morphologies as all-atom simulations and experiments. Moreover, the compressibility modulus, order parameter of lipid tails, and thickness of the phospholipid monolayer are quantitatively in line with the all-atom simulations and experiments. This model also captures the sensitive changes in the pressure-area isotherms of mixed DPPC/POPC monolayers with altered mixing ratios, indicating that the model is promising for applications with complex natural phospholipid monolayers. These results demonstrate a significant improvement of quantitative phospholipid monolayer simulations over previous coarse-grained models.

Modeling lipid-protein interactions for coarse-grained lipid and Cα protein models

Biological membranes that play major roles in diverse functions are composed of numerous lipids and proteins, making them an important target for coarse-grained (CG) molecular dynamics (MD) simulations. Recently, we have developed the CG implicit solvent lipid force field (iSoLF) that has a resolution compatible with the widely used Cα protein representation [D. Ugarte La Torre and S. Takada, J. Chem. Phys. 153, 205101 (2020)]. In this study, we extended it and developed a lipid-protein interaction model that allows the combination of the iSoLF and the Cα protein force field, AICG2+. The hydrophobic-hydrophilic interaction is modeled as a modified Lennard-Jones potential in which parameters were tuned partly to reproduce the experimental transfer free energy and partly based on the free energy profile normal to the membrane surface from previous all-atom MD simulations. Then, the obtained lipid-protein interaction is tested for the configuration and placement of transmembrane proteins, water-soluble proteins, and peripheral proteins, showing good agreement with prior knowledge. The interaction is generally applicable and is implemented in the publicly available software, CafeMol.

Geometry transformation of ionic surfactants and adsorption behavior on water/n-decane-interface: calculation by molecular dynamics simulation and DFT study

Understanding the effect of surfactant structure on their ability to modify interfacial properties is of great scientific and industrial interest. In this work, we have synthesized four amide based ionic surfactants under acidic or basic conditions, including CTHA·HCl, CTEA·HCl, CTHA⁻Na⁺ and CTEA⁻Na⁺. Experiments have proved that the anionic surfactant with polyethylene oxide groups (CTEA⁻Na⁺) had the lowest surface tension on the water/n-decane interface. Molecular dynamics simulations have been applied to investigate the structural effect on the adsorption behavior of four different surfactants. The surface tension, interface thickness, interface formation energy, density profiles, order parameters, radial distribution function on the water/n-decane interfaces were calculated and compared. During the equilibrium states, we found that the interface configuration of two cationic surfactants are almost linear while the two anionic surfactants are changed to bending shapes due to the different positions of the hydrophilic head groups. Further DFT study and wavefunction analysis of surfactants have shown that CTEA⁻Na⁺ can form stronger vdW interactions with n-decane molecules due to a more neutral electrostatic potential distribution. Meanwhile, the introduction of polyethylene oxide groups has offered more H-bonding sites and resulted in more concentrated H-bonding interactions with water molecules. The difference of weak interactions may contribute to the conformational change and finally affect the interface properties of these ionic surfactants.

The difference of weak interactions may contribute to the conformational change and finally affect the interface properties of these ionic surfactants.

Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure

Lipid droplets (LDs) are intracellular organelles responsible for lipid storage, and they emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly triglycerides (TG), between the two leaflets of the ER membrane. LD biogenesis takes place at ER sites that are marked by the protein seipin, which subsequently recruits additional proteins to catalyze LD formation. Deletion of seipin, however, does not abolish LD biogenesis, and its precise role in controlling LD assembly remains unclear. Here, we use molecular dynamics simulations to investigate the molecular mechanism through which seipin promotes LD formation. We find that seipin clusters TG, as well as its precursor diacylglycerol, inside its unconventional ring-like oligomeric structure and that both its luminal and transmembrane regions contribute to this process. This mechanism is abolished upon mutations of polar residues involved in protein-TG interactions into hydrophobic residues. Our results suggest that seipin remodels the membrane of specific ER sites to prime them for LD biogenesis.

Development of coarse-grained force field for alcohols: an efficient meta-multilinear interpolation parameterization algorithm

Coarse-grained (CG) molecular dynamics are powerful tools to access a mesoscopic phenomenon and simultaneously record microscopic details, but currently the CG force fields (FFs) are still limited by low parameterization efficiency and poor accuracy especially for polar molecules. In this work, we developed a Meta-Multilinear Interpolation Parameterization (Meta-MIP) algorithm to optimize the CG FFs for alcohols. This algorithm significantly boosts parameterization efficiency by constructing on-the-fly local databases to cover the global optimal parameterization path. In specific, an alcohol molecule is mapped to a heterologous model composed of an OH bead and a hydrocarbon portion which consists of alkane beads representing two to four carbon atoms. Non-bonded potentials are described by soft Morse functions that have no tail-corrections but can still retain good continuities at truncation distance. Nearly all of the properties in terms of density, heat of vaporization, surface tension, and solvation free energy for alcohols predicted by the current FFs deviate from experimental values by less than 7%. This Meta-MIP algorithm can be readily applied to force field development for a wide variety of molecules or functional groups, in many situations including but not limited to CG FFs.

CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations

Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.

Modeling Gas-Liquid Interfaces by Dissipative Particle Dynamics: Adsorption and Surface Tension of Cetyl Trimethyl Ammonium Bromide at the Air-Water Interface

Adsorption of surfactants at gas-liquid interfaces that causes reduction in the surface tension is a classical problem in colloid and interface science with multiple practical applications in oil and gas recovery, separations, cosmetics, personal care, and biomedicine. Here, we develop an original coarse-grained model of the liquid-gas interface within the conventional dissipative particle dynamics (DPD) framework with the goal of quantitatively predicting the surface tension in the presence of surfactants. As a practical case-study example, we explore the adsorption of the cationic surfactant cetyl trimethyl ammonium bromide (CTAB) on the air-water interface. The gas phase is modeled as a DPD fluid composed of fictitious hard-core "gas" beads with exponentially decaying repulsive potentials to prevent penetration of the liquid phase components. A rigorous parametrization scheme is proposed based on matching the bulk and interfacial properties of water and octane taken as the reference compounds. Quantitative agreement between the simulated and experimental surface tension of CTAB solutions is found for a wide range of bulk surfactant concentrations (∼10^-3 to ∼1 mmol/L) with the reduction of the surface tension from ∼72 mN/m (pure water) to the limiting value of ∼37.5 mN/m at the critical micelle concentration. The gas phase DPD model with the proposed parametrization scheme can be extended and applied to modeling various gas-liquid interfaces with surfactant and lipid monolayers, such as bubble suspensions, foams, froths, etc.

Learning Coarse-Grained Potentials for Binary Fluids

For a multiple-fluid system, CG models capable of accurately predicting the interfacial properties as a function of curvature are still lacking. In this work, we propose a new probabilistic machine learning (ML) model for learning CG potentials for binary fluids. The water-hexane mixture is selected as a typical immiscible binary liquid-liquid system. We develop a new CG force field (FF) using the Shinoda-DeVane-Klein (SDK) FF framework and compute parameters in this CG FF using the proposed probabilistic ML method. It is shown that a standard response-surface approach does not provide a unique set of parameters, as it results in a loss function with multiple shallow minima. To address this challenge, we develop a probabilistic ML approach where we compute the probability density function (PDF) of parameters that minimize the loss function. The PDF has a well-defined peak corresponding to a unique set of parameters in the CG FF that reproduces the desired properties of a liquid-liquid interface. We compare the performance of the new CG FF with several existing FFs for the water-hexane mixture, including two atomistic and three CG FFs with respect to modeling the interface structure and thermodynamic properties. It is demonstrated that the new FF significantly improves the CG model prediction of both the interfacial tension and structure for the water-hexane mixture.

Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations

The asymmetric lipid composition in plasma membranes within the inner leaflet is not typically suitable for domain formation. Thus elucidation of the likelihood of the formation or stability of a raft-like domain in the inner leaflet is necessary. Herein we investigated the phase behavior of asymmetric membranes using coarse-grained molecular dynamics simulations. The lipid leaflet comprising dioleoylphosphatidylcholine (DOPC) and cholesterol (Chol) does not typically show well-developed domains in symmetric bilayer membranes; however, it does separate into liquid ordered (L_o) and liquid disordered (L_d) phases when the opposing leaflet containing sphingomyelin (SM), DOPC, and Chol demonstrates domain formation. We determine that interdigitated acyl chains modulated the partitioning of Chol in the opposing leaflet, resulting in phase separation. Similarly, the acyl chain length of SM within the opposing leaflet affected the phase behavior of the leaflet. Our results reveal the crucial role of interdigitation in determining the phase status in asymmetric membranes.

Cellular absorption of small molecules: free energy landscapes of melatonin binding at phospholipid membranes

Free energy calculations are essential to unveil mechanisms at the atomic scale such as binding of small solutes and their translocation across cell membranes, eventually producing cellular absorption. Melatonin regulates biological rhythms and is directly related to carcinogenesis and neurodegenerative disorders. Free energy landscapes obtained from well-tempered metadynamics simulations precisely describe the characteristics of melatonin binding to specific sites in the membrane and reveal the role of cholesterol in free energy barrier crossing. A specific molecular torsional angle and the distance between melatonin and the center of the membrane along the normal to the membrane Z-axis have been considered as suitable reaction coordinates. Free energy barriers between two particular orientations of the molecular structure (folded and extended) have been found to be of about 18 kJ/mol for z-distances of about 1–2 nm. The ability of cholesterol to expel melatonin out of the internal regions of the membrane towards the interface and the external solvent is explained from a free energy perspective. The calculations reported here offer detailed free energy landscapes of melatonin embedded in model cell membranes and reveal microscopic information on its transition between free energy minima, including the location of relevant transition states, and provide clues on the role of cholesterol in the cellular absorption of small molecules.

MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics

Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories.

Coexistence of Lipid Phases Stabilizes Interstitial Water in the Outer Layer of Mammalian Skin

The lipid matrix in the outer layer of mammalian skin, the stratum corneum, has been previously investigated by multiple biophysical techniques aimed at identifying hydrophilic and lipophilic pathways of permeation. Although consensus is developing over the microscopic structure of the lipid matrix, no molecular-resolution model describes the permeability of all chemical species simultaneously. Using molecular dynamics simulations of a model mixture of skin lipids, the self-assembly of the lipid matrix lamellae has been studied. At higher humidity, the resulting lamellar phase is maintained by partitioning excess water into isolated droplets of controlled size and spatial distribution. The droplets may fuse together to form intralamellar water channels, thereby providing a pathway for the permeation of hydrophilic species. These results reconcile competing data on the outer skin's structure and broaden the scope of molecular-based methods to improve the safety of topical products and to advance transdermal drug delivery.

Antagonist Effects of l-Phenylalanine and the Enantiomeric Mixture Containing d-Phenylalanine on Phospholipid Vesicle Membrane

One of the congenital flaws of metabolism, phenylketonuria (PKU), is known to be related to the self-assembly of toxic fibrillar aggregates of phenylalanine (Phe) in blood at elevated concentrations. Our experimental findings using l-phenylalanine (l-Phe) at millimolar concentration suggest the formation of fibrillar morphologies in the dry phase, which in the solution phase interact strongly with the model membrane composed of 1,2-diacyl-sn-glycero-phosphocholine (LAPC) lipid, thereby decreasing the rigidity (or increasing the fluidity) of the membrane. The hydrophobic interaction, in addition to the electrostatic attraction of Phe with the model membrane, is found to be responsible for such phenomena. On the contrary, various microscopic observations reveal that such fibrillar morphologies of l-Phe are severely ruptured in the presence of its enantiomer d-phenylalanine (d-Phe), thereby converting the fibrillar morphologies into crushed flakes. Various biophysical studies, including the solvation dynamics experiment, suggest that this l-Phe in the presence of d-Phe, when interacting with the same model membrane, now reverts the rigidity of the membrane, i.e., increases the rigidity of the membrane, which was lost due to interaction with l-Phe exclusively. Fluorescence anisotropy measurements also support this reverse rigid character of the membrane in the presence of an enantiomeric mixture of amino acids. A comprehensive understanding of the interaction of Phe with the model membrane is further pursued at the single-molecular fluorescence detection level using fluorescence correlation spectroscopy (FCS) experiments. Therefore, our experimental conclusion interprets a linear correlation between increased permeability and enhanced fluidity of the membrane in the presence of l-Phe and certifies d-Phe as a therapeutic modulator of l-Phe fibrillar morphologies. Further, the study proposes that the rigidity of the membrane lost due to interaction with l-Phe was reinstated-in fact, increased-in the presence of the enantiomeric mixture containing both d- and l-Phe.

Computer simulations of protein-membrane systems

The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.