Enhanced Adsorption Response of pH-Sensitive Peptides: The Role of Membrane Acidity.

pH-sensitive peptides bind and traverse lipid membranes in response to changes in pH. They can be used to target tumors and other acidic tissues. We investigate the influence of acidic lipids on the pH-driven adsorption of recently synthesized peptides. Using a statistical-thermodynamic theory that takes into account the acid-base chemistry of peptides and lipids, we find that the presence of acidic lipids amplifies changes in peptide surface concentration when transitioning from high to low pH. We study cyclic and linear peptides, containing tryptophan, glutamic acid, and arginine residues, examining their behavior in both neutral and acidic membranes. Membrane binding consistently results from the shallow insertion of tryptophan residues with hydrophilic residues facing the aqueous solution. Regardless of the pH, the peptide's geometry predominantly determines the orientation and distribution of residues. Notably, we find that not only the extent of adsorption is pH-sensitive but also the underlying adsorption mechanism: it is barrier-free at low pH but hindered by a large free energy barrier at high pH. Hence, under more acidic conditions, pH-sensitive peptides show facilitated adsorption both kinetically and thermodynamically.

Membrane Binding Strength vs Pore Formation Cost─What Drives the Membrane Permeation of Nanoparticles Coated with Cell-Penetrating Peptides?

Cell-penetrating peptides (CPPs) enable the transport of nanoparticles through cell membranes. Using molecular simulations, we conduct an in-depth investigation into the thermodynamic forces governing the passive translocation of CPP-coated nanoparticles across lipid bilayers, contrasting their behavior with that of bare particles to dissect the contribution of the peptides. Our analysis unveils a distinctive two-stage translocation mechanism, where the adsorption energy of the particles overcomes the cost of forming a hydrophilic transmembrane pore. Proper evaluation of the translocation mechanisms is only possible when using two reaction coordinates, in particular, one that explicitly includes the density of the lipids on the binding site of the particle. An analysis of adsorption and activation free energies in terms of a simple kinetic model provides a clearer understanding of the CPP effect. Experimental validation using nonendocytic cells confirms the superior membrane permeation of CPP-coated particles. Our findings have implications for the rational design of more efficient cell-permeating particles.

Voltage-Induced Adsorption of Cationic Nanoparticles on Lipid Membranes.

We evaluate the effects of an applied electric potential on the adsorption/desorption mechanism of cationic nanoparticles on lipid membranes. By applying a molecular theory that allows calculating nanoparticle adsorption isotherms and free-energy profiles, we identify the conditions under which the external voltage promotes the adsorption of nanoparticles coated with cell penetrating peptides. We consider symmetric and asymmetric membranes made of neutral and acidic lipids and cover a wide range of environmental conditions (external voltage, pH, salt, and nanoparticles concentration) relevant to both electrochemical experiments and biological systems. For neutral membranes at low concentration of salt, a moderate external voltage (<100 mV) induces spontaneous adsorption of nanoparticles. For membranes containing a small fraction of anionic lipids, the external potential has little effect on the interfacial concentration of nanoparticles, and the membrane surface charge dominates the adsorption behavior. In all cases, the membrane-particle effective interactions, and its dependence on the external bias, are strongly modulated by the concentration of salt. At 100 mM NaCl, the external potential has almost no effect on the adsorption free energy profiles. In general, we provide a theoretical framework to evaluate the conditions under which nanoparticles are thermodynamically adsorbed or kinetically restrained to the vicinity of the membrane, and to assess the impact of the nanoparticles on the interfacial electrostatic properties.

Noria and its derivatives as hosts for chemically and thermally robust Type II porous liquids.

Porous Liquids (PLs) are a new class of material that possess both fluidity and permanent porosity. As such they can act as enhanced, selective solvents and may ultimately find applications which are not possible for porous solids, such as continuous flow separation processes. Type II PLs consist of empty molecular hosts dissolved in size-excluded solvents and to date have mainly been based on hosts that have limited chemical and thermal stability. Here we identify Noria, a rigid cyclic oligomer as a new host for the synthesis of more robust Type II PLs. Although the structure of Noria is well-documented, we find that literature has overlooked the true composition of bulk Noria samples. We find that bulk samples typically consist of Noria (ca. 40%), a Noria isomer, specifically a resorcinarene trimer, "R3" (ca. 30%) and other unidentified oligomers (ca. 30%). Noria has been characterised crystallographically as a diethyl ether solvate and its 1H NMR spectrum fully assigned for the first time. The previously postulated but unreported R3 has also been characterised crystallographically as a dimethyl sulfoxide solvate, which confirms its alternative connectivity to Noria. Noria and R3 have low solubility which precludes their use in Type II PLs, however, the partially ethylated derivative Noria-OEt dissolves in the size-excluded solvent 15-crown-5 to give a new Type II PL. This PL exhibits enhanced uptake of methane (CH4) gas supporting the presence of empty pores in the liquid. Detailed molecular dynamics simulations support the existence of pores in the liquid and show that occupation of the pores by CH4 is favoured. Overall, this work revises the general accepted composition of bulk Noria samples and shows that Noria derivatives are appropriate for the synthesis of more robust Type II PLs.

Nanoparticles modified with cell penetrating peptides: Assessing adsorption on membranes containing acidic lipids.

Cell-penetrating peptides (CPP) are poly-cationic molecules that facilitate the cellular uptake of nano-sized cargoes. Accumulation of the cargoes on the cell surface regulates the cargoes internalization rate and constitutes a critical step prior membrane crossing. In this work, we characterize the adsorption of nanoparticles coated with CPP on membranes containing acidic lipids. We describe how the particle-membrane interactions and the extent of adsorption, depend on the size of the particles, the number of grafted CPP molecules, and the composition of the solution in contact with the membrane. Our results are obtained by applying a molecular theory that takes into account electrostatic and steric interactions, entropic effects, and the acid-base equilibrium of all titratable molecules. It also takes into account the shape, protonation state, charge distribution and conformational flexibility of the peptide-grafted particles. Adsorption free energy profiles allow to quantify the adsorption energy, and reveal that nanoparticles attachment and detachment from the membrane surface are restrained by free energy barriers. At physiological pH, the surface binding of the nanoparticles is ultimately driven by the deprotonation of acidic lipids; the adsorption free energy is more sensitive to the concentration of salt or particles in solution than to the number of grafted CPP molecules. At variance, the height of the adsorption/desorption barriers increases with the CPP load. Our results indicate that electrostatic interactions, modulated by entropic effects, provide the driving force and regulate the adsorption kinetics of CPP-coated particles on acidic membranes.

Surface charge density and fatty acids enhance the membrane permeation rate of CPP-cargo complexes.

The CPP-effect makes reference to the process by which the membrane translocation rate of a cargo is enhanced by chemical functionalization with cell-penetrating peptides (CPPs). In this work we combine a simple kinetic model with free-energy calculations to explore the energetic basis of the CPP-effect. Two polyglicines are selected as model hydrophilic cargoes, and nona-arginine as a prototypical CPP. We assess the cargo carrying efficiency of nona-arginine by comparing the adsorption and insertion energies of the cargoes, the cargo-free CPPs, and the CPP-cargo complexes, into lipid membranes of varying composition. We also analyze the effect of modifying the type and concentration of anionic lipids, and the implication of these factors on the translocation rate of the CPP-cargo complex. Of particular interest is the evaluation of the catalytic role of palmitic acid (palmitate) as a promoter of the CPP-effect. We also analyse the influence of the size of the cargo on the membrane adsorption and insertion energies. Our results show that the efficiency of nona-arginine as a transmembrane carrier of simple hydrophilic molecules is modulated by the size of the cargo, and is strongly enhanced by increasing the concentration of anionic lipids and of ionized fatty acids in the membrane.

Thermodynamics of cell penetrating peptides on lipid membranes: sequence and membrane acidity regulate surface binding.

Cell-penetrating peptides (CPPs) are molecules that traverse cell membranes and facilitate the cellular uptake of nano-sized cargoes. In this work we characterize the adsorption of amphipathic and purely cationic CPPs on membranes containing acidic lipids. We describe how the peptide primary sequence, the location of amino-acids within the sequence, the membrane composition, and the pH of the environment, determine both the surface concentration of the peptides and the molecular organization of the interface. Our results are obtained by applying a molecular theory that takes into account the size, shape, protonation state, charge distribution and conformational flexibility of the peptides, as well as the acid-base chemistry of the lipids. We find that peptide adsorption and binding free energy result from a balance between electrostatic and van der Waals interactions, and between chemical and entropic effective forces. We observe that, within a range of physiologically relevant parameters, acidic lipids respond to pH in ways that fully promote or deplete the surface accumulation of CPPs. Membrane acidity emerges thus as a crucial parameter to consider when designing CPP-based cargo-delivery vehicles.

Interaction of a Polyarginine Peptide with Membranes of Different Mechanical Properties.

The membrane translocation efficiency of cell penetrating peptides (CPPs) has been largely studied, and poly-arginines have been highlighted as particularly active CPPs, especially upon negatively charged membranes. Here we inquire about the influence of membrane mechanical properties in poly-arginine adsorption, penetration and translocation, as well as the subsequent effect on the host membrane. For this, we selected anionic membranes exhibiting different rigidity and fluidity, and exposed them to the nona-arginine KR9C. Three different membrane compositions were investigated, all of them having 50% of the anionic lipid 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DOPG), thus, ensuring a high affinity of the peptide for membrane surfaces. The remaining 50% was a saturated PC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC), an unsaturated PC (1,2-dioleoyl-sn-glycero-3-phosphocholine, DOPC) or a mixture of DOPC with cholesterol. Peptide-membrane interactions were studied using four complementary models for membranes: Langmuir monolayers, Large Unilamellar Vesicles, Black Lipid Membranes and Giant Unilamellar Vesicles. The patterns of interaction of KR9C varied within the different membrane compositions. The peptide strongly adsorbed on membranes with cholesterol, but did not incorporate or translocate them. KR9C stabilized phase segregation in DPPC/DOPG films and promoted vesicle rupture. DOPC/DOPG appeared like the better host for peptide translocation: KR9C adsorbed, inserted and translocated these membranes without breaking them, despite softening was observed.

Hopanoids Like Sterols Form Compact but Fluid Films.

Hopanoids are pentacyclic molecules present in membranes from some bacteria, recently proposed as sterol surrogates in these organisms. Diplopterol is an abundant hopanoid that, similar to sterols, does not self-aggregate in lamellar structures when pure, but forms monolayers at the air-water interface. Here, we analyze the interfacial behavior of pure diplopterol and compare it with sterols from different organisms: cholesterol from mammals, ergosterol from fungi, and stigmasterol from plants. We prepared Langmuir monolayers of the compounds and studied their surface properties using different experimental approaches and molecular dynamics simulations. Our results indicate that the films formed by diplopterol, despite being compact with low mean molecular areas, high surface potentials, and high refractive index, depict shear viscosity values similar to that for fluid films. Altogether, our results reveal that hopanoids have similar interfacial behavior than that of sterols, and thus they may have the capacity of modulating bacterial membrane properties in a similar way sterols do in eukaryotes.

Adsorption and insertion of polyarginine peptides into membrane pores: The trade-off between electrostatics, acid-base chemistry and pore formation energy.

The mechanism that arginine-rich cell penetrating peptides (ARCPPs) use to translocate lipid membranes is not entirely understood. In the present work, we develop a molecular theory that allows to investigate the adsorption and insertion of ARCPPs on membranes bearing hydrophilic pores. This method accounts for size, shape, conformation, protonation state and charge distribution of the peptides; it also describes the state of protonation of acidic membrane lipids. We present a systematic investigation of the effect of pore size, peptide concentration and sequence length on the extent of peptide adsorption and insertion into the pores. We show that adsorption on the intact (non-porated) lipid membrane plays a key role on peptide translocation. For peptides shorter than nona-arginine, adsorption on the intact membrane increases significantly with chain length, but it saturates for longer peptides. However, this adsorption behavior only occurs at relatively low peptide concentrations; increasing peptide concentration favors adsorption of the shorter molecules. Adsorption of longer peptides increases the intact membrane negative charge as a result of further deprotonation of acidic lipids. Peptide insertion into the pores depends non-monotonically on pore radius, which reflects the short range nature of the effective membrane-peptide interactions. The size of the pore that promotes maximum adsorption depends on the peptide chain length. Peptide translocation is a thermally activated process, so we complement our thermodynamic approach with a simple kinetic model that allows to rationalize the ARCPPs translocation rate in terms of the free energy gain of adsorption, and the energy cost of creating a transmembrane pore with peptides in it. Our results indicate that strategies to improve translocation efficiency should focus on enhancing peptide adsorption.

Insights into mechanochemical reactions at the molecular level: simulated indentations of aspirin and meloxicam crystals.

Although solvent-free mechanochemical synthesis continues to gain ever greater importance, the molecular scale processes that occur during such reactions remain largely uncharacterised. Here, we apply computational modelling to indentations between particles of crystals of aspirin and meloxicam under a variety of conditions to mimic the early stages of their mechanochemical cocrystallisation reaction. The study also extends to the effects of the presence of small amounts of solvent. It is found that, despite the solid crystalline nature of the reactants and the presence of little or no solvent, mixing occurs readily at the molecular level even during relatively low-energy collisions. When indented crystals are subsequently drawn apart, a connective neck formed by a mixture of the reactant molecules is observed, suggesting plastic-like behaviour of the reacting materials. Overall the work reveals some striking new insights including (i) relatively facile mixing of crystals under solvent-free conditions, (ii) no appreciable local temperature increases, (iii) localised amorphisation at the contact region and neck of the reacting crystals, and (iv) small amounts of solvent have relatively little effect during this early stage of the reaction, suggesting that their accelerating effect on the reaction may be exerted at later stages.

Mechanisms of Iodide⁻Triiodide Exchange Reactions in Ionic Liquids: A Reactive Molecular-Dynamics Exploration.

Efficient charge transport has been observed in iodine-doped, iodide-based room-temperature ionic liquids, yielding high ionic conductivity. To elucidate preferred mechanistic pathways for the iodide ( I - )-to-triiodide ( I 3 - ) exchange reactions, we have performed 10 ns reactive molecular-dynamics calculations in the liquid state for 1-butyl-3-methylimidazolium iodide ([BMIM][I]) at 450 to 750 K. Energy-barrier distributions for the iodine-swapping process were determined as a function of temperature, employing a charge-reassignment scheme drawn in part from electronic-structure calculations. Bond-exchange events were observed with rate-determining energy barriers ranging from ~0.19 to 0.23 ± 0.06 eV at 750 and 450 K, respectively, with an approximately Arrhenius temperature dependence for iodine self-diffusivity and reaction kinetics, although diffusion dominates/limits the bond-exchange events. This charge transfer is not dissimilar in energetics to those in solid-state superionic conductors.

Elucidating mysteries of phase-segregated membranes: mobile-lipid recruitment facilitates pores' passage to the fluid phase.

Phase segregation of multicomponent lipid bilayers leads to, under phase-coexistence conditions, domain formation, featuring delimitation by essentially one-dimensional borders. (Micro-)phase segregation of bilayers is proposed to influence the physiological behaviour of cell membranes and provides the driving force for lipid-raft formation. Experiments show a maximum in the electrical-conductivity of membranes at the phase-transition point, which has been conjectured to arise from border-nucleated transmembrane-conducting defects or pores. However, recent electroporation experiments on phase-segregated bilayers demonstrate electro-pore detection in the liquid disordered phase (Ld), wherein they diffuse over macroscopic periods without absorption into the liquid ordered phase (Lo). Here, we scrutinise transmembrane-pore formation via molecular dynamics simulations on a multicomponent phase-segregated bilayer. We find that pores created in Lo domains always migrate spontaneously to the Ld phase, via 'recruitment' of unsaturated lipids to the pore's rim to transport the pore to the fluid phase under a large stress-field driving force. Once in Ld domains, pores migrate towards their centre, never returning or pinning to Lo. These findings are explained by thermodynamics. By comparing the free-energy cost for creating pores in the bulk of Ld and Lo membranes, and in the phase-segregated system, we show that it is always more energetically tractable to create pores in Ld domains, independent of the pore size.

Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes.

A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of the binding mechanism that is performed using the coordinate demonstrates that the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.

Negative Dipole Potentials and Carboxylic Polar Head Groups Foster the Insertion of Cell-Penetrating Peptides into Lipid Monolayers.

Cell-penetrating peptides (CPPs) are polycationic sequences of amino acids recognized as some of the most effective vehicles for delivering membrane-impermeable cargos into cells. CPPs can traverse cell membranes by direct translocation, and assessing the role of lipids on the membrane permeation process is important to convene a complete model of the CPP translocation. In this work, we focus on the biophysical basis of peptide-fatty acid interactions, analyzing how the acid-base and electrostatic properties of the lipids determine the CPP adsorption and incorporation into a Langmuir monolayer, focusing thus on the first two stages of the direct translocation mechanism. We sense the binding and insertion of the peptide into the lipid structure by measuring the changes in the surface pressure, the surface potential, and the reflectivity of the interface. We show that, beyond the presence of anionic moieties, negative dipole potentials and carboxylic polar head groups significantly promote the insertion of the peptide into the monolayer. On the basis of our results, we propose the appearance of stable CPP-lipid complexes whose kinetics of formation depends on the length of the lipids' hydrocarbon chains.

On the Mechanism of the Iodide-Triiodide Exchange Reaction in a Solid-State Ionic Liquid.

Efficient charge transport has been observed in iodide-based room-temperature ionic liquids when doped with iodine. To investigate preferred pathways for the iodide (I-)-to-triiodide (I3-) exchange reaction and to clarify the origin of this high ionic conductivity, we have conducted electronic structure calculations in the crystal state of 1-butyl-3-methylimidazolium iodide ([BMIM][I]). Energy barriers for the different stages of the iodine-swapping process, including the reorientation of the I-···I3- moiety, were determined from minimum energy paths as a function of a reaction coordinate. Hirshfeld charges and structural parameters, such as bond lengths and angles, were monitored during the reaction. Several bond-exchange events were observed with energy barriers ranging from 0.17 to 0.48 eV and coinciding with the formation of a twisted I-···I3- complex. Striking similarities were observed in the mechanics and energetics of this charge-transfer process in relation to solid-state superionic conductors.

Molecular Explanation for the Abnormal Flux of Material into a Hot Spot in Ester Monolayers.

Langmuir monolayers of certain surfactants show a negative derivative of the surface pressure with respect to temperature. In these monolayers, a local temperature gradient leads to local yielding of the solid phase to a kinetically flowing liquid, so that the material flows toward the hotter regions that act as sinks. The accumulation of material leads to the formation of nonequilibrium multilamellar bubbles of different sizes. Here we investigate the molecular factors leading to such a peculiar behavior. First, we identify the required structural molecular moieties, and second we vary the composition of the subphase in order to analyze its influence. We conclude that esters appear to be unique in two key aspects: they form monolayers whose compression isotherms shift to lower areas as the temperature increases, and thus collapse into a hot spot; and they bind weakly to the aqueous subphase, i.e., water does not attach to the monolayer at the molecular level, but only supports it. Molecular simulations for a selected system confirm and help explain the observed behavior: surfactant molecules form a weak hydrogen bonding network, which is disrupted upon heating, and also the molecular tilting changes with temperature, leading to changes in the film density.

Liquids with permanent porosity.

Porous solids such as zeolites and metal-organic frameworks are useful in molecular separation and in catalysis, but their solid nature can impose limitations. For example, liquid solvents, rather than porous solids, are the most mature technology for post-combustion capture of carbon dioxide because liquid circulation systems are more easily retrofitted to existing plants. Solid porous adsorbents offer major benefits, such as lower energy penalties in adsorption-desorption cycles, but they are difficult to implement in conventional flow processes. Materials that combine the properties of fluidity and permanent porosity could therefore offer technological advantages, but permanent porosity is not associated with conventional liquids. Here we report free-flowing liquids whose bulk properties are determined by their permanent porosity. To achieve this, we designed cage molecules that provide a well-defined pore space and that are highly soluble in solvents whose molecules are too large to enter the pores. The concentration of unoccupied cages can thus be around 500 times greater than in other molecular solutions that contain cavities, resulting in a marked change in bulk properties, such as an eightfold increase in the solubility of methane gas. Our results provide the basis for development of a new class of functional porous materials for chemical processes, and we present a one-step, multigram scale-up route for highly soluble 'scrambled' porous cages prepared from a mixture of commercially available reagents. The unifying design principle for these materials is the avoidance of functional groups that can penetrate into the molecular cage cavities.

Designing and understanding permanent microporosity in liquids.

Standard microporous materials are typically crystalline solids that exhibit a regular array of cavities of uniform size and shape. Packing and directional bonding between molecular building blocks give rise to interstitial pores that confer size and shape-specific sorption properties to the material. In the liquid state interstitial cavities are transient. However, permanent and intrinsic "pores" can potentially be built into the structure of the molecules that constitute the liquid. With the aid of computer simulations we have designed, synthesised and characterised a series of liquids composed of hollow cage-like molecules, which are functionalised with hydrocarbon chains to make them liquid at accessible temperatures. Experiments and simulations demonstrate that chain length and size of terminal chain substituents can be used to tune, within certain margins, the permanence of intramolecular cavities in such neat liquids. Simulations identify a candidate "porous liquid" in which 30% of the cages remain empty in the liquid state. Absorbed methane molecules selectively occupy these empty cavities.

H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552.

In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase-cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase-cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent. Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein-protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein-ligand systems.