Atomistic simulations of anionic Au144(SR)60 nanoparticles interacting with asymmetric model lipid membranes

Absorption of Polypropylene in Dipalmitoylphosphatidylcholine Membranes: The Role of Molecular Weight and Initial Configuration of Polymer Chains

We study by molecular dynamics simulations the absorption of polypropylene (PP) chains within a dipalmitoylphosphatidylcholine (DPPC) lipid membrane in aqueous solvent. DPPC represents the most abundant phospholipid in biological membranes, while PP is one of the most common synthetic polymers diffused in the anthropic environment. By following in detail the absorption process, and the corresponding structural modification undergone by the membrane, we show how the initial configuration and the PP molecular weight determine the overall behavior of the system. Specifically, if PP chains initially lie on the DPPC surface, they are fully absorbed; likewise, polymers initially included within the membrane cannot escape from. On the other hand, if polymers are placed sufficiently apart from the membrane, they have time to join together and coalesce into a few nanoparticles. At contact, such nanoparticles may completely dissolve (for low molecular weight) and then be absorbed. For high molecular weight, not all of them dissolve, and therefore the system attains a condition in which some of the chains are absorbed, while others form a residual nanoparticle staying outside (but in contact with) the membrane. Such a state─albeit energetically unfavorable with respect to a condition in which all PP chains are absorbed─remains stable, at the least over a substantial simulation time, extending in our study up to 1.6 μs. The tendency for polymers to spontaneously form aggregates, which then prefer to stay in contact with the membrane, is further corroborated by calculation of the DPPC-nanoparticle potential of mean force.

Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity

The study of molecular recognition patterns is crucial for understanding the interactions between inorganic (nano)particles and biomolecules. In this review we focus on hydroxyls (OH) exposed at the surface of oxide particles (OxPs) which can play a key role in molecular initiating events leading to OxPs toxicity. We discuss here the main analytical methods available to characterize surface OH from a quantitative and qualitative point of view, covering thermogravimetry, titration, ζ potential measurements, and spectroscopic approaches (NMR, XPS). The importance of modelling techniques (MD, DFT) for an atomistic description of the interactions between membranes/proteins and OxPs surfaces is also discussed. From this background, we distilled a new approach methodology (NAM) based on the combination of IR spectroscopy and bioanalytical assays to investigate the molecular interactions of OxPs with biomolecules and membranes. This NAM has been already successfully applied to SiO₂ particles to identify the OH patterns responsible for the OxPs' toxicity and can be conceivably extended to other surface-hydroxylated oxides.

Effect of substrate charge density on the adsorption of intrinsically disordered protein amyloid β40: a molecular dynamics study

The inhibitory effect of negatively charged gold nanoparticles (AuNPs) on amyloidogenic protein fibrillation has been established from experiments and computer simulations. Here, we investigate the effect of the charge density (σ) of gold (Au) surfaces on the adsorption of the intrinsically disordered amyloid β40 (Aβ40) monomer using molecular dynamics (MD) simulations. On the basis of the binding free energy, some key residues (ARG5, LYS16, LYS28, LEU17-ALA21, ILE31-VAL38) were found to be responsible for preventing the β-sheet formation, which is known to be a precursor for fibrillation. Until a critical charge density (σ_c) of -0.167 e nm^-2, the key residues remained adsorbed on the Au slab. A saturation in the number of condensed counterions (Na⁺) on Aβ40 was also observed at σ_c. Beyond σ_c, the condensation of Na⁺ occurs only on the Au slab, leading to competition between positively charged key residues and condensed ions. This competition was found to be responsible for the lack of adsorption of the key residues, leading to β-sheet formation for σ > -0.167 e nm^-2. This study suggests that if the key residues are not adsorbed, then β-sheet formation is observed, which can then lead to the development of proto-fibrils and subsequently fibrillation. Therefore the surface should have an optimal charge density to be an effective inhibitor of fibrillation.

Monovalent ion-mediated charge-charge interactions drive aggregation of surface-functionalized gold nanoparticles

Monolayer-protected metal nanoparticles (NPs) are not only promising materials with a wide range of potential industrial and biological applications, but they are also a powerful tool to investigate the behaviour of matter at nanoscopic scales, including the stability of dispersions and colloidal systems. This stability is dependent on a delicate balance between attractive and repulsive interactions that occur in the solution, and it is described in quantitative terms by the classic Derjaguin-Landau-Vewey-Overbeek (DLVO) theory, that posits that aggregation between NPs is driven by van der Waals interactions and opposed by electrostatic interactions. To investigate the limits of this theory at the nanoscale, where the continuum assumptions required by the DLVO theory break down, here we investigate NP dimerization by computing the Potential of Mean Force (PMF) of this process using fully atomistic MD simulations. Serendipitously, we find that electrostatic interactions can lead to the formation of metastable NP dimers at physiological ion concentrations. These dimers are stabilized by complexes formed by negatively charged ligands belonging to distinct NPs that are bridged by positively charged monovalent ions present in solution. We validate our findings by collecting tomographic EM images of NPs in solution and by quantifying their radial distribution function, that shows a marked peak at interparticle distance comparable with that of MD simulations. Taken together, our results suggest that not only van der Waals interactions, but also electrostatic interactions mediated by monovalent ions at physiological concentrations, contribute to attraction between nano-sized charged objects at very short length scales.

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.

Atomistic Molecular Dynamics Simulation Study on the Interaction between Atomically Precise Thiolate-Protected Gold Nanoclusters and Phospholipid Membranes

The interaction of atomically precise monolayer thiolate (SR) protected gold nanoclusters (Au NCs) with the phospholipid membranes has been studied by the all-atom molecular dynamics (AAMD) simulations. The effect of cluster size, type, and the surface charge density of protection ligand was studied. The simulation results show gold nanoclusters with different size and surface modifications have much different transmembrane behaviors. The Au₂₅(SR)₁₈ cluster was found to possess the best affinity to the phospholipid membranes among six atomically accurate clusters Au₂₅(SR)₁₈, Au₃₆(SR)₂₄, Au₄₄(SR)₂₈, Au₆₈(SR)₃₂, Au₁₄₄(SR)₆₀, and Au₃₁₄(SR)₉₆. Using the Au₂₅ NC as a model, this work also found that the aggregation mode of the surface ligands and the surface charge density are the important factors affecting the interaction between the gold nanoclusters and the phospholipid membranes. Moreover, the balance of hydrophilic and hydrophobic ligands on the surface of Au NCs is beneficial to the high permeability.

Adsorption of the amyloid β40 monomer on charged gold nanoparticles and slabs: a molecular dynamics study

Negatively charged nanoparticles are known to inhibit the fibrillation of amyloidogenic protein amyloid β (Aβ40), though the overall charge on the protein is negative. In this work a molecular dynamics study is reported to investigate the interaction of Aβ40 on negatively charged gold nanoparticles (3-5 nm) and charged (positive and negative) and neutral gold slabs. The equilibrium structures of Aβ40 on gold surfaces are characterized using residue-specific contacts on the gold surface, secondary structure analysis and binding free energy calculations. The simulation results reveal that the Aβ40 protein in water interconverts into β-sheets, which are building blocks of the mature fibrils, whereas on gold nanoparticles Aβ40 unfolds and adsorbs. Both the negatively charged gold nanoparticles and gold slabs arrest the formation of β-sheets in Aβ40, whereas the positively charged gold slab does not inhibit the formation of β-sheets. The residue-specific interactions between Aβ40 and the gold surfaces are important in governing the adsorption of Aβ40 on charged surfaces.

Non-disruptive uptake of anionic and cationic gold nanoparticles in neutral zwitterionic membranes

The potential toxicity of ligand-protected nanoparticles (NPs) on biological targets is crucial for their clinical translation. A number of studies are aimed at investigating the molecular mechanisms shaping the interactions between synthetic NPs and neutral plasma membranes. The role played by the NP surface charge is still widely debated. We compare, via liposome leakage assays, the perturbation induced by the penetration of sub-6 nm anionic and cationic Au NPs into model neutral lipid membranes composed of the zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our charged Au NPs are functionalized by a mixture of the apolar 1-octanethiol and a ω-charged thiol which is either the anionic 11-mercapto-1-undecanesulfonate or the cationic (11-mercaptoundecyl)-N,N,N-trimethylammonium. In both cases, the NP uptake in the bilayer is confirmed by quartz crystal microbalance investigations. Our leakage assays show that both negatively and positively charged Au NPs do not induce significant membrane damage on POPC liposomes when penetrating into the bilayer. By means of molecular dynamics simulations, we show that the energy barrier for membrane penetration is the same for both NPs. These results suggest that the sign of the NP surface charge, per se, does not imply different physicochemical mechanisms of interaction with zwitterionic lipid membranes.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules

The molecular features that dictate interactions between functionalized nanoparticles and biomolecules are not well understood. This is in part because for highly charged nanoparticles in solution, establishing a clear connection between the molecular features of surface ligands and common experimental observables such as ζ potential requires going beyond the classical models based on continuum and mean field models. Motivated by these considerations, molecular dynamics simulations are used to probe the electrostatic properties of functionalized gold nanoparticles and their interaction with a charged peptide in salt solutions. Counterions are observed to screen the bare ligand charge to a significant degree even at the moderate salt concentration of 50 mM. As a result, the apparent charge density and ζ potential are largely insensitive to the bare ligand charge densities, which fall in the range of ligand densities typically measured experimentally for gold nanoparticles. While this screening effect was predicted by classical models such as the Manning condensation theory, the magnitudes of the apparent surface charge from microscopic simulations and mean-field models are significantly different. Moreover, our simulations found that the chemical features of the surface ligand (e.g., primary vs. quaternary amines, heterogeneous ligand lengths) modulate the interfacial ion and water distributions and therefore the interfacial potential. The importance of interfacial water is further highlighted by the observation that introducing a fraction of hydrophobic ligands enhances the strength of electrostatic binding of the charged peptide. Finally, the simulations highlight that the electric double layer is perturbed upon binding interactions. As a result, it is the bare charge density rather than the apparent charge density or ζ potential that better correlates with binding affinity of the nanoparticle to a charged peptide. Overall, our study highlights the importance of molecular features of the nanoparticle/water interface and underscores a set of design rules for the modulation of electrostatic driven interactions at nano/bio interfaces.

Size-dependent interaction of hydrophilic/hydrophobic ligand functionalized cationic and anionic nanoparticles with lipid bilayers

We study the nature of nanoparticle (NPs)-membrane interaction as a function of nanoparticle size for different functionalization using molecular dynamics simulation. Zinc sulphide quantum dots of size, 2 nm and 4 nm are used as model NPs, and DLPC and DPPC lipid bilayers are used as model membranes. We use coarse-grained polarizable MARTINI model (MPW) to simulate the NPs and lipid bilayers. Our simulation results show that uncharged bare NPs penetrate the lipid bilayers and embed themselves within the hydrophobic core of the bilayer both in the gel and fluid phases. NPs of size 4 nm are shown to disrupt the bilayer. The bilayer recovers from the damages caused by smaller NPs of size 2 nm. In case of either purely hydrophilic or hybrid (with hydrophilic/hydrophobic ratio of 2:1) ligand-functionalized NPs of smaller size (shell size 2 nm), only cationic NPs bind to the bilayer. However, for larger NPs with a shell size of 4 nm, both anionic and cationic hybrid functionalized NPs bind to the bilayer. The performance of standard Martini (SM) force field for the charged NP/bilayer systems has also been tested and compared with the results obtained using MPW model. Although the overall trend that the cationic NPs interact strongly with the bilayers than their anionic counterparts has been captured correctly using SM, the adsorption behaviour of the functionalized NPs differ significantly in the SM force field. The interaction of anionic NPs with both fluid and gel bilayers has been observed to be least accurately represented in the SM force field.

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 at Biomimetic Interfaces: Combined Experimental and Simulation Study on Charged Gold Nanoparticles/Lipid Bilayer Interfaces

The poor understanding of the interaction of nanomaterials with biologically relevant interfaces is recognized as one of the major issues currently limiting the development of nanomedicine. The central purpose of this study is to compare experimental (confocal microscopy, fluorescence correlation spectroscopy, X-ray reflectivity) and computational (molecular dynamics simulations) results to thoroughly describe the interaction of cationic gold nanoparticles (AuNPs) with mixed zwitterionic/anionic lipid membranes. The adhesion of AuNPs to the lipid membrane is investigated on different length scales from a structural and dynamical point of view; with this approach, a series of complex phenomena, spanning from lipid extraction, localized membrane disruption, lateral phase separation, and slaved diffusion, are characterized and interpreted from a molecular level to macroscopic observations.

Anionic nanoparticle-lipid membrane interactions: the protonation of anionic ligands at the membrane surface reduces membrane disruption

Monolayer-protected gold nanoparticles (Au NPs) are promising biomedical tools with applications in diagnosis and therapy, thanks to their biocompatibility and versatility. Here we show how the NP surface functionalization can drive the mechanism of interaction with lipid membranes. In particular, we show that the spontaneous protonation of anionic carboxylic groups on the NP surface can make the NP-membrane interaction faster and less disruptive.

The interaction between anionic Au nanoparticles and model lipid membranes is facilitated by the spontaneous protonation of the NP ligand carboxylate groups, COO⁻˙ → COOH, in the lipid headgroup region.

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.

Polylysine-grafted Au144 nanoclusters: birth and growth of a healthy surface-plasmon-resonance-like band

Poly(amino acid)-coated gold nanoparticles hold promise in biomedical applications, particularly because they combine the unique physicochemical properties of the gold core, excellent biocompatibility, and easy functionalization of the poly(amino acid)-capping shell. Here we report a novel method for the preparation of robust hybrid core-shell nanosystems consisting of a Au144 cluster and a densely grafted polylysine layer. Linear polylysine chains were grown by direct N-carboxyanhydride (NCA) polymerization onto ligands capping the gold nanocluster. The density of the polylysine chains and the thickness of the polymer layer strongly depend on the amount and concentration of the NCA monomer and the initiator. The optical spectra of the so-obtained core-shell nanosystems show a strong surface plasmon resonance (SPR)-like band at 531 nm. In fact, despite maintenance of the gold cluster size and the absence of interparticle aggregation, the polylysine-capped clusters behave as if they have a diameter nearly 4 times larger. To the best of our knowledge, this is the first observation of the growth of a fully developed, very stable SPR-like band for a gold nanocluster of such dimensions. The robust polylysine protective shell makes the nanoparticles very stable under conditions of chemical etching, in the presence of glutathione, and at different pH values, without gold core deshielding or alteration of the SPR-like band. This polymerization method can conceivably be extended to prepare core-shell nanosystems based on other mono- or co-poly(amino acids).

Counterintuitive cooperative endocytosis of like-charged nanoparticles in cellular internalization: computer simulation and experiment

The nanoparticles (NPs) functionalized with charged ligands are of particular significance due to their potential drug/gene delivery and biomedical applications. However, the molecular mechanism of endocytosis of the charged NPs by cells, especially the effect of the NP-NP and NP-biomembrane interactions on the internalization pathways is still poorly understood. In this work, we systematically investigate the internalization behaviors of the positively charged NPs by combining experiment technology and dissipative particle dynamics (DPD) simulation. We experimentally find an interesting but highly counterintuitive phenomenon, i.e. the multiple positively charged NPs prefer to enter cells cooperatively although the like-charged NPs have obvious electrostatic repulsion. Furthermore, we adopt the DPD simulation to confirm the experimental findings, and reveal that the mechanism of the cooperative endocytosis between like-charged NPs is definitely caused by the interplay of particle size, the charged ligand density on particle surface and local concentration of NPs. Importantly, we not only observe the normal cooperative endocytosis of like-charged NPs in cell biomembrane like neutral NP case, but also predict the 'bud' cooperative endocytosis of like-charged NPs which is absence in the neutral NP case. The results indicate that electrostatic repulsion between the positively charged nanoparticles plays an important role in the 'bud' cooperative endocytosis of like-charged NPs.

Modeling the Hydrophobicity of Nanoparticles and Their Interaction with Lipids and Proteins

We present a method of modeling nanoparticle (NP) hydrophobicity using coarse-grained molecular dynamics (CG MD) simulations, and apply this to the interaction of lipids with nanoparticles. To model at a coarse-grained level the wettability or hydrophobicity of a given material, we choose the MARTINI coarse-grained force field, and determine through simulation the contact angles of MARTINI water droplets residing on flat regular surfaces composed of various MARTINI bead types (C1, C2, etc.). Each surface is composed of a single bead type in each of three crystallographic symmetries (FCC, BCC, and HCP). While this method lumps together several atoms (for example, one cerium and two oxygens of CeO₂) into a single CG bead, we can still capture the overall hydrophobicity of the actual material by choosing the MARTINI bead type that gives the best fit of the contact angle to that of the actual material, as determined by either experimental or all-atom simulations. For different MARTINI bead types, the macroscopic contact angle is obtained by extrapolating the microscopic contact angles of droplets of eight different sizes (containing N_w = 3224-22978 water molecules) to infinite droplet size. For each droplet, the contact angle was computed from a best fit of a circular curve to the droplet interface extrapolated to the first layer of the surface. We then examine how small nanoparticles of differing wettability interact with MARTINI dipalmitoylphosphotidylcholine (DPPC) lipids and SP-C peptides (a component of lung surfactant). The DPPC shows a transition from tails coating the nanoparticle to a hemimicelle coating the water-wet NP, as the contact angle of a water droplet on the surface is lowered below ∼60°. The results are relevant to developing a taxonomy describing the potential nanotoxicity of nanoparticle interactions with components in the lung.

Molecular dynamics simulations on the effect of size and shape on the interactions between negative Au18(SR)14, Au102(SR)44 and Au144(SR)60 nanoparticles in physiological saline

Molecular dynamics simulations employing all-atom force fields have become a reliable way to study binding interactions quantitatively for a wide range of systems. In this work, we employ two recently developed methods for the calculation of dissociation constants KD between gold nanoparticles (AuNPs) of different sizes in a near-physiological environment through the potential of mean force (PMF) formalism: the method of geometrical restraints developed by Woo et al. and formalized by Gumbart et al. and the method of hybrid Steered Molecular Dynamics (hSMD). Obtaining identical results (within the margin of error) from both approaches on the negatively charged Au18(SR)14 NP, functionalized by the negatively charged 4-mercapto-benzoate (pMBA) ligand, we draw parallels between their energetic and entropic interactions. By applying the hSMD method on Au102(SR)44 and Au144(SR)60, both of them near-spherical in shape and functionalized by pMBA, we study the effects of size and shape on the binding interactions. Au18 binds weakly with KD = 13mM as a result of two opposing effects: its large surface curvature hindering the formation of salt bridges, and its large ligand density on preferential orientations favoring their formation. On the other hand, Au102 binds more strongly with KD = 30μM and Au144 binds the strongest with KD = 3.2nM.

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.

Role of charged lipids in membrane structures - Insight given by simulations

Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids such as phosphatidylinositols and phosphatidylserines are involved in several examples of such effects. Molecular dynamics simulations have proved an invaluable tool in exploring these aspects. This so-called computational microscope can provide both complementing explanations for the experimental results and guide experiments to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane components, mainly proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters

We present transferable AMBER-compatible force field parameters for thiolate-protected gold nanoclusters. Five different sized clusters containing both organo-soluble and water-soluble thiolate ligands served as test systems in MD simulations, and parameters were validated against DFT and experimental results. The cluster geometries remain intact during the MD simulations in various solvents, and structural fluctuations and energetics showed agreement with DFT calculations. Experimental diffusion coefficients and crystal structures were also reproduced with sufficient accuracy. The presented parameter set contains the minimum number of cluster-specific parameters enabling the use of these parameters for several different gold nanoclusters. The parameterization of ligands can also be extended to different types of ligands.

NANOGOLD decorated by pHLIP peptide: comparative force field study

The potential of gold nanoparticles (AuNPs) in therapeutic and diagnostic cancer applications is becoming increasingly recognized, which focuses on their efficient and specific delivery from passive accumulation in tumour tissue to directly targeting tumor-specific biomarkers. AuNPs functionalized by pH low insertion peptide (pHLIP) have recently revealed the capability of targeting acidic tissues and inserting into cell membranes. However, the structure of AuNP-pHLIP conjugates and fundamental gold-peptide interactions still remain unknown. In this study, we have developed a series of molecular dynamics (MD) models reproducing a small gold nanoparticle coupled to pHLIP. We focus on Au135 nanoparticles that comprise a nearly spherical Au core (diameter ∼ 1.4 nm) functionalized with a monomaleimide moiety, mimicking a commercially available monomaleimido NANOGOLD® labelling agent. To probe the structure and folding of pHLIP, which is attached covalently to the maleimide NANOGOLD particle, we have benchmarked the performances of a series of popular, all-atom force fields (FF), including those of OPLS-AA, AMBER03, three variations of CHARMM FFs, as well as united-atom GROMOS G53A6 FF. We found that CHARMMs and OPLSAA FFs predict that in an aqueous salt solution at a neutral pH, pHLIP is partially bound onto the gold surface through some short hydrophobic peptide stretches, while at the same time, a large portion of peptide remains in solution. In contrast, AMBER03 and G53A6 FFs revealed the formation of compact, tightly bound peptide configurations adsorbed onto the nanoparticle core. To reproduce the experimental physical picture of the peptide adsorption onto gold in unfolded and unstructured conformations, our study suggests CHARMM36 and OPLS-AA FFs as a tool of choice for the computational studies of NANOGOLD decorated by pHLIP.

Molecular-level insight into the interactions of DNA with phospholipid bilayers: barriers and triggers

A zwitterionic phospholipid bilayer represents a repulsive barrier for DNA binding; this barrier can be overcome through adsorption of divalent cations to the bilayer surface.

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles

Nanometer-sized gold particles (AuNPs) are of peculiar interest because their behaviors in an aqueous solution are sensitive to changes in environmental factors including the size and shape of the solute ions. In order to determine these important characteristics, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates (4-mercaptobenzoate, pMBA) in eight aqueous solutions having ions of varying sizes and shapes (Na(+), K(+), tetramethylamonium cation TMA(+), tris-ammonium cation TRS(+), Cl(-), and OH(-)). For each solution, we computed the reversible work (potential of mean of force) to bring two nanoparticles together as a function of their separation distance. We found that the behavior of pMBA protected Au144 nanoparticles can be readily modulated by tuning their aqueous environmental factors (pH and solute ion combinations). We examined the atomistic details on how the sizes and shapes of solute ions quantitatively factor in the definitive characteristics of nanoparticle-environment and nanoparticle-nanoparticle interactions. We predict that tuning the concentrations of nonspherical composite ions such as TRS(+) in an aqueous solution of AuNPs be an effective means to modulate the aggregation propensity desired in biomedical and other applications of small charged nanoparticles.

Ligand-modulated interactions between charged monolayer-protected Au144(SR)60 gold nanoparticles in physiological saline

In order to determine how functionalized gold nanoparticles (AuNPs) interact in a near-physiological environment, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates selected from one of these five (5) types: 11-mercapto-1-undecanesulfonate -SC11H22(SO3(-)), 5-mercapto-1-pentanesulfonate -SC5H10(SO3(-)), 5-mercapto-1-pentaneamine -SC5H10(NH3(+)), 4-mercapto-benzoate -SPh(COO(-)), or 4-mercapto-benzamide -SPh(CONH3(+)). These thiolates were selected to elucidate how the aggregation behavior of AuNPs depends on ligand parameters, including the charge of the terminal group (anionic vs. cationic), and its length and conformational flexibility. For this purpose, each functionalized AuNP was paired with a copy of itself, placed in an aqueous cell, neutralized by 120 Na(+)/Cl(-) counter-ions and salinated with a 150 mM concentration of NaCl, to form five (5) systems of like-charged AuNPs pairs in a saline. We computed the potential of mean force (the reversible work of separation) as a function of the intra-pair distance and, based on which, the aggregation affinities. We found that the AuNPs coated with negatively charged, short ligands have very high affinities. Structurally, a significant number of Na(+) counter-ions reside on a plane between the AuNPs, mediating the interaction. Each such ion forms a "salt bridge" (or "ionic bonds") to both of the AuNPs when they are separated by its diameter plus 0.2-0.3 nm. The positively charged AuNPs have much weaker affinities, as Cl(-) counter-ions form fewer and weaker salt bridges between the AuNPs. In the case of Au144(SC11H22(SO3(-)))60 pair, the flexible ligands fluctuate much more than the other four cases. The large fluctuations disfavor the forming of salt bridges between two AuNPs, but enable hydrophobic contact between the exposed hydrocarbon chains of the two AuNPs, which are subject to an effective attraction at a separation much greater than the AuNP diameter and involve a higher concentration of counter ions in the inter-pair space.