PIP2 Is An Electrostatic Catalyst for Vesicle Fusion by Lowering the Hydration Energy: Arresting Vesicle Fusion by Masking PIP2.

Lipids are key factors in regulating membrane fusion. Lipids are not only structural components to form membranes but also active catalysts for vesicle fusion and neurotransmitter release, which are driven by soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. SNARE proteins seem to be partially assembled before fusion, but the mechanisms that arrest vesicle fusion before Ca2+ influx are still not clear. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2) electrostatically triggers vesicle fusion as an electrostatic catalyst by lowering the hydration energy and that a myristoylated alanine-rich C-kinase substrate (MARCKS), a PIP2-binding protein, arrests vesicle fusion in a vesicle docking state where the SNARE complex is partially assembled. Vesicle-mimicking liposomes fail to reproduce vesicle fusion arrest by masking PIP2, indicating that native vesicles are essential for the reconstitution of physiological vesicle fusion. PIP2 attracts cations to repel water molecules from membranes, thus lowering the hydration energy barrier.

Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer.

Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.

Lanthanide transport in angstrom-scale MoS2-based two-dimensional channels.

Rare earth elements (REEs), critical to modern industry, are difficult to separate and purify, given their similar physicochemical properties originating from the lanthanide contraction. Here, we systematically study the transport of lanthanide ions (Ln3+) in artificially confined angstrom-scale two-dimensional channels using MoS2-based building blocks in an aqueous environment. The results show that the uptake and permeability of Ln3+ assume a well-defined volcano shape peaked at Sm3+. This transport behavior is rooted from the tradeoff between the barrier for dehydration and the strength of interactions of lanthanide ions in the confinement channels, reminiscent of the Sabatier principle. Molecular dynamics simulations reveal that Sm3+, with moderate hydration free energy and intermediate affinity for channel interaction, exhibit the smallest dehydration degree, consequently resulting in the highest permeability. Our work not only highlights the distinct mass transport properties under extreme confinement but also demonstrates the potential of dialing confinement dimension and chemistry for greener REEs separation.

Anomalously enhanced ion transport and uptake in functionalized angstrom-scale two-dimensional channels.

Emulating angstrom-scale dynamics of the highly selective biological ion channels is a challenging task. Recent work on angstrom-scale artificial channels has expanded our understanding of ion transport and uptake mechanisms under confinement. However, the role of chemical environment in such channels is still not well understood. Here, we report the anomalously enhanced transport and uptake of ions under confined MoS2-based channels that are ~five angstroms in size. The ion uptake preference in the MoS2-based channels can be changed by the selection of surface functional groups and ion uptake sequence due to the interplay between kinetic and thermodynamic factors that depend on whether the ions are mixed or not prior to uptake. Our work offers a holistic picture of ion transport in 2D confinement and highlights ion interplay in this regime.

Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State.

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.

Antibacterial Mechanism of Multifunctional MXene Nanosheets: Domain Formation and Phase Transition in Lipid Bilayer.

MXenes, two-dimensional metal carbides or nitrides with multifunctional surfaces, are one of the most promising antibacterial nanoscale materials. However, their putative bactericidal mechanism is elusive. To study their bactericidal mechanism, we investigated the interaction between a MXene nanosheet and a model bacterial membrane by molecular dynamics simulations and found that an adsorbed MXene on a membrane surface induced a local phase transition in a domain where the fluidity of the phospholipid in this domain at room temperature was comparable with that of the gel phase. The domain also showed a denser and thinner phospholipid membrane structure than the peripheral phospholipids. By comparing it with our previous experiments of the bactericidal activity of MXenes, we proposed the leakage of intercellular molecules at the phase boundary defects as a possible bactericidal mechanism of MXenes that leads to cell lysis. This study provides a useful model for tailoring new bactericidal nanomaterials.

Supramolecular Peptide Hydrogel-Based Soft Neural Interface Augments Brain Signals through a Three-Dimensional Electrical Network.

Recording neural activity from the living brain is of great interest in neuroscience for interpreting cognitive processing or neurological disorders. Despite recent advances in neural technologies, development of a soft neural interface that integrates with neural tissues, increases recording sensitivity, and prevents signal dissipation still remains a major challenge. Here, we introduce a biocompatible, conductive, and biostable neural interface, a supramolecular ß-peptide-based hydrogel that allows signal amplification via tight neural/hydrogel contact without neuroinflammation. The non-biodegradable ß-peptide forms a multihierarchical structure with conductive nanomaterial, creating a three-dimensional electrical network, which can augment brain signal efficiently. By achieving seamless integration in brain tissue with increased contact area and tight neural tissue coupling, the epidural and intracortical neural signals recorded with the hydrogel were augmented, especially in the high frequency range. Overall, our tissuelike chronic neural interface will facilitate a deeper understanding of brain oscillation in broad brain states and further lead to more efficient brain-computer interfaces.

Dynamic Properties of Water Confined in Graphene-Based Membrane: A Classical Molecular Dynamics Simulation Study.

We performed molecular dynamics simulations of water molecules inside a hydrophobic membrane composed of stacked graphene sheets. By decreasing the density of water molecules inside the membrane, we observed that water molecules form a droplet through a hydrogen bond with each other in the hydrophobic environment that stacked graphene sheets create. We found that the water droplet translates as a whole body rather than a dissipate. The translational diffusion coefficient along the graphene surface increases as the number of water molecules in the droplet decreases, because the bigger water droplet has a stronger van der Waals interaction with the graphene surface that hampers the translational motion. We also observed a longer hydrogen bond lifetime as the density of water decreased, because the hydrophobic environment limits the libration motion of the water molecules. We also calculated the reorientational correlation time of the water molecules, and we found that the rotational motion of confined water inside the membrane is anisotropic and the reorientational correlation time of confined water is slower than that of bulk water. In addition, we employed steered molecular dynamics simulations for guiding the target molecule, and measured the free energy profile of water and ion penetration through the interstice between graphene sheets. The free energy profile of penetration revealed that the optimum interlayer distance for desalination is ~10 Å, where the minimum distance for water penetration is 7 Å. With a 7 Å interlayer distance between the graphene sheets, water molecules are stabilized inside the interlayer space because of the van der Waals interaction with the graphene sheets where sodium and chloride ions suffer from a 3-8 kcal/mol energy barrier for penetration. We believe that our simulation results would be a significant contribution for designing a new graphene-based membrane for desalination.

Highly Stable, Ultrasmall Polymer-Grafted Nanobins (usPGNs) with Stimuli-Responsive Capability.

Highly stable and stimuli/pH-responsive ultrasmall polymer-grafted nanobins (usPGNs) have been developed by grafting a small amount (10 mol %) of short (4.3 kDa) cholesterol-terminated poly(acrylic acid) (Chol-PAA) into an ultrasmall unilamellar vesicle (uSUV). The usPGNs are stable against fusion and aggregation over several weeks, exhibiting over 10-fold enhanced cargo retention in biologically relevant media at pH 7.4 in comparison with the parent uSUV template. Coarse-grained molecular dynamics (CGMD) simulations confirm that the presence of the cholesterol moiety can greatly stabilize the lipid bilayer. They also show extended PAA chain conformations that can be interpreted as causing repulsion between colloidal particles, thus stabilizing them against fusion. Notably, CGMD predicted a clustering of the Chol-PAA chains on the lipid bilayer under acidic conditions due to intra- and interchain hydrogen bonding, leading to the destabilization of local membrane areas. This explains the experimental observation that usPGNs can be triggered to release a significant amount of cargo upon acidification to pH 5. These developments put the lipid-bilayer-embedded Chol-PAA in stark contrast with traditional poly(acrylic acid) systems where the molar mass (Mn) of the polymer chains must exceed 16.5 kDa to achieve stimuli-responsive changes in conformation. They also distinguish the small usPGNs from the much-larger polymer-caged nanobin platform where the Chol-PAA chains must be covalently cross-linked to engender stimuli-responsive behaviors.

Nature-Inspired Construction of Two-Dimensionally Self-Assembled Peptide on Pristine Graphene.

Peptide assemblies have received significant attention because of their important role in biology and applications in bionanotechnology. Despite recent efforts to elucidate the principles of peptide self-assembly for developing novel functional devices, peptide self-assembly on two-dimensional nanomaterials has remained challenging. Here, we report nature-inspired two-dimensional peptide self-assembly on pristine graphene via optimization of peptide-peptide and peptide-graphene interactions. Two-dimensional peptide self-assembly was designed based on statistical analyses of >104 protein structures existing in nature and atomistic simulation-based structure predictions. We characterized the structures and surface properties of the self-assembled peptide formed on pristine graphene. Our study provides insights into the formation of peptide assemblies coupled with two-dimensional nanomaterials for further development of nanobiocomposite devices.

Molecular Transport Junctions Created By Self-Contacting Gapped Nanowires.

Molecular transport junctions (MTJs) are important components in molecular electronic devices. However, the synthesis of MTJs remains a significant challenge, as the dimensions of the junction must be tailored for each experiment, based on the molecular lengths. A novel methodology is reported for forming MTJs, taking advantage of capillary and van der Waals forces.

Xe affinities of water-soluble cryptophanes and the role of confined water.

Given their relevance to drug design and chemical sensing, host-guest interactions are of broad interest in molecular science. Natural and synthetic host molecules provide vehicles for understanding selective molecular recognition in aqueous solution. Here, cryptophane-Xe host-guest systems are considered in aqueous media as a model molecular system that also has important applications. 129Xe-cryptophane systems can be used in the creation of biosensors and powerful contrast agents for magnetic resonance imaging applications. Detailed molecular information on the determinants of Xe affinity is difficult to obtain experimentally. Thus, molecular simulation and free energy perturbation methods were applied to estimate the affinities of Xe for six water-soluble cryptophanes. The calculated affinities correlated well with the previously measured experimental values. The simulations provided molecular insight on the differences in affinities and the roles of conformational fluctuations, solvent, and counter ions on Xe binding to these host molecules. Displacement of confined water from the host interior cavity is a key component of the binding equilibrium, and the average number of water molecules within the host cavity is correlated with the free energy of Xe binding to the different cryptophanes. The findings highlight roles for molecular simulation and design in modulating the relative strengths of host-guest and host-solvent interactions.

Molecular dynamics simulations and electronic excited state properties of a self-assembled peptide amphiphile nanofiber with metalloporphyrin arrays.

We have employed molecular dynamics simulations and quantum chemistry methods to study the structures and electronic absorption properties of a novel type of photonic nanowire gel constructed by the self-assembly of peptide amphiphiles (PAs) and the chromophore-(PPIX)Zn molecules. Using molecular dynamics simulations, structures of the self-assembled fiber were determined with atomistic detail, including the distribution of chromophores along the nanofiber and the relative distances and orientations of pairs of chromophores. In addition, quantum chemistry calculations were used to determine the electronic structure and absorption properties of the chromophores in the fiber, so as to assess the capabilities of the nanofiber for photonics applications. The calculations show that the PA nanofiber provides an effective scaffold for the chromophores in which the chromophores form several clusters in which nearest neighbor chromophores are separated by less than 20 Å. The calculations also indicate that the chromophores can be in both the hydrophilic shell and hydrophobic core portions of the fiber. There are only small spectral shifts to the B-band of the porphyrins arising from the inhomogeneous microelectronic environment provided by the fiber. However, there are much stronger electronic interactions between nearby pairs of chromophores, leading to a more significant red shift of the B-band that is similar to what is found in the experiments and to significant excitonic coupling that is seen in circular dichroism spectra. This electronic interaction between chromophores associated with the PA nanofiber structure is crucial to future applications of these fibers for light-harvesting applications.

Cell death versus cell survival instructed by supramolecular cohesion of nanostructures.

Many naturally occurring peptides containing cationic and hydrophobic domains have evolved to interact with mammalian cell membranes and have been incorporated into materials for non-viral gene delivery, cancer therapy or treatment of microbial infections. Their electrostatic attraction to the negatively charged cell surface and hydrophobic interactions with the membrane lipids enable intracellular delivery or cell lysis. Although the effects of hydrophobicity and cationic charge of soluble molecules on the cell membrane are well known, the interactions between materials with these molecular features and cells remain poorly understood. Here we report that varying the cohesive forces within nanofibres of supramolecular materials with nearly identical cationic and hydrophobic structure instruct cell death or cell survival. Weak intermolecular bonds promote cell death through disruption of lipid membranes, while materials reinforced by hydrogen bonds support cell viability. These findings provide new strategies to design biomaterials that interact with the cell membrane.

Origins of the helical wrapping of phenyleneethynylene polymers about single-walled carbon nanotubes.

The highly charged, conjugated polymer poly[p-{2,5-bis(3-propoxysulfonicacidsodiumsalt)}phenylene]ethynylene (PPES) has been shown to wrap single-wall carbon nanotubes (SWNTs), adopting a robust helical superstructure. Surprisingly, PPES adopts a helical rather than a linear conformation when adhered to SWNTs. The complexes formed by PPES and related polymers upon helical wrapping of a SWNT are investigated using atomistic molecular dynamics (MD) simulations in the presence and absence of aqueous solvent. In simulations of the PPES/SWNT system in an aqueous environment, PPES spontaneously takes on a helical conformation. A potential of mean force, ΔA(ξ), is calculated as a function of ξ, the component of the end-to-end vector of the polymer chain projected on the SWNT axis; ξ is a monotonic function of the polymer's helical pitch. ΔA(ξ) provides a means to quantify the relative free energies of helical conformations of the polymer when wrapped about the SWNT. The aqueous system possesses a global minimum in ΔA(ξ) at the experimentally observed value of the helical pitch. The presence of this minimum is associated with preferred side chain conformations, where the side chains adopt conformations that provide van der Waals contact between the tubes and the aliphatic components of the side chains, while exposing the anionic sulfonates for aqueous solvation. The simulations provide a free energy estimate of a 0.2 kcal/mol/monomer preference for the helical over the linear conformation of the PPES/SWNT system in an aqueous environment.

Steered molecular dynamics studies of the potential of mean force for peptide amphiphile self-assembly into cylindrical nanofibers.

Steered molecular dynamics (SMD) simulations were applied to determine the potential of mean force for the self-assembly of peptide amphiphile (PA) nanofibers, specifically considering a single PA adding to a growing cylindrical nanofiber at 310 K. It is found that the free energy, enthalpy, and entropy differences for this assembly process are -67 kcal/mol, -71.5 kcal/ml, and -14.5 cal/(mol K), respectively, and therefore that enthalpy provides the driving force for self-assembly to form a fiber. A pairwise interaction analysis shows that both electrostatic and van der Waals interactions play important roles in the self-assembly process, with the van der Waals interaction being the larger effect. The mechanistic picture that emerges from this work is that as the PA is pulled from the fiber, the interaction evolves through three stages: (1) initially electrostatic interactions between the charged head of the pulled PA and other PAs, and between the pulled PA and solvent are dominant, (2) after the charged head emerges, the rest of the peptide comes out, with both PA-solvent electrostatic interactions and van der Waals interactions being significant, and (3) in the last step, the alkane tail emerges, dominated by van der Waals interactions with either peptide or solvent.

Modeling the self-assembly of peptide amphiphiles into fibers using coarse-grained molecular dynamics.

We have studied the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber starting from a homogeneous mixture of PAs in water using coarse-grained molecular dynamics simulations. Nine independent 16 µs runs all show spontaneous fiber formation in which the PA molecules first form spherical micelles, and then micelles form a three-dimensional network via van der Waals interactions. As the hydrophobic core belonging to the different micelles merge, the three-dimensional network disappears and a fiber having a diameter of ∼80 Å appears. In agreement with atomistic simulation results, water molecules are excluded from the hydrophobic core and penetrate to ∼15 Å away from the axis of fiber. About 66% of the surface of fiber is covered with the IKVAV epitope, and ∼92% of the epitope is exposed to water molecules.

A- to B-form transition in DNA between gold surfaces.

Molecular dynamics simulations have been performed to characterize the conformation of DNA that is present when DNA links gold nanoparticles to form nanoparticle superlattice crystals. To model the DNA-linked gold nanoparticles, four strands of DNA are used to connect two gold surfaces, with a small interstrand separation and high added salt to match experiment. A-form DNA was assumed for the initial conformation, as this form of DNA has a length per base-pair that matches lengths that have been inferred from X-ray measurements. The DNA structure was monitored for 40 ns, and the distributions of the slide and z(p) coordinates were obtained from the simulations. We find that all the double-stranded DNA (ds-DNA) strands transform from A- to B-DNA during the simulations. In addition, single-stranded DNAa (ss-DNAs) that are used to connect the ds-DNA to each surface are found to become adsorbed on the gold surfaces during this process, and the ds-DNAs bend (∼143°) at their junctions with the two gold surfaces to accommodate the observed distance between gold surfaces using B-form DNA. We infer from this that the short length of DNA between the gold surfaces is not due to the presence of A-DNA.

Multiscale Simulation as a Framework for the Enhanced Design of Nanodiamond-Polyethylenimine-based Gene Delivery.

Nanodiamonds (NDs) are emerging carbon platforms with promise as gene/drug delivery vectors for cancer therapy. Specifically, NDs functionalized with the polymer polyethylenimine (PEI) can transfect small interfering RNAs (siRNA) in vitro with high efficiency and low cytotoxicity. Here we present a modeling framework to accurately guide the design of ND-PEI gene platforms and elucidate binding mechanisms between ND, PEI, and siRNA. This is among the first ND simulations to comprehensively account for ND size, charge distribution, surface functionalization, and graphitization. The simulation results are compared with our experimental results both for PEI loading onto NDs and for siRNA (C-myc) loading onto ND-PEI for various mixing ratios. Remarkably, the model is able to predict loading trends and saturation limits for PEI and siRNA, while confirming the essential role of ND surface functionalization in mediating ND-PEI interactions. These results demonstrate that this robust framework can be a powerful tool in ND platform development, with the capacity to realistically treat other nanoparticle systems.

Triggered release of pharmacophores from [Ni(HAsO3)]-loaded polymer-caged nanobin enhances pro-apoptotic activity: a combined experimental and theoretical study.

Nanoscale drug delivery platforms can provide an attractive therapeutic strategy for cancer treatments, as they can substantially reduce the adverse side effects associated with toxic small-molecule anticancer agents. For enhanced therapeutic efficacy to be achieved with such platforms, a tumor-specific drug-release trigger is a critical requirement. This article reports the use of a pH-sensitive polymer network that surrounds a nanoscale liposome core to trigger the release of both encapsulated hydrophilic, membrane-impermeable Ni(II) cations and amphipathic, membrane-permeable As(III) anticancer agents under acidic conditions commonly encountered in hypoxic tumor tissues and late endosomes. Computational modeling studies provide clear evidence that the acid-triggered drug-release mechanism for this polymer-caged nanobin (PCN) platform arises from a pH- and temperature-responsive conformation change of the cross-linked polymer cage. As a result, the simultaneous release of both of the active agents in this multicomponent therapeutic enhances the pro-apoptotic activity of As(III) while diminishing its acute toxicity, potentially reducing the undesirable side effects commonly associated with this free drug. The ability to engender acid-triggered release of drugs co-encapsulated inside a liposomal template makes drug delivery using PCN an attractive strategy for triggered drug release.