Unveiling Interactions of Tumor-Targeting Nanoparticles with Lipid Bilayers Using a Titratable Martini Model

pH-responsive nanoparticles are ideal vehicles for drug delivery and are widely used in cell imaging in targeted therapy of cancer, which usually has a weakly acidic microenvironment. In this work, we constructed a titratable molecular model for nanoparticles grafted with ligands of pH-sensitive carboxylic acids and investigated the interactions between the nanoparticles and the lipid bilayer in varying pH environments. We mainly examined the effect of the grafting density of the pH-sensitive ligands of the nanoparticles on the interactions of the nanoparticles with the lipid bilayer. The results show that the nanoparticles can penetrate the lipid bilayer only when the pH value is lower than a critical value, which can be readily modulated to the specific pH value of the tumor microenvironment by changing the ligand grafting density. This work provides some insights into modulating the interactions between the pH-sensitive nanoparticles and cellular membranes to realize targeted drug delivery to tumors based on their specific pH environment.

Effect of Functional Groups in Lipid Molecules on the Stability of Nanostructured Lipid Carriers: Experimental and Computational Investigations

Lipid nanoparticles have been used as drug carriers for decades. Many lipid types have been screened for both solid lipid nanoparticles and nanostructured lipid carriers (NLCs). Specifically, for NLCs that are composed of lipids in the solid form mixed with lipids in the liquid form, compatibility of lipid combination and phase behavior play a significant role in the NLC quality. In this study, stearic acid (STA) and cetyl palmitate (CTP) were used as solid lipids, and oleic acid (OLA), isopropyl palmitate (IPP), and caprylic/capric triglycerides were used as liquid lipids. NLCs were prepared at solid:liquid ratios of 50:50, 70:30, and 90:10, respectively. The characteristics and stability of the prepared NLCs were investigated. Laboratory results showed that the solid lipid had a greater influence on the particle size than the liquid lipid. Meanwhile, cetyl palmitate, an ester compound, provides higher NLC stability compared to stearic acid, a carboxylic acid compound. A MARTINI-based coarse-grained molecular dynamics simulation was used to simulate the lipid droplet in water. The distribution of lipid molecules in the droplet was characterized by the polar group density distribution. Different spatial arrangements of the lipid headgroup and lipid molecules, when CTP or STA was used as solid lipids, might contribute to the different stabilities of prepared NLCs. The understanding of mixed lipid systems via simulations will be a significant tool for screening the type of lipids for drug carriers and other pharmaceutical applications.

Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology

Sea spray aerosol (SSA) ejected through bursting bubbles at the ocean surface is a complex mixture of salts and organic species. Submicrometer SSA particles have long atmospheric lifetimes and play a critical role in the climate system. Composition impacts their ability to form marine clouds, yet their cloud-forming potential is difficult to study due to their small size. Here, we use large-scale molecular dynamics (MD) simulations as a "computational microscope" to provide never-before-seen views of 40 nm model aerosol particles and their molecular morphologies. We investigate how increasing chemical complexity impacts the distribution of organic material throughout individual particles for a range of organic constituents with varying chemical properties. Our simulations show that common organic marine surfactants readily partition between both the surface and interior of the aerosol, indicating that nascent SSA may be more heterogeneous than traditional morphological models suggest. We support our computational observations of SSA surface heterogeneity with Brewster angle microscopy on model interfaces. These observations indicate that increased chemical complexity in submicrometer SSA leads to a reduced surface coverage by marine organics, which may facilitate water uptake in the atmosphere. Our work thus establishes large-scale MD simulations as a novel technique for interrogating aerosols at the single-particle level.

How Azide Ion/Hydrazoic Acid Passes Through Biological Membranes: An Experimental and Computational Study

Hydrazoic acid (HN₃) and its deprotonated form azide ion (N₃^-) (AHA) are toxic because they inhibit the cytochrome c oxidase complex IV (CoX IV) embedded in the inner mitochondrial membrane that forms part of the enzyme complexes involved in cellular respiration. Critical to its toxicity is the inhibition of CoX IV in the central nervous system and cardiovascular system. Hydrazoic acid is an ionizable species and its affinity for membranes, and the associated permeabilities, depend on the pH values of aqueous media on both sides of the membranes. In this article, we address the permeability of AHA through the biological membrane. In order to understand the affinity of the membrane for the neutral and ionized form of azide, we measured the octanol/water partition coefficients at pH values of 2.0 and 8.0, which are 2.01 and 0.00034, respectively. Using a Parallel Artificial Membrane Permeability Assay (PAMPA) experiment, we measured the effective permeability through the membrane, which is logP_e - 4.97 and - 5.26 for pH values of 7.4 and pH 8.0, respectively. Experimental permeability was used to validate theoretical permeability, which was estimated by numerically solving a Smoluchowski equation for AHA diffusion through the membrane. We demonstrated that the rate of permeation through the cell membrane of 8.46·10⁴ s^-1 is much higher than the rate of the chemical step of CoX IV inhibition by azide of 200 s^-1. The results of this study show that transport through the membrane does not represent the rate-limiting step and therefore does not control the rate of CoX IV inhibition in the mitochondria. However, the observed dynamics of azide poisoning is controlled by circulatory transport that takes place on a time scale of minutes.

Partitioning into phosphatidylcholine-cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation

Membrane-water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field. The methodology is general and can also be used for other applications where coarse-grained simulations are appropriate. This article addresses the effect on membrane-water partitioning of adding cholesterol to POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Nine contrasting neutral, zwitterionic and charged solutes are tested. Agreement between experiment and simulation is generally good, with the most challenging cases being permanently charged solutes. For all solutes, partitioning is found to be insensitive to membrane cholesterol concentration up to 25% mole fraction. Hence, for assessment of bioaccumulation into a range of membranes (such as those found in fish), partitioning data measured in pure lipid membranes are still informative.

Increasing the Realism of in Silico pHLIP Peptide Models with a Novel pH Gradient CpHMD Method

The pH-low insertion peptides (pHLIP) are pH-dependent membrane inserting peptides, whose function depends on the cell microenvironment acidity. Several peptide variants have been designed to improve upon the wt-sequence, particularly the state transition kinetics and the selectivity for tumor pH. The variant 3 (Var3) peptide is a 27 residue long peptide, with a key titrating residue (Asp-13) that, despite showing a modest performance in liposomes (pK^ins ∼ 5.0), excelled in tumor cell experiments. To help rationalize these results, we focused on the pH gradient in the cell membrane, which is one of the crucial properties that are not present in liposomes. We extended our CpHMD-L method and its pH replica-exchange (pHRE) implementation to include a pH gradient and mimic the pHLIP-membrane microenvironment in a cell where the internal pH is fixed (pH 7.2) and the external pH is allowed to change. We showed that, by properly modeling the pH-gradient, we can correctly predict the experimentally observed loss and gain of performance in tumor cells experiments by the wt and Var3 sequences, respectively. In sum, the pH gradient implementation allowed for more accurate and realistic pK_a estimations and was a pivotal step in bridging the in silico data and the in vivo cell experiments.

Extending the Stochastic Titration CpHMD to CHARMM36m

The impact of pH on proteins is significant but often neglected in molecular dynamics simulations. Constant-pH Molecular Dynamics (CpHMD) is the state-of-the-art methodology to deal with these effects. However, it still lacks widespread adoption by the scientific community. The stochastic titration CpHMD is one of such methods that, until now, only supported the GROMOS force field family. Here, we extend this method's implementation to include the CHARMM36m force field available in the GROMACS software package. We test this new implementation with a diverse group of proteins, namely, lysozyme, Staphylococcal nuclease, and human and E. coli thioredoxins. All proteins were conformationally stable in the simulations, even at extreme pH values. The RMSE values (pK_a prediction vs experimental) obtained were very encouraging, in particular for lysozyme and human thioredoxin. We have also identified a few residues that challenged the CpHMD simulations, highlighting scenarios where the method still needs improvement independently of the force field. The CHARMM36m all-atom implementation was more computationally efficient when compared with the GROMOS 54A7, taking advantage of a shorter nonbonded interaction cutoff and a less frequent neighboring list update. The new extension will allow the study of pH effects in many systems for which this force field is particularly suited, i.e., proteins, membrane proteins, lipid bilayers, and nucleic acids.

Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier

We have designed a protocol combining constant-pH molecular dynamics (CpHMD) simulations with an umbrella sampling (US) scheme (US-CpHMD) to study the mechanism of ADP/ATP transport (import and export) by their inner mitochondrial membrane carrier protein [ADP/ATP carrier (AAC)]. The US scheme helped overcome the limitations of sampling the slow kinetics involved in these substrates' transport, while CpHMD simulations provided an unprecedented realism by correctly capturing the associated protonation changes. The import of anionic substrates along the mitochondrial membrane has a strong energetic disadvantage due to a smaller substrate concentration and an unfavorable membrane potential. These limitations may have created an evolutionary pressure on AAC to develop specific features benefiting the import of ADP. In our work, the potential of mean force profiles showed a clear selectivity in the import of ADP compared to ATP, while in the export, no selectivity was observed. We also observed that AAC sequestered both substrates at longer distances in the import compared to the export process. Furthermore, only in the import process do we observe transient protonation of both substrates when going through the AAC cavity, which is an important advantage to counteract the unfavorable mitochondrial membrane potential. Finally, we observed a substrate-induced disruption of the matrix salt-bridge network, which can promote the conformational transition (from the C- to M-state) required to complete the import process. This work unraveled several important structural features where the complex electrostatic interactions were pivotal to interpreting the protein function and illustrated the potential of applying the US-CpHMD protocol to other transport processes involving membrane proteins.

Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization

pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.

Investigating the morphological transitions in an associative surfactant ternary system

Associative surfactants systems involving polar oils have recently been shown to stabilize immiscible liquids by forming nanostructures at the liquid interface and have been used to print soft materials. Although these associating surfactant systems show great promise for creating nanostructured soft materials, a fundamental understanding of the self-assembly process is still unknown. In this study, a ternary phase diagram for a system of cationic surfactant cetylpyridinium chloride monohydrate (CPCl), a polar oil (oleic acid), and water is established using experiment and simulation, to study the equilibrium phase behavior. A combination of visual inspection, small-angle X-ray scattering (SAXS), and rheological measurements was employed to establish the phase behavior and properties of the self-assembled materials. Dissipative particle dynamics (DPD) is used to simulate the formation of the morphologies in this system and support the experimental results. The ternary phase diagram obtained from the simulations agrees with the experimental results, indicating the robustness of the computational simulation as a supplement to the mesoscale experimental systems. We observe that morphological transitions (e.g., micelle-to-bilayer and vesicle-to-lamellar) are in agreement between experiments and simulations across the ternary diagram. DPD simulations correctly predict that associative surfactant systems form new nanoscale phases due to the co-assembly of the components. The established ternary phase diagram and the DPD model pave the way towards predicting and controlling the formation of different mesostructures like lamellar or vesicles, opening new avenues to tailor and synthesize desired morphologies for applications related to liquid-in-liquid 3D printing.

Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules

Characterizing the biophysical properties of bacterial membranes is critical for understanding the protective nature of the microbial envelope, interaction of biological membranes with exogenous materials, and designing new antibacterial agents. Presented here are molecular dynamics simulations for two cationic quaternary ammonium compounds, and the anionic and nonionic form of a fatty acid molecule interacting with a Staphylococcus aureus bacterial inner membrane. The effect of the tested materials on the properties of the model membranes are evaluated with respect to various structural properties such as the lateral pressure profile, lipid tail order parameter, and the bilayer’s electrostatic potential. Conducting asymmetric loading of molecules in only one leaflet, it was observed that anionic and cationic amphiphiles have a large impact on the Staphylococcus aureus membrane’s electrostatic potential and lateral pressure profile as compared to a symmetric distribution. Nonintuitively, we find that the cationic and anionic molecules induce a similar change in the electrostatic potential, which points to the complexity of membrane interfaces, and how asymmetry can induce biophysical consequences. Finally, we link changes in membrane structure to the rate of electroporation for the membranes, and again find a crucial impact of introducing asymmetry to the system. Understanding these physical mechanisms provides critical insights and viable pathways for the rational design of membrane-active molecules, where controlling the localization is key.

Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review

Scientific and consumer interest in healthy foods (also known as functional foods), nutraceuticals and cosmeceuticals has increased in the recent years, leading to an increased presence of these products in the market. However, the regulations across different countries that define the type of claims that may be made, and the degree of evidence required to support these claims, are rather inconsistent. Moreover, there is also controversy on the effectiveness and biological mode of action of many of these products, which should undergo an exhaustive approval process to guarantee the consumer rights. Computational approaches constitute invaluable tools to facilitate the discovery of bioactive molecules and provide biological plausibility on the mode of action of these products. Indeed, methodologies like QSAR, docking or molecular dynamics have been used in drug discovery protocols for decades and can now aid in the discovery of bioactive food components. Thanks to these approaches, it is possible to search for new functions in food constituents, which may be part of our daily diet, and help to prevent disorders like diabetes, hypercholesterolemia or obesity. In the present manuscript, computational studies applied to this field are reviewed to illustrate the potential of these approaches to guide the first screening steps and the mechanistic studies of nutraceutical, cosmeceutical and functional foods.

Fast bilayer-micelle fusion mediated by hydrophobic dipeptides

To understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak. In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles, inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which form hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allows for identifying the transition state for fusion. Free-energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending on the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.

Using coarse-grained molecular dynamics to rationalize biomolecule solubilization mechanisms in ionic liquid-based colloidal systems

Solubilizing agents are widely used to extract poorly soluble compounds from biological matrices. Aqueous solutions of surfactants and hydrotropes are commonly used as solubilizers, however, the underlying mechanism that determines their action is still roughly understood. Among these, ionic liquids (IL) are often used not only for solubilization of a target compound but in liquid-liquid extraction processes. Molecular dynamics simulations can shed light into this issue by providing a microscopic insight of the interactions between solute and solubilising agents. In this work, a new coarse-grained (CG) model was developed under the MARTINI framework for gallic acid (GA) while the CG models of three quaternary ammonium ionic liquids and salts (QAILS) were obtained from literature. Three QAILS were selected bearing in mind their potential solubilising mechanisms: trimethyl-tetradecylammonium chloride ([N1,1,1,14]Cl) as a surfactant, tetrabutylammonium chloride ([N4,4,4,4]Cl) as a hydrotrope, and tributyl-tetradecylammonium chloride ([N4,4,4,14]Cl) as a system combining the characteristics of the other compounds. Throughout this hydrotrope-to-surfactant spectrum and considering the most prevalent GA species across the pH range, the solvation of GA at two concentration levels in aqueous QAILS solutions were studied and discussed. The results of this study indicate that dispersive interactions between the QAILS and GA are generally the driving force in the GA solubilization. However, electrostatic interactions play an increasingly significant role as the GA becomes deprotonated, affecting their placement within the micelle and ultimately the solvation mechanism. The hydrotropic mechanism seen in [N4,4,4,4]Cl corroborates recent models based on the formation of a hydrotrope-solute aggregates driven by dispersive forces. This work contributes to the application of a transferable approach to partition and solubilization studies using molecular dynamics, which could complement experimental assays and quickly screen molecular candidates for these processes.

Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena

Phosphorylation is a ubiquitous post-translational modification in proteins, and the phosphate group is present constitutively or transiently in most biological building blocks. These phosphorylated biomolecules are involved in many high-affinity binding/unbinding events that rely predominantly on electrostatic interactions. To build accurate models of these molecules, we need an improved description of the atomic partial charges for all relevant protonation states. In this work, we showed that the commonly used protocols to derive atomic partial charges using well-solvated molecules are inadequate to model the protonation equilibria in binding events. We introduced a protocol based on PB/MC calculations with a single representative conformation (of both protonation states) and used the resulting pK_a estimations to help manually curate the atomic partial charges. The final charge set, which is fully compatible with the GROMOS 54A7 force field, proved to be very effective in modeling the protonation equilibrium in different phosphorylated peptides in the free (tetrapeptides, pentapeptides, and pY1021) and protein-complexed forms (pY1021/PLC-γ1 complex). This was particularly important in the case of the pY1021 bound to the SH2 domain of PLC-γ1, where only our curated charge set captured the correct protonation equilibrium at the neutral to slightly acidic pH range. The binding/unbinding phenomena in that pH range are biologically relevant, and to improve our models, we need to go beyond the commonly used protocols and obtain revised force field parameters for these molecules.

Influence of Bile Composition on Membrane Incorporation of Transient Permeability Enhancers

Transient permeability enhancers (PEs), such as caprylate, caprate, and salcaprozate sodium (SNAC), improve the bioavailability of poorly permeable macromolecular drugs. However, the effects are variable across individuals and classes of macromolecular drugs and biologics. Here, we examined the influence of bile compositions on the ability of membrane incorporation of three transient PEs—caprylate, caprate, and SNAC—using coarse-grained molecular dynamics (CG-MD). The availability of free PE monomers, which are important near the absorption site, to become incorporated into the membrane was higher in fasted-state fluids than that in fed-state fluids. The simulations also showed that transmembrane perturbation, i.e., insertion of PEs into the membrane, is a key mechanism by which caprylate and caprate increase permeability. In contrast, SNAC was mainly adsorbed onto the membrane surface, indicating a different mode of action. Membrane incorporation of caprylate and caprate was also influenced by bile composition, with more incorporation into fasted- than fed-state fluids. The simulations of transient PE interaction with membranes were further evaluated using two experimental techniques: the quartz crystal microbalance with dissipation technique and total internal reflection fluorescence microscopy. The experimental results were in good agreement with the computational simulations. Finally, the kinetics of membrane insertion was studied with CG-MD. Variation in micelle composition affected the insertion rates of caprate monomer insertion and expulsion from the micelle surface. In conclusion, this study suggests that the bile composition and the luminal composition of the intestinal fluid are important factors contributing to the interindividual variability in the absorption of macromolecular drugs administered with transient PEs.

Titratable Martini model for constant pH simulations

In this work, we deliver a proof of concept for a fast method that introduces pH effects into classical coarse-grained (CG) molecular dynamics simulations. Our approach is based upon the latest version of the popular Martini CG model to which explicit proton mimicking particles are added. We verify our approach against experimental data involving several different molecules and different environmental conditions. In particular, we compute titration curves, pH dependent free energies of transfer, and lipid bilayer membrane affinities as a function of pH. Using oleic acid as an example compound, we further illustrate that our method can be used to study passive translocation in lipid bilayers via protonation. Finally, our model reproduces qualitatively the expansion of the macromolecule dendrimer poly(propylene imine) as well as the associated pKa shift of its different generations. This example demonstrates that our model is able to pick up collective interactions between titratable sites in large molecules comprising many titratable functional groups.

Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations

The structure and interactions of proteins play a critical role in determining the quality attributes of many foods, beverages, and pharmaceutical products. Incorporating a multiscale understanding of the structure-function relationships of proteins can provide greater insight into, and control of, the relevant processes at play. Combining data from experimental measurements, human sensory panels, and computer simulations through machine learning allows the construction of statistical models relating nanoscale properties of proteins to the physicochemical properties, physiological outcomes, and tastes of foods. This review highlights several examples of advanced computer simulations at molecular, mesoscale, and multiscale levels that shed light on the mechanisms at play in foods, thereby facilitating their control. It includes a practical simulation toolbox for those new to in silico modeling.

Lipid-Protein Interactions in Langmuir Monolayers under Dynamically Varied Conditions

In the Langmuir monolayer technique, a single layer of molecules is formed on a water subphase. This approach was used to mimic the antitumoricidal lipid-protein complex of oleic acid and bovine α-lactalbumin called the BAMLET complex. Our previous studies have shown that at the interface, the BAMLET complex is stabilized by the hydrophobic forces supported by the hydrogen bonds. This study provides an insight into the influence of calcium ions and the experimental conditions (temperature and subphase pH) on the stability of the complex at the interface. The Langmuir technique was expanded using a dosing pump to exchange the subphase and deliver additional substances to the system. We investigated the interactions between oleic acid monolayer and α-lactalbumin in the presence of Ca²⁺ in the bulk and the effect of varied experimental conditions on the complex stability. The role of calcium ions in this system is important because (in addition to low pH and relatively high temperature) it affects the conformational changes within the protein molecule and facilitates the transition of α-lactalbumin into the molten globule state. A partially unfolded state is required to form the BAMLET complex. We found that the mixed monolayer spread at the interface is stable despite drastic changes in the process conditions and remains stable even after the subphase exchange. This study of molecular interactions explored by the Langmuir technique with peristaltic pump enabled to understand the role of Ca²⁺ in BAMLET complex formation.

Coupling Phase Behavior of Fatty Acid Containing Membranes to Membrane Bio-Mechanics

Biological membranes constantly modulate their fluidity for proper functioning of the cell. Modulation of membrane properties via regulation of fatty acid composition has gained a renewed interest owing to its relevance in endocytosis, endoplasmic reticulum membrane homeostasis, and adaptation mechanisms in the deep sea. Endowed with significant degrees of freedom, the presence of free fatty acids can alter the curvature of membranes which in turn can alter the response of curvature sensing proteins, thus defining adaptive ways to reconfigure membranes. Most significantly, recent experiments demonstrated that polyunsaturated lipids facilitate membrane bending and fission by endocytic proteins – the first step in the biogenesis of synaptic vesicles. Despite the vital roles of fatty acids, a systematic study relating the interactions between fatty acids and membrane and the consequent effect on the bio-mechanics of membranes under the influence of fatty acids has been sparse. Of specific interest is the vast disparity in the properties of cis and trans fatty acids, that only differ in the orientation of the double bond and yet have entirely unique and opposing chemical properties. Here we demonstrate a combined X-ray diffraction and membrane fluctuation analysis method to couple the structural properties to the biophysical properties of fatty acid-laden membranes to address current gaps in our understanding. By systematically doping pure dioleoyl phosphatidylcholine (DOPC) membranes with cis fatty acid and trans fatty acid we demonstrate that the presence of fatty acids doesn’t always fluidize the membrane. Rather, an intricate balance between the curvature, molecular interactions, as well as the amount of specific fatty acid dictates the fluidity of membranes. Lower concentrations are dominated by the nature of interactions between the phospholipid and the fatty acids. Trans fatty acid increases the rigidity while decreasing the area per lipid similar to the properties depicted by the addition of saturated fatty acids to lipidic membranes. Cis fatty acid however displays the accepted view of having a fluidizing effect at small concentrations. At higher concentrations curvature frustration dominates, leading to increased rigidity irrespective of the type of fatty acid. These results are consistent with theoretical predictions as detailed in the manuscript.

Hierarchically structured phase separated biopolymer hydrogels create tailorable delayed burst release during gastrointestinal digestion

The on demand delivery of novel peptide actives, traditional pharmaceuticals, nutrients and/or vitamins is a ever present challenge due to the digestive and metabolic degradation of the active and the delivery vehicle. Biodegradable biopolymer hydrogels have long held promise as candidates for creating tailored release profiles due to the ability to control gel porosity. The present study describes the creation of novel hierarchical biopolymer hydrogels for the controlled release of lipids/lipophilic actives pharmaceutical ingredients (APIs), and mathematically describes the mechanisms that affect the timing of release. The creation of phase separated protein/polysaccharide core (6.6 wt% gelatin, 40 wt% Oil in water emulsion) shell structures (7 g/L xanthan with 70-140 g/L β-lactoglobulin) altered enzyme mass transport processes. This core shell structure enabled the creation of a tailorable burst release of API during gastrointestinal digestion where there is a delay in the onset of release, without affecting the kinetics of release. The timing of the delay could be readily programmed (with release of between 60 and 240 min) by controlling either the thickness or protein concentration (between 70 g/L and 140 g/L β-lactoglobulin) of the outer mixed biopolymer hydrogel shell (7 g/L xanthan with 70-140 g/L β-lactoglobulin). Enzyme diffusion measurements demonstrated that surface erosion was the main degradation mechanism. A kinetic model was created to describe the delayed burst release behaviour of APIs encapsulated within the core, and successfully predicted the influence of shell thickness and shell protein density on the timing of gastro-intestinal release (in vitro). Our work highlights the creation of a novel family of core-shell hydrogel oral dosage forms capable of programmable delivery of lipids/lipophilic APIs. These findings could have considerable implications for the delivery of peptides, poorly soluble drugs, or the programmed delivery of lipids within the gastrointestinal tract.

Calculation of apparent pKa values of saturated fatty acids with different lengths in DOPC phospholipid bilayers

We performed all-atom molecular dynamics simulations and calculated free energy profiles and apparent pKa values for neutral and anionic forms of single myristic (C14:0), palmitic (C16:0) and stearic (C18:0) fatty acid embedded in a DOPC bilayer and explicit water solvent. We showed that the neutral forms of the fatty acids are stabilized inside the bilayer by hydrogen bonding of a fatty acid carboxylic group with DOPC phosphate and carbonyl groups. In contrast to the neutral form, the anionic forms of the fatty acids are shifted towards the water-membrane interface and are instead stabilized by hydrogen bonding to interfacial water. By using umbrella sampling simulations, we calculated free energies of stabilization and revealed that the free energy of stabilization inside the bilayer increases with the chain length for both the neutral and deprotonated forms. On the other hand, the free energies of flip-flop of both the neutral and anionic forms are constant upon the prolongation of the fatty acid. Based on the free energy curves, we also calculated apparent fatty acid pKa,app values in the bilayer, which are 7.0, 7.2 and 6.3 for myristic, palmitic and stearic acid and are increased by several pKa units compared to the corresponding pKa values in water. By further analysis of the calculated curves we found that spontaneous protonation of fatty acid anions takes place in the bilayer interior at ca. 1.4 nm from the bilayer center for all studied fatty acids.

Temperature, pH, and Molecular Packing Effects on the Penetration of Oleic Acid Monolayer by α-Lactalbumin

Recently, we reported on the interfacial behavior of mixed oleic acid (OA)-α-lactalbumin monolayer and its relevance in the formation of tumoricidal HAMLET (human α-lactalbumin made lethal to tumor cells)-like complex. This complex is probably formed in the gastrointestinal tract, but it has not been proved so far. The molecular base and the underlying physicochemical forces leading to such complexation remain to be known as well. There are also several other issues related with the complex stoichiometry that need to be fully explained. This study provides insight into the mechanism of temperature, pH, and physical state of monolayer-dependent binding of OA by the milk protein- apo-α-lactalbumin. Using the Langmuir and Langmuir-Blodgett approaches, we investigated the interactions between the OA monolayer and the apo-bovine α-lactalbumin (BLA III) at different pH, temperatures, and molecular packing. We found that the most favorable conditions for the formation of mixed OA-BLA III film are relevant to the gastric environment. The stabilization of OA-BLA III at the interface is associated with the conformational changes of protein in the presence of fatty acids induced by low pH and high temperature in the expanded monolayer. Our approach helps to understand the molecular mechanism of HAMLET/bovine α-lactalbumin made lethal to tumor cells formation in vivo.

Aggregation Behavior of Medium Chain Fatty Acids Studied by Coarse-Grained Molecular Dynamics Simulation

Medium chain fatty acids (MCFA) are digestion products of lipid-rich food and lipid-based formulations, and they are used as transient permeability enhancers in formulation of poorly permeable compounds. These molecules may promote drug absorption by several different processes, including solubilization, increased membrane fluidity, and increased paracellular transport through opening of the tight junctions. Therefore, understanding the aggregation behavior of MCFAs is important. A number of studies have measured the critical micelle concentration (CMC) of MCFAs experimentally. However, CMC is highly dependent on system conditions like pH, temperature, and the ionic strength of the buffer used in different experimental techniques. In this study, we investigated the aggregation behavior of four different MCFAs using the coarse-grained molecular dynamics (CG-MD) simulations with the purpose to explore if CG-MD can be used to study MCFA interactions occurring in water. The ratio of deprotonated and non-charged MCFA molecules were manipulated to assess aggregation behavior under different pH conditions and within the box sizes of 22 × 22 × 44 nm³ and 44 nm³ for 1 μs. CMCs were calculated by performing CG-MD simulations with an increasing number of MCFAs. The resulting aggregate size distribution and number of free MCFA molecules were used to determine the CMC. The CMCs from simulations for C₈, C₁₀, and C₁₂ were 1.8–3.5-fold lower than the respective CMCs determined experimentally by the Wilhelmy method. However, the variation of MCFA aggregate sizes and morphologies at different pH conditions is consistent with previous experimental observation. Overall, this study suggests that CG-MD is suitable for studying colloidal systems including various MCFAs.

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.

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

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

Reservoir pH replica exchange

We present the reservoir pH replica exchange (R-pH-REM) method for constant pH simulations. The R-pH-REM method consists of a two-step procedure; the first step involves generation of one or more reservoirs of conformations. Each reservoir is obtained from a standard or enhanced molecular dynamics simulation with a constrained (fixed) protonation state. In the second step, fixed charge constraints are relaxed, as the structures from one or more reservoirs are periodically injected into a constant pH or a pH-replica exchange (pH-REM) simulation. The benefit of this two-step process is that the computationally intensive part of conformational search can be decoupled from constant pH simulations, and various techniques for enhanced conformational sampling can be applied without the need to integrate such techniques into the pH-REM framework. Simulations on blocked Lys, KK, and KAAE peptides were used to demonstrate an agreement between pH-REM and R-pH-REM simulations. While the reservoir simulations are not needed for these small test systems, the real need arises in cases when ionizable molecules can sample two or more conformations separated by a large energy barrier, such that adequate sampling is not achieved on a time scale of standard constant pH simulations. Such problems might be encountered in protein systems that exploit conformational transitions for function. A hypothetical case is studied, a small molecule with a large torsional barrier; while results of pH-REM simulations depend on the starting structure, R-pH-REM calculations on this model system are in excellent agreement with a theoretical model.

Membrane-Induced p Ka Shifts in wt-pHLIP and Its L16H Variant

The pH (low) insertion peptides (pHLIPs) is a family of peptides that are able to insert into a lipid bilayer at acidic pH. The molecular mechanism of pHLIPs insertion, folding, and stability in the membrane at low pH is based on multiple protonation events, which are challenging to study at the molecular level. More specifically, the relation between the experimental p K of insertion (p K^exp) of pHLIPs and the p K_a of the key residues is yet to be clarified. We carried out a computational study, complemented with new experimental data, and established the influence of (de)protonation of titrable residues on the stability of the peptide membrane-inserted state. Constant-pH molecular dynamics simulations were employed to calculate the p K_a values of these residues along the membrane normal. In the wt-pHLIP, we identified Asp14 as the key residue for the stability of the membrane-inserted state, and its p K_a value is strongly correlated with the experimental p K^exp measured in thermodynamics studies. Also, in order to narrow down the pH range at which pHLIP is stable in the membrane, we designed a new pHLIP variant, L16H, where Leu in the 16th position was replaced by a titrable His residue. Our results showed that the L16H variant undergoes two transitions. The calculated p K_a and experimentally observed p K^exp values are in good agreement. Two distinct p K^exp values delimit a pH range where the L16H peptide is stably inserted in the membrane, while, outside this range, the membrane-inserted state is destabilized and the peptide exits from the bilayer. pHLIP peptides have been successfully used to target cancer cells for the delivery of diagnostics and therapeutic agents to acidic tumors. The fine-tuning of the stability of the pHLIP inserted state and its restriction to a narrow well-defined pH range might allow the design of new peptides, able to discriminate between tissues with different extracellular pH values.

Micelle Formation in Alkyl Sulfate Surfactants Using Dissipative Particle Dynamics

We use dissipative particle dynamics (DPD) to study micelle formation in alkyl sulfate surfactants, with alkyl chain lengths ranging from 6 to 12 carbon atoms. We extend our recent DPD force field [ J. Chem. Phys. 2017 , 147 , 094503 ] to include a charged sulfate chemical group and aqueous sodium ions. With this model, we achieve good agreement with the experimentally reported critical micelle concentrations (CMCs) and can match the trend in mean aggregation numbers versus alkyl chain length. We determine the CMC by fitting a charged pseudophase model to the dependence of the free surfactant on the total surfactant concentration above the CMC and compare it with a direct operational definition of the CMC as the point at which half of the surfactant is classed as micellar and half as monomers and submicellar aggregates. We find that the latter provides the best agreement with experimental results. Finally, with the same model, we are able to observe the sphere-to-rod morphological transition for sodium dodecyl sulfate (SDS) micelles and determine that it corresponds to SDS concentrations in the region of 300-500 mM.

Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers

Electrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer (J. Chem. Theory Comput. 2014,10, 5483-5492). In this work, we investigate how two limit approaches to the ionic strength treatment (implicitly with GRF or using full system neutralization with either GRF or PME) can influence the conformational space of the second-generation PAMAM dendrimer. Constant-pH MD simulations were used to map PAMAM's conformational space at its full pH range (from 2.5 to 12.5). Our simulations clearly captured the coupling between protonation and conformation in PAMAM. Interestingly, the dendrimer conformational distribution was almost independent of the ionic strength treatment methods, which is in contrast to what we have observed in charged lipid bilayers. Overall, our results confirm that both GRF with implicit ionic strength and a fully neutralized system with PME are valid approaches to model charged globular systems, using the GROMOS 54A7 force field.

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.

Biological fate of food nanoemulsions and the nutrients they carry – internalisation, transport and cytotoxicity of edible nanoemulsions in Caco-2 intestinal cells

Internalisation of edible food nanoemulsions by CaCo-2 intestinal cells. The structure of edible nanoemulsions increases five times upon incorporation of reactive/ROS producing nutrients/APIs.

Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

Coarse-grained molecular simulations reveal the influence of pH and flow on the self-assembly of DFAG-OPV3-GAFD optoelectronic peptides.

Inhibition of TRPV1 channels by a naturally occurring omega-9 fatty acid reduces pain and itch

The transient receptor potential vanilloid 1 (TRPV1) ion channel is mainly found in primary nociceptive afferents whose activity has been linked to pathophysiological conditions including pain, itch and inflammation. Consequently, it is important to identify naturally occurring antagonists of this channel. Here we show that a naturally occurring monounsaturated fatty acid, oleic acid, inhibits TRPV1 activity, and also pain and itch responses in mice by interacting with the vanilloid (capsaicin)-binding pocket and promoting the stabilization of a closed state conformation. Moreover, we report an itch-inducing molecule, cyclic phosphatidic acid, that activates TRPV1 and whose pruritic activity, as well as that of histamine, occurs through the activation of this ion channel. These findings provide insights into the molecular basis of oleic acid inhibition of TRPV1 and also into a way of reducing the pathophysiological effects resulting from its activation.

TRPV1 channels are known to mediate pathological pain and itch. Here, the authors find a naturally occurring fatty acid, oleic acid, acts as a TRPV1 antagonist and can modulate capsaicin and histamine-mediated pain and itch response in mouse models.

Oleic acid phase behavior from molecular dynamics simulations

Fatty acid aggregation is important for a number of diverse applications: from origins of life research to industrial applications to health and disease. Experiments have characterized the phase behavior of oleic acid mixtures, but the molecular details are complex and hard to probe with many experiments. Coarse-grained molecular dynamics computer simulations and free energy calculations are used to model oleic acid aggregation. From random dispersions, we observe the aggregation of oleic acid monomers into micelles, vesicles, and oil phases, depending on the protonation state of the oleic acid head groups. Worm-like micelles are observed when all the oleic acid molecules are deprotonated and negatively charged. Vesicles form spontaneously if significant amounts of both neutral and negative oleic acid are present. Oil phases form when all the fatty acids are protonated and neutral. This behavior qualitatively matches experimental observations of oleic acid aggregation. To explain the observed phase behavior, we use umbrella sampling free energy calculations to determine the stability of individual monomers in aggregates compared to water. We find that both neutral and negative oleic acid molecules prefer larger aggregates, but neutral monomers prefer negatively charged aggregates and negative monomers prefer neutral aggregates. Both neutral and negative monomers are most stable in a DOPC bilayer, with implications on fatty acid adsorption and cellular membrane evolution. Although the CG model qualitatively reproduces oleic acid phase behavior, we show that an updated polarizable water model is needed to more accurately predict the shift in pKa for oleic acid in model bilayers.

The importance of membrane defects-lessons from simulations

The defects and pores within lipid membranes are scientifically interesting and have a number of biological applications. Although lipid bilayers are extremely thin hydrophobic barriers, just ∼3 nm thick, they include diverse chemistry and have complex structures. Bilayers are soft and dynamic, and as a result, they can bend and deform in response to different stimuli by means of structural changes in their component lipids. Though defects occur within these structures, their transience and small size have made it difficult to characterize them. However, with recent advances in computer power and computational modeling techniques, researchers can now use simulations as a powerful tool to probe the mechanism and energies of defect and pore formation in a number of situations. In this Account, we present results from our detailed molecular dynamics computer simulations of hydrophilic pores and related defects in lipid bilayers at an atomistic level. Electroporation can be used to increase the permeability of cellular membranes, with potential therapeutic applications. Atomistic simulations of electroporation have illustrated the molecular details of this process, including the importance of water dipole interactions at the water-membrane interface. Characterization of the lipid-protein interactions provides an important tool for understanding transmembrane protein structure and thermodynamic stability. Atomistic simulations give a detailed picture of the free energies of model peptides and side chains in lipid membranes; the energetic cost of defect formation strongly influences the energies of interactions between lipids and polar and charged residues. Many antimicrobial peptides form hydrophilic pores in lipid membranes, killing bacteria or cancer cells. On the basis of simulation data, at least some of these peptides form defects and pores near the center of the bilayer, with a common disordered structure where hydrated headgroups form an approximately toroidal shape. The localization and trafficking of lipids supports general membrane structure and a number of important signaling cascades, such as those involving ceramide, diacylglycerol, and cholesterol. Atomistic simulations have determined the rates and free energies of lipid flip-flop. During the flip-flop of most phosphatidylcholine lipids, a hydrophilic pore forms when the headgroup moves near the center of the bilayer. Simulations have provided novel insight into many features of defects and pores in lipid membranes. Simulation data from very different systems and models show how water penetration and defect formation can determine the free energies of many membrane processes. Bilayers can deform and allow transient defects and pores when exposed to a diverse range of stimuli. Future work will explore many aspects of membrane defects with increased resolution and scope, including the study of more complex lipid mixtures, membrane domains, and large-scale membrane remodeling. Such studies will examine processes including vesicle budding and fusion, non-bilayer lipid phases, and interactions between lipid bilayers and other biomolecules. Simulations provide information that complements experimental studies, allowing microscopic insight into experimental observations and suggesting novel hypotheses and experiments. These studies should enable a deeper understanding of the role of lipid bilayers in cellular biology and support the development of future lipid-based biotechnology.