Free energy change for insertion of charged, monolayer-protected nanoparticles into lipid bilayers

Self-assembly of amphiphilic homopolymers grafted onto spherical nanoparticles: complete embedded minimal surfaces and a machine learning algorithm for their recognition

By means of computer modelling, the self-assembly of amphiphilic A-graft-B macromolecules, grafted onto a spherical nanoparticle, is studied. In a solvent, that is poor for side pendants, the macromolecules self-assemble into thin membrane-like ABBA bilayers deviated from spherical nanoparticles. The bilayers form morphological structures that depend on the grafting density and macromolecular polymerization degree and can be referred to as the classical family of complete embedded minimal surfaces. The plane disk, catenoid, helicoid, Costa and Enneper surfaces as well as "double" helicoid and "complex minimal surface" were identified, and the fields of their stability were defined. The surfaces can be grouped according to the sequences of conformal transformations that transform them into each other. These surfaces arise in different experiments situationally. Results are summarized in a pie diagram constructed using a machine learning algorithm based on matching grafting points with a specially created planar graphic image.

Polydots, soft nanoparticles, at membrane interfaces

Soft nanoparticles (NPs) are emerging candidates for nano medicine, particularly for intercellular imaging and targeted drug delivery. Their soft nature, manifested in their dynamics, allows translocation into organisms without damaging their membranes. A crucial step towards incorporating soft dynamic NPs in nano medicine, is to resolve their interrelation with membranes. Here using atomistic molecular dynamics (MD) simulations we probe the interaction of soft NPs formed by conjugated polymers with a model membrane. These NPs, often termed polydots, are confined to their nano dimensions without any chemical tethers, forming dynamic long lived nano structures. Specifically, polydots formed by dialkyl para poly phenylene ethylene (PPE), with a varying number of carboxylate groups tethered to the alkyl chains to tune the interfacial charge of the surface of the NP are investigated at the interface with a model membrane that consists of di-palmitoyl phosphatidylcholine (DPPC). We find that even though polydots are controlled only by physical forces, they retain their NP configuration as they transcend the membrane. Regardless of their size, neutral polydots spontaneously penetrate the membrane whereas carboxylated polydots must be driven in, with a force that depends on the charge at their interface, all without significant disruption to the membrane. These fundamental results provide a means to control the position of the nanoparticles with respect to the membrane interfaces, which is key to their therapeutic use.

Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions

Functional peptides are now widely used in a myriad of biomedical and clinical contexts, from cancer therapy and tumor targeting to the treatment of bacterial and viral infections. Underlying this diverse range of applications are the non-specific interactions that can occur between peptides and cell membranes, which, in many contexts, result in spontaneous internalization of the peptide within cells by avoiding energy-driven endocytosis. For this to occur, the amphipathicity and surface structural flexibility of the peptides play a crucial role and can be regulated by the presence of specific molecular residues that give rise to precise molecular events. Nevertheless, most of the mechanistic details regulating the encounter between peptides and the membranes of bacterial or animal cells are still poorly understood, thus greatly limiting the biomimetic potential of these therapeutic molecules. In this arena, finely engineered nanomaterials-such as small amphiphilic gold nanoparticles (AuNPs) protected by a mixed thiol monolayer-can provide a powerful tool for mimicking and investigating the physicochemical processes underlying peptide-lipid interactions. Within this perspective, we present here a critical review of membrane effects induced by both amphiphilic AuNPs and well-known amphiphilic peptide families, such as cell-penetrating peptides and antimicrobial peptides. Our discussion is focused particularly on the effects provoked on widely studied model cell membranes, such as supported lipid bilayers and lipid vesicles. Remarkable similarities in the peptide or nanoparticle membrane behavior are critically analyzed. Overall, our work provides an overview of the use of amphiphilic AuNPs as a highly promising tailor-made model to decipher the molecular events behind non-specific peptide-lipid interactions and highlights the main affinities observed both theoretically and experimentally. The knowledge resulting from this biomimetic approach could pave the way for the design of synthetic peptides with tailored functionalities for next-generation biomedical applications, such as highly efficient intracellular delivery systems.

Cholesterol Hinders the Passive Uptake of Amphiphilic Nanoparticles into Fluid Lipid Membranes

Plasma membranes represent pharmacokinetic barriers for the passive transport of site-specific drugs within cells. When engineered nanoparticles (NPs) are considered as transmembrane drug carriers, the plasma membrane composition can affect passive NP internalization in many ways. Among these, cholesterol-regulated membrane fluidity is probably one of the most biologically relevant. Herein, we consider small (2-5 nm in core diameter) amphiphilic gold NPs capable of spontaneously and nondisruptively entering the lipid bilayer of plasma membranes. We study their incorporation into model 1,2-dioleoyl-sn-glycero-3-phosphocholine membranes with increasing cholesterol content. We combine dissipative quartz crystal microbalance experiments, atomic force microscopy, and molecular dynamics simulations to show that membrane cholesterol, at biologically relevant concentrations, hinders the molecular mechanism for passive NP penetration within fluid bilayers, resulting in a dramatic reduction in the amount of NP incorporated.

Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations

The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.

Amphiphilic gold nanoparticles perturb phase separation in multidomain lipid membranes

Amphiphilic gold nanoparticles with diameters in the 2-4 nm range are promising as theranostic agents thanks to their spontaneous translocation through cell membranes. This study addresses the effects that these nanoparticles may have on a distinct feature of plasma membranes: lipid lateral phase separation. Atomic force microscopy, quartz crystal microbalance, and molecular dynamics are combined to study the interaction between model neuronal membranes, which spontaneously form ordered and disordered lipid domains, and amphiphilic gold nanoparticles having negatively charged surface functionalization. Nanoparticles are found to interact with the bilayer and form bilayer-embedded ordered aggregates. Nanoparticles also suppress lipid phase separation, in a concentration-dependent fashion. A general, yet simple thermodynamic model is developed to show that the change of lipid-lipid enthalpy is the dominant driving force towards the nanoparticle-induced destabilization of phase separation.

Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils

Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.

HaloFlippers: A General Tool for the Fluorescence Imaging of Precisely Localized Membrane Tension Changes in Living Cells

Tools to image membrane tension in response to mechanical stimuli are badly needed in mechanobiology. We have recently introduced mechanosensitive flipper probes to report quantitatively global membrane tension changes in fluorescence lifetime imaging microscopy (FLIM) images of living cells. However, to address specific questions on physical forces in biology, the probes need to be localized precisely in the membrane of interest (MOI). Herein we present a general strategy to image the tension of the MOI by tagging our newly introduced HaloFlippers to self-labeling HaloTags fused to proteins in this membrane. The critical challenge in the construction of operational HaloFlippers is the tether linking the flipper and the HaloTag: It must be neither too taut nor too loose, be hydrophilic but lipophilic enough to passively diffuse across membranes to reach the HaloTags, and allow partitioning of flippers into the MOI after the reaction. HaloFlippers with the best tether show localized and selective fluorescence after reacting with HaloTags that are close enough to the MOI but remain nonemissive if the MOI cannot be reached. Their fluorescence lifetime in FLIM images varies depending on the nature of the MOI and responds to myriocin-mediated sphingomyelin depletion as well as to osmotic stress. The response to changes in such precisely localized membrane tension follows the validated principles, thus confirming intact mechanosensitivity. Examples covered include HaloTags in the Golgi apparatus, peroxisomes, endolysosomes, and the ER, all thus becoming accessible to the selective fluorescence imaging of membrane tension.

The aggregation of striped nanoparticles in mixed phospholipid bilayers

The unique and adjustable properties of nanoparticles present enormous opportunities for their use as targeted drug delivery vectors. For example, nanoparticles functionalized with key surface ligands have been shown to pass through phospholipid bilayers without causing localised disruption. However, the further effects nanoparticles have on multi-component phospholipid bilayers remain unclear. We use coarse-grained computational models to investigate the structural properties of mixed phospholipid bilayers in the presence of ligand-functionalized nanoparticles. Model bilayers are composed of DPPC, DUPC, DFPC and cholesterol, and the nanoparticles are striped with a hydrophobic-ligand band and charged-ligand spherical caps. Our results show that nanoparticles aggregate near unsaturated phospholipid regions, phospholipid bilayer phase-separation is promoted in the presence of nanoparticles, and the heterogeneous components of a phospholipid bilayer play a significant role in the lateral organization of nanoparticles. This study highlights the need for considering the complexity of realistic phospholipid bilayers when optimising ligand functionalized nanoparticles for efficient drug delivery vectors.

Interfacing the Cell with "Biomimetic Membrane Proteins"

Integral membrane proteins mediate a myriad of cellular processes and are the target of many therapeutic drugs. Enhancement and extension of the functional scope of membrane proteins can be realized by membrane incorporation of engineered nanoparticles designed for specific diagnostic and therapeutic applications. In contrast to hydrophobic insertion of small amphiphilic molecules, delivery and membrane incorporation of particles on the nanometric scale poses a crucial barrier for technological development. In this perspective, the transformative potential of biomimetic membrane proteins (BMPs), current state of the art, and the barriers that need to be overcome in order to advance the field are discussed.

Nanoparticles and organized lipid assemblies: from interaction to design of hybrid soft devices

This contribution reviews the state of art on hybrid soft matter assemblies composed of inorganic nanoparticles (NP) and lamellar or non-lamellar lipid bilayers. After a short outline of the relevant energetic contributions, we address the interaction of NPs with synthetic lamellar bilayers, meant as cell membrane mimics. We then review the design of hybrid nanostructured materials composed of lipid bilayers and some classes of inorganic NPs, with particular emphasis on the effects on the amphiphilic phase diagram and on the additional properties contributed by the NPs. Then, we present the latest developments on the use of lipid bilayers as coating agents for inorganic NPs. Finally, we remark on the main achievements of the last years and our vision for the development of the field.

The Role of Temperature and Lipid Charge on Intake/Uptake of Cationic Gold Nanoparticles into Lipid Bilayers

Understanding the molecular mechanisms governing nanoparticle-membrane interactions is of prime importance for drug delivery and biomedical applications. Neutron reflectometry (NR) experiments are combined with atomistic and coarse-grained molecular dynamics (MD) simulations to study the interaction between cationic gold nanoparticles (AuNPs) and model lipid membranes composed of a mixture of zwitterionic di-stearoyl-phosphatidylcholine (DSPC) and anionic di-stearoyl-phosphatidylglycerol (DSPG). MD simulations show that the interaction between AuNPs and a pure DSPC lipid bilayer is modulated by a free energy barrier. This can be overcome by increasing temperature, which promotes an irreversible AuNP incorporation into the lipid bilayer. NR experiments confirm the encapsulation of the AuNPs within the lipid bilayer at temperatures around 55 °C. In contrast, the AuNP adsorption is weak and impaired by heating for a DSPC-DSPG (3:1) lipid bilayer. These results demonstrate that both the lipid charge and the temperature play pivotal roles in AuNP-membrane interactions. Furthermore, NR experiments indicate that the (negative) DSPG lipids are associated with lipid extraction upon AuNP adsorption, which is confirmed by coarse-grained MD simulations as a lipid-crawling effect driving further AuNP aggregation. Overall, the obtained detailed molecular view of the interaction mechanisms sheds light on AuNP incorporation and membrane destabilization.

pH-Dependent aggregation and pH-independent cell membrane adhesion of monolayer-protected mixed charged gold nanoparticles

Design of pH-responsive monolayer-protected gold nanoparticles (AuNPs) that are mixed charged, with the ability to switch their net surface charge, based on the stimuli of environmental pH is a promising technique in nanomedicine. However, understanding of pH-responsive mixed charged AuNP behavior in terms of their stability and cellular interaction are still limited. In this work, we study the aggregation of pH-responsive AuNPs and their interaction with model lipid bilayers by adopting Martini coarse-grained (CG) molecular dynamics simulations. The surface of these AuNPs is decorated by both positively and negatively charged ligands. The AuNP is positively charged at low pH values due to protonation of negatively charged ligands. Its net charge is lowered at higher pH by increasing the ratio of deprotonated negatively charged ligands. We find that the AuNPs are severely aggregated at moderate pH value, where each AuNP has an overall neutral charge, whereas they are stable and dispersed at both low and high pH values. Further free energy analysis reveals that the energy barrier at a larger separation distance than the location of the hydrophobic driving force potential well, plays a key role that determines the stability of monolayer-protected AuNPs at different pH values. This energy barrier is dramatically decreased at moderate pH value, leading to severe aggregation of AuNPs. By investigating the interaction between AuNPs and model lipid bilayers, we find that all the AuNPs adhere onto the lipid bilayer, independent of the pH value. Moreover, the lipids present originally in the bilayer are extracted by the AuNPs through a process of protrusion and upward climbing. The extraction of lipids can cause dehydration and disruption of the bilayers when multiple AuNPs are adhered. Free energy analysis reveals that the penetration of AuNPs will induce a dramatic free energy increase because of deformation of the ligands with hydrophilic functional end groups. We have systematically studied the stability of pH-responsive AuNPs and their interactions with lipid bilayers by simulation, which might pave the way for the design of pH-responsive monolayer protected AuNPs for biomedical applications.

Lipid bilayer disruption induced by amphiphilic Janus nanoparticles: the non-monotonic effect of charged lipids

In this study, we report the complex effects of charged lipids on the interaction between amphiphilic Janus nanoparticles and lipid bilayers. Janus nanoparticles are cationic on one hemisphere and hydrophobic on the other. We show that the nanoparticles, beyond threshold concentrations, induce holes in both cationic and anionic lipid bilayers mainly driven by hydrophobic interactions. However, the formation of these defects is non-monotonically dependent on ionic lipid composition. The electrostatic attraction between the particles and anionic lipid bilayers enhances particle adsorption and lowers the particle concentration threshold for defect initiation, but leads to more localized membrane disruption. Electrostatic repulsion leads to reduced particle adsorption on cationic bilayers and extensive defect formation that peaks at intermediate contents of cationic lipids. This study elucidates the significant role lipid composition plays in influencing how amphiphilic Janus nanoparticles interact with and perturb lipid membranes.

Molecular Modeling of Surfactant Micellization Using Solvent-Accessible Surface Area

We report a new implicit solvent simulation model for studying the self-assembly of surfactants, where the hydrophobic interactions were captured by calculating the relative changes of the solvent-accessible surface area (SASA) of the hydrophobic domains. Using histogram-reweighting grand canonical Monte Carlo simulations, we demonstrate that this approach allows us to match both the experimental critical micelle concentrations (cmc) and micellar aggregation numbers simultaneously with a single phenomenological surface tension γ_SASA for the poly(oxyethylene) monoalkyl ether (C _mE _n) surfactants in aqueous solutions. Excellent transferability is observed: the same model can accurately predict the experimental cmc and aggregation numbers for the C _mE _n surfactants with the alkyl lengths m between 6 and 12 and the poly(oxyethylene) lengths n between 1 and 9. The SASA-based implicit solvent model put forward in this work is general and may be applied to study more complex amphiphilic systems such as surfactants with branched alkyl chains or surfactant-hydrocarbon mixtures.

Energy landscape for the insertion of amphiphilic nanoparticles into lipid membranes: A computational study

Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown to enter cells via a non-endocytic, non-disruptive pathway that could be valuable for biomedical applications. The same NPs were also found to insert into a series of model cell membranes as a precursor to cellular uptake, but the insertion mechanism remains unclear. Previous simulations have demonstrated that an amphiphilic NP can insert into a single leaflet of a planar lipid bilayer, but in this configuration all charged end groups are localized to one side of the bilayer and it is unknown if further insertion is thermodynamically favorable. Here, we use atomistic molecular dynamics simulations to show that an amphiphilic NP can reach the bilayer midplane non-disruptively if charged ligands iteratively "flip" across the bilayer. Ligand flipping is a favorable process that relaxes bilayer curvature, decreases the nonpolar solvent-accessible surface area of the NP monolayer, and increases attractive ligand-lipid electrostatic interactions. Analysis of end group hydration further indicates that iterative ligand flipping can occur on experimentally relevant timescales. Supported by these results, we present a complete energy landscape for the non-disruptive insertion of amphiphilic NPs into lipid bilayers. These findings will help guide the design of NPs to enhance bilayer insertion and non-endocytic cellular uptake, and also provide physical insight into a possible pathway for the translocation of charged biomacromolecules.

Nanoparticles Self-Assembly within Lipid Bilayers

Coarse-grained molecular dynamics simulations are used to model the self-assembly of small hydrophobic nanoparticles (NPs) within the interior of lipid bilayers. The simulation results reveal the conditions under which NPs form clusters and lattices within lipid bilayers of planar and spherical shapes, depending on the NP-lipid coupling strengths. The formation of nanopores within spherical bilayers with self-assembled planar NPs is also described. These observations can provide guidance in the preparation of functional bio-inorganic systems.

Hydrogel-Based Drug Delivery Nanosystems for the Treatment of Brain Tumors

Chemotherapy is commonly associated with limited effectiveness and unwanted side effects in normal cells and tissues, due to the lack of specificity of therapeutic agents to cancer cells when systemically administered. In brain tumors, the existence of both physiological barriers that protect tumor cells and complex resistance mechanisms to anticancer drugs are additional obstacles that hamper a successful course of chemotherapy, thus resulting in high treatment failure rates. Several potential surrogate therapies have been developed so far. In this context, hydrogel-based systems incorporating nanostructured drug delivery systems (DDS) and hydrogel nanoparticles, also denoted nanogels, have arisen as a more effective and safer strategy than conventional chemotherapeutic regimens. The former, as a local delivery approach, have the ability to confine the release of anticancer drugs near tumor cells over a long period of time, without compromising healthy cells and tissues. Yet, the latter may be systemically administered and provide both loading and targeting properties in their own framework, thus identifying and efficiently killing tumor cells. Overall, this review focuses on the application of hydrogel matrices containing nanostructured DDS and hydrogel nanoparticles as potential and promising strategies for the treatment and diagnosis of glioblastoma and other types of brain cancer. Some aspects pertaining to computational studies are finally addressed.

Rupture of Lipid Membranes Induced by Amphiphilic Janus Nanoparticles

The surface coatings of nanoparticles determine their interaction with biomembranes, but studies have been limited almost exclusively to nanoparticles with a uniform surface chemistry. Although nanoparticles are increasingly made with complex surface chemistries to achieve multifunctionalities, our understanding of how a heterogeneous surface coating affects particle-biomembrane interaction has been lagging far behind. Here we report an investigation of this question in an experimental system consisting of amphiphilic "two-faced" Janus nanoparticles and supported lipid membranes. We show that amphiphilic Janus nanoparticles at picomolar concentrations induce defects in zwitterionic lipid bilayers. In addition to revealing the various effects of hydrophobicity and charge in particle-bilayer interactions, we demonstrate that the Janus geometry-the spatial segregation of hydrophobicity and charges on particle surface-causes nanoparticles to bind more strongly to bilayers and induce defects more effectively than particles with uniformly mixed surface functionalities. We combine experiments with computational simulation to further elucidate how amphiphilic Janus nanoparticles extract lipids to rupture intact lipid bilayers. This study provides direct evidence that the spatial arrangement of surface functionalities on a nanoparticle, rather than just its overall surface chemistry, plays a crucial role in determining how it interacts with biological membranes.

Modulating interactions between ligand-coated nanoparticles and phase-separated lipid bilayers by varying the ligand density and the surface charge

The interactions between nanoparticles and lipid bilayers are critical in applications of nanoparticles in nanomedicine, cell imaging, toxicology, and elsewhere. Here, we investigate the interactions between nanoparticles coated with neutral and/or charged ligands and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. Both penetration and adsorption processes as well as the final distribution of the nanoparticles can be readily modulated by varying the ligand density and the surface charge of the nanoparticles. Completely hydrophobic (neutral) nanoparticles with larger size initially preferentially penetrate into the liquid-disordered region of the lipid bilayer and finally transfer into the liquid-ordered region; partially hydrophilic nanoparticles with low or moderate surface charge tend to either distribute in the liquid-disordered region or be adsorbed on the surface of the lipid bilayer, while strongly hydrophilic nanoparticles with high surface charge always reside on the surface of the lipid bilayer. Interactions of the nanoparticles with the lipid bilayers are affected by the surface charge of nanoparticles, hydrophobic mismatch, bending of the ligands, and the packing state of the lipids. Insight in these factors can be used to improve the efficiency of designing nanoparticles for specific applications.

Gold nanoparticles with patterned surface monolayers for nanomedicine: current perspectives

Molecular self-assembly is a topic attracting intense scientific interest. Various strategies have been developed for construction of molecular aggregates with rationally designed properties, geometries, and dimensions that promise to provide solutions to both theoretical and practical problems in areas such as drug delivery, medical diagnostics, and biosensors, to name but a few. In this respect, gold nanoparticles covered with self-assembled monolayers presenting nanoscale surface patterns-typically patched, striped or Janus-like domains-represent an emerging field. These systems are particularly intriguing for use in bio-nanotechnology applications, as presence of such monolayers with three-dimensional (3D) morphology provides nanoparticles with surface-dependent properties that, in turn, affect their biological behavior. Comprehensive understanding of the physicochemical interactions occurring at the interface between these versatile nanomaterials and biological systems is therefore crucial to fully exploit their potential. This review aims to explore the current state of development of such patterned, self-assembled monolayer-protected gold nanoparticles, through step-by-step analysis of their conceptual design, synthetic procedures, predicted and determined surface characteristics, interactions with and performance in biological environments, and experimental and computational methods currently employed for their investigation.

Trigger-Responsive Gene Transporters for Anticancer Therapy

In the current era of gene delivery, trigger-responsive nanoparticles for the delivery of exogenous nucleic acids, such as plasmid DNA (pDNA), mRNA, siRNAs, and miRNAs, to cancer cells have attracted considerable interest. The cationic gene transporters commonly used are typically in the form of polyplexes, lipoplexes or mixtures of both, and their gene transfer efficiency in cancer cells depends on several factors, such as cell binding, intracellular trafficking, buffering capacity for endosomal escape, DNA unpacking, nuclear transportation, cell viability, and DNA protection against nucleases. Some of these factors influence other factors adversely, and therefore, it is of critical importance that these factors are balanced. Recently, with the advancements in contemporary tools and techniques, trigger-responsive nanoparticles with the potential to overcome their intrinsic drawbacks have been developed. This review summarizes the mechanisms and limitations of cationic gene transporters. In addition, it covers various triggers, such as light, enzymes, magnetic fields, and ultrasound (US), used to enhance the gene transfer efficiency of trigger-responsive gene transporters in cancer cells. Furthermore, the challenges associated with and future directions in developing trigger-responsive gene transporters for anticancer therapy are discussed briefly.

Grafting Charged Species to Membrane-Embedded Scaffolds Dramatically Increases the Rate of Bilayer Flipping

The cell membrane is a barrier to the passive diffusion of charged molecules due to the chemical properties of the lipid bilayer. Surprisingly, recent experiments have identified processes in which synthetic and biological charged species directly transfer across lipid bilayers on biologically relevant time scales. In particular, amphiphilic nanoparticles have been shown to insert into lipid bilayers, requiring the transport of charged species across the bilayer. The molecular factors facilitating this rapid insertion process remain unknown. In this work, we use atomistic molecular dynamics simulations to calculate the free energy barrier associated with "flipping" charged species across a lipid bilayer for species that are grafted to a membrane-embedded scaffold, such as a membrane-embedded nanoparticle. We find that the free energy barrier for flipping a grafted ligand can be over 7 kcal/mol lower than the barrier for translocating an isolated, equivalent ion, yielding a 5 order of magnitude decrease in the corresponding flipping time scale. Similar results are found for flipping charged species grafted to either nanoparticle or protein scaffolds. These results reveal new mechanistic insight into the flipping of charged macromolecular components that might play an important, yet overlooked, role in signaling and charge transport in biological settings. Furthermore, our results suggest guidelines for the design of synthetic materials capable of rapidly flipping charged moieties across the cell membrane.

What is the role of curvature on the properties of nanomaterials for biomedical applications?

The use of nanomaterials for drug delivery and theranostics applications is a promising paradigm in nanomedicine, as it brings together the best features of nanotechnolgy, molecular biology, and medicine. To fully exploit the synergistic potential of such interdisciplinary strategy, a comprehensive description of the interactions at the interface between nanomaterials and biological systems is not only crucial, but also mandatory. Routine strategies to engineer nanomaterial-based drugs comprise modifying their surface with biocompatible and targeting ligands, in many cases resorting to modular approaches that assume additive behavior. However, emergent behavior can be observed when combining confinement and curvature. The final properties of functionalized nanomaterials become dependent not only on the properties of their constituents but also on the geometry of the nano-bio interface, and on the local molecular environment. Modularity no longer holds, and the coupling between interactions, chemical equilibrium, and molecular organization has to be directly addressed in order to design smart nanomaterials with controlled spatial functionalization envisioning optimized biomedical applications. Nanoparticle's curvature becomes an integral part of the design strategy, enabling to control and engineer the chemical and surface properties with molecular precision. Understanding how nanoparticle size, morphology, and surface chemistry are interrelated will put us one step closer to engineering nanobiomaterials capable of mimicking biological structures and their behaviors, paving the way into applications and the possibility to elucidate the use of curvature by biological systems. WIREs Nanomed Nanobiotechnol 2016, 8:334-354. doi: 10.1002/wnan.1365 For further resources related to this article, please visit the WIREs website.

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.

Gold nanoparticles in model biological membranes: A computational perspective

The electronic, optical, catalytic, and magnetic properties of metal nanoparticles (NPs) make them extremely interesting for biomedical applications. In this rapidly moving field, monolayer-protected gold nanoparticles emerge both as a reference system and as promising candidates for drug and gene delivery, photothermal treatment, and imaging applications. Despite the technological relevance, there is still poor understanding of the molecular processes driving the interactions of metal nanoparticles with cells, and with cell membranes in particular. In this paper we review molecular-level computational studies of the interaction between monolayer-protected gold NPs and model lipid membranes. Our review comprises a brief description of the most relevant experimental results in this field and of the questions they raised, followed by a description of the computational achievements reported so far. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Decorating Nanoparticle Surface for Targeted Drug Delivery: Opportunities and Challenges

The size, shape, stiffness (composition) and surface properties of nanoparticles (NPs) have been recognized as key design parameters for NP-mediated drug delivery platforms. Among them, the surface functionalization of NPs is of great significance for targeted drug delivery. For instance, targeting moieties are covalently coated on the surface of NPs to improve their selectively and affinity to cancer cells. However, due to a broad range of possible choices of surface decorating molecules, it is difficult to choose the proper one for targeted functions. In this work, we will review several representative experimental and computational studies in selecting the proper surface functional groups. Experimental studies reveal that: (1) the NPs with surface decorated amphiphilic polymers can enter the cell interior through penetrating pathway; (2) the NPs with tunable stiffness and identical surface chemistry can be selectively accepted by the diseased cells according to their stiffness; and (3) the NPs grafted with pH-responsive polymers can be accepted or rejected by the cells due to the local pH environment. In addition, we show that computer simulations could be useful to understand the detailed physical mechanisms behind these phenomena and guide the design of next-generation NP-based drug carriers with high selectivity, affinity, and low toxicity. For example, the detailed free energy analysis and molecular dynamics simulation reveals that amphiphilic polymer-decorated NPs can penetrate into the cell membrane through the "snorkeling" mechanism, by maximizing the interaction energy between the hydrophobic ligands and lipid tails. We anticipate that this work will inspire future studies in the design of environment-responsive NPs for targeted drug delivery.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems

Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Biological Responses to Engineered Nanomaterials: Needs for the Next Decade

The interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.

Pathway for insertion of amphiphilic nanoparticles into defect-free lipid bilayers from atomistic molecular dynamics simulations

Gold nanoparticles (NPs) have been increasingly used in biological applications that involve potential contact with cellular membranes. As a result, it is essential to gain a physical understanding of NP-membrane interactions to guide the design of next-generation bioactive nanoparticles. In previous work, we showed that charged, amphiphilic NPs can fuse with lipid bilayers after contact between protruding solvent-exposed lipid tails and the NP monolayer. Fusion was only observed at the high-curvature edges of large bilayer defects, but not in low-curvature regions where protrusions are rarely observed. Here, we use atomistic molecular dynamics simulations to show that the same NPs can also fuse with low-curvature bilayers in the absence of defects if NP-protrusion contact occurs, generalizing the results of our previous work. Insertion proceeds without applying biasing forces to the NP, driven by the hydrophobic effect, and involves the transient generation of bilayer curvature. We further find that NPs with long hydrophobic ligands can insert a single ligand into the bilayer core in a manner similar to the binding of peripheral proteins. Such anchoring may precede insertion, revealing potential methods for engineering NP monolayers to enhance NP-bilayer fusion in systems with a low likelihood of lipid tail protrusions. These results reveal new pathways for NP-bilayer fusion and provide fundamental insight into behavior at the nano-bio interface.

Nanoparticle hardness controls the internalization pathway for drug delivery

Nanoparticle (NP)-based drug delivery systems offer fundamental advantages over current therapeutic agents that commonly display a longer circulation time, lower toxicity, specific targeted release, and greater bioavailability. For successful NP-based drug delivery it is essential that the drug-carrying nanocarriers can be internalized by the target cells and transported to specific sites, and the inefficient internalization of nanocarriers is often one of the major sources for drug resistance. In this work, we use the dissipative particle dynamics simulation to investigate the effect of NP hardness on their internalization efficiency. Three simplified models of NP platforms for drug delivery, including polymeric NP, liposome and solid NP, are designed here to represent increasing nanocarrier hardness. Simulation results indicate that NP hardness controls the internalization pathway for drug delivery. Rigid NPs can enter the cell by a pathway of endocytosis, whereas for soft NPs the endocytosis process can be inhibited or frustrated due to wrapping-induced shape deformation and non-uniform ligand distribution. Instead, soft NPs tend to find one of three penetration pathways to enter the cell membrane via rearranging their hydrophobic and hydrophilic segments. Finally, we show that the interaction between nanocarriers and drug molecules is also essential for effective drug delivery.

Amphiphilic interactions of ionic liquids with lipid biomembranes: a molecular simulation study

Current bottlenecks in the large-scale commercial use of many ionic liquids (ILs) include their high costs, low biodegradability, and often unknown toxicities. As a proactive effort to better understand the molecular mechanisms of ionic liquid toxicities, the work herein presents a comprehensive molecular simulation study on the interactions of 1-n-alkyl-3-methylimidazolium-based ILs with a phosphatidylcholine (PC) lipid bilayer. We explore the effects of increasing alkyl chain length (n = 4, 8, and 12) in the cation and anion hydrophobicity on the interactions with the lipid bilayer. Bulk atomistic molecular dynamics (MD) simulations performed at millimolar (mM) IL concentrations show spontaneous insertion of cations into the lipid bilayer regardless of the alkyl chain length and a favorable orientational preference once a cation is inserted. Cations also exhibit the ability to "flip" inside the lipid bilayer (as is common for amphiphiles) if partially inserted with an unfavorable orientation. Moreover, structural analysis of the lipid bilayer show that cationic insertion induces roughening of the bilayer surface, which may be a precursor to bilayer disruption. To overcome the limitation in the timescale of our simulations, free energies for a single IL cation and anion insertion have been determined based on potential of mean force calculations. These results show a decrease in free energy in response to both short and long alkyl chain IL cation insertion, and likewise for a single hydrophobic anion insertion, but an increase in free energy for the insertion of a hydrophilic chloride anion. Both bulk MD simulations and free energy calculations suggest that toxicity mechanisms toward biological systems are likely caused by ILs behaving as ionic surfactants. [Yoo et al., Soft Matter, 2014].

How hydrophobic nanoparticles aggregate in the interior of membranes: A computer simulation

Lipid-based dispersion of hydrophobic nanoparticles (NPs) not only gives fundamental insight into how nanomaterials distribute in live cells and organisms, but also provides a quite general route to designing nanocarrier agents in triggered drug delivery and medical imaging. It is not clearly understood how hydrophobic NPs arrange in the interior of a membrane. In this paper, with computer simulation techniques, we demonstrate that hydrophobic NPs having a diameter compared to the hydrophobic thickness of the membrane are capable of clustering in the hydrophobic interior of a cell membrane. Except from the isotropic aggregation, an unexpected linear arrangement of spherical NPs, which is still not found from experiments, is identified here. The free-energy costs associated with linear and isotropic aggregations are computed explicitly to interpret aggregation behavior and the obtained phase diagrams give us a comprehensive understanding of where linear aggregation is expected. In this work we also shows that NP size and membrane tension play key roles in determining the NP aggregate, while the effects of NP concentration and membrane curvature seem to be relatively weak.

A spontaneous penetration mechanism of patterned nanoparticles across a biomembrane

Recent experimental studies have shown the ability of tailoring the nanoparticle (NP)-cell interaction via the engineering of NP surfaces. Although the considerable progress has been made in design of patterned NPs for drug delivery, the effect of surface pattern on the NP-cell interaction is not fully understood yet. In this work, we used a dissipative particle dynamics method to systematically investigate the effects of NP surface pattern on its penetration across a membrane. For stripy NPs or patchy NPs having a large stripe width or patch size, an "insertion-rotation" penetration mechanism is found. Results indicate that stripy NPs and patchy NPs coated with narrow stripes or small patches can directly penetrate the cell membrane with a less constrained rotation. By considering the spontaneous penetration of many NPs into a vesicle, we found that NP aggregation would lead to the shape change of the vesicle, and therefore cause the leakage of encapsulated solvent or membrane rupture, implying the possible cytotoxicity. In short, this work gives a fundamental understanding for the penetration mechanism of the ligand patterned NPs, which provides useful reference for the design of NPs for controllable cell penetrability and targeted delivery of drugs.

Surface presentation of functional peptides in solution determines cell internalization efficiency of TAT conjugated nanoparticles

Functionalizing nanoparticles with cell-penetrating peptides is a popular choice for cellular delivery. We investigated the effects of TAT peptide concentration and arrangement in solution on functionalized nanoparticles' efficacy for membrane permeation. We found that cell internalization correlates with the positive charge distribution achieved prior to nanoparticle encountering interactions with membrane. We identified a combination of solution based properties required to maximize the internalization efficacy of TAT-functionalized nanoparticles.