Structure and dynamics of model pore insertion into a membrane

Coarse-grained modeling of polystyrene-modified CNTs and their interactions with lipid bilayers

In the present work, we describe Martini3 coarse-grained models of polystyrene and carboxyl-terminated polystyrene functionalized carbon nanotubes (CNTs) and investigate their interactions with lipid bilayers with and without cholesterol (CHOL) using molecular dynamics simulations. By changing the polystyrene chain length and grafting density at the end ring of the CNTs at two different nanotube concentrations, we observe the translocation of nanoparticles as well as changes in the lipid bilayer properties. Our results show that all developed models passively diffuse into the membranes without causing any damage to the membrane integrity, although high concentrations of CNTs induce structural and elastic changes in lipid bilayers. In the presence of CHOL, increasing CNT concentration results in decreased rates of CHOL transmembrane motions. On the other hand, CNTs are prone to lipid and polystyrene blockage, which affects their equilibrated configurations, and tilting behavior within the membranes. Hence, we demonstrate that polystyrene-functionalized CNTs are promising drug-carrier agents. However, polystyrene chain length and grafting density are important factors to consider to enhance the efficiency of drug delivery.

Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery

To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.

Applications of cyclic peptide nanotubes (cPNTs)

Self-assembled cyclic peptide nanotubes (cPNTs) have recently drawn particular attention as one of the most intriguing nanostructures in the field of nanotechnology. Given their unique features including high surface area, increased drug loading, environmental stability, enhanced permeation, and modifiable drug release, these hollow tubular structures can be constructed with cyclic di-, tri-, tetra-, hexa-, octa-, and decapeptides with various amino acid sequences, enantiomers, and functionalized side chains and can be applied for antiviral and antibacterial drugs, drug delivery and gene delivery vectors, organic electronic devices, and ionic or molecular channels. Recent publications have presented promising results regarding the use of cPNTs as drugs or biomedical devices. However, there is an urgent need for the further in vivo nanotoxicity and safety testing of these nanotubes to evaluate their suitability in different fields.

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations

Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T=260, 285, 310, 335 and 360K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared.

Role of metal oxide nanoparticles in histopathological changes observed in the lung of welders

Background

Although major concerns exist regarding the potential consequences of human exposure to nanoparticles (NP), no human toxicological data is currently available. To address this issue, we took welders, who present various adverse respiratory outcomes, as a model population of occupational exposure to NP.

The aim of this study was to evaluate if welding fume-issued NP could be responsible, at least partially, in the lung alterations observed in welders.

Methods

A combination of imaging and material science techniques including ((scanning) transmission electron microscopy ((S)TEM), energy dispersive X-ray (EDX), and X-ray microfluorescence (μXRF)), was used to characterize NP content in lung tissue from 21 welders and 21 matched control patients. Representative NP were synthesized, and their effects on macrophage inflammatory secretome and migration were evaluated, together with the effect of this macrophage inflammatory secretome on human lung primary fibroblasts differentiation.

Results

Welding-related NP (Fe, Mn, Cr oxides essentially) were identified in lung tissue sections from welders, in macrophages present in the alveolar lumen and in fibrous regions. In vitro macrophage exposure to representative NP (Fe₂O₃, Fe₃O₄, MnFe₂O₄ and CrOOH) induced the production of a pro-inflammatory secretome (increased production of CXCL-8, IL-1ß, TNF-α, CCL-2, −3, −4, and to a lesser extent IL-6, CCL-7 and −22), and all but Fe₃O₄ NP induce an increased migration of macrophages (Boyden chamber). There was no effect of NP-exposed macrophage secretome on human primary lung fibroblasts differentiation.

Conclusions

Altogether, the data reported here strongly suggest that welding-related NP could be responsible, at least in part, for the pulmonary inflammation observed in welders. These results provide therefore the first evidence of a link between human exposure to NP and long-term pulmonary effects.

Multiscale molecular dynamics simulations of membrane proteins

The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.

Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class

Aggregation of transmembrane proteins is important for many biological processes, such as protein sorting and cell signaling, and also for in vitro processes such as two-dimensional crystallization. We have used large-scale simulations to study the lateral organization and dynamics of lipid bilayers containing multiple inserted proteins. Using coarse-grained molecular dynamics simulations, we have studied model membranes comprising ∼7000 lipids and 16 identical copies of model cylindrical proteins of either α-helical or β-barrel types. Through variation of the lipid tail length and hence the degree of hydrophobic mismatch, our simulations display levels of protein aggregation ranging from negligible to extensive. The nature and extent of aggregation are shown to be influenced by membrane curvature and the shape or orientation of the protein. Interestingly, a model β-barrel protein aggregates to form one-dimensional strings within the bilayer plane, whereas a model α-helical bundle forms two-dimensional clusters. Overall, it is clear that the nature and extent of membrane protein aggregation is dependent on several aspects of the proteins and lipids, including hydrophobic mismatch, protein class and shape, and membrane curvature.

Modeling the self-assembly of lipids and nanotubes in solution: forming vesicles and bicelles with transmembrane nanotube channels

Via dissipative particle dynamics (DPD), we simulate the self-assembly of end-functionalized, amphiphilic nanotubes and lipids in a hydrophilic solvent. Each nanotube encompasses a hydrophobic stalk and two hydrophilic ends, which are functionalized with end-tethered chains. With a relatively low number of the nanotubes in solution, the components self-assemble into stable lipid-nanotube vesicles. As the number of nanotubes is increased, the system exhibits a vesicle-to-bicelle transition, resulting in stable hybrid bicelle. Moreover, our results reveal that the nanotubes cluster into distinct tripod-like structures within the vesicles and aggregate into a ring-like assembly within the bicelles. For both the vesicles and bicelles, the nanotubes assume trans-membrane orientations, with the tethered hairs extending into the surrounding solution or the encapsulated fluid. Thus, the hairs provide a means of regulating the transport of species through the self-assembled structures. Our findings provide guidelines for creating nanotube clusters with distinctive morphologies that might be difficult to achieve through more conventional means. The results also yield design rules for creating synthetic cell-like objects or microreactors that can exhibit biomimetic functionality.

Interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations

Voltage sensors (VS) domains couple the activation of ion channels/enzymes to changes in membrane voltage. We used molecular dynamics simulations to examine interactions with lipids of several VS homologs. VSs in intact channels in the activated state are exposed to phospholipids, leading to a characteristic local distortion of the lipid bilayer which decreases its thickness by ∼10 Å. This effect is mediated by a conserved hydrophilic stretch in the S4-S5 segment linking the VS and the pore domains, and may favor gating charges crossing the membrane. In cationic lipid bilayers lacking phosphate groups, VSs form fewer contacts with lipid headgroups. The S3-S4 paddle motifs show persistent interactions of individual lipid molecules, influenced by the hairpin loop. In conclusion, our results suggest common interactions with phospholipids for various VS homologs, providing insights into the molecular basis of their stabilization in the membrane and how they are altered by lipid modification.

The energetics of transmembrane helix insertion into a lipid bilayer

Free energy profiles for insertion of a hydrophobic transmembrane protein α-helix (M2 from CFTR) into a lipid bilayer have been calculated using coarse-grained molecular dynamics simulations and umbrella sampling to yield potentials of mean force along a reaction path corresponding to translation of a helix across a lipid bilayer. The calculated free energy of insertion is smaller when a bilayer with a thinner hydrophobic region is used. The free energies of insertion from the potentials of mean force are compared with those derived from a number of hydrophobicity scales and with those derived from translocon-mediated insertion. This comparison supports recent models of translocon-mediated insertion and in particular suggests that: 1), helices in an about-to-be-inserted state may be located in a hydrophobic region somewhat thinner than the core of a lipid bilayer; and/or 2), helices in a not-to-be-inserted state may experience an environment more akin (e.g., in polarity/hydrophobicity) to the bilayer/water interface than to bulk water.

Forming transmembrane channels using end-functionalized nanotubes

Using dissipative particle dynamics (DPD) simulations, we examine the interaction between amphiphilic nanotubes and lipid bilayer membranes. The nanotubes are represented by a hydrophobic shaft that is end-functionalized with hydrophilic groups. Nanotubes that are capped by a monolayer of hydrophilic beads or also encompass hydrophilic "hairs" on just one end of the shaft are found to spontaneously penetrate and assume a transmembrane position; the process, however, depends critically on the membrane tension. On the other hand, nanotubes that include hydrophilic hairs at both ends of the hydrophobic shaft are not observed to spontaneously self-organize into the bilayer. When the membrane is stretched to form a pore, the nanotubes with two hairy ends adsorb on the edge of the pore and become localized in the membrane, thus forming a transmembrane channel. The findings from these studies provide guidelines for creating biomimetic nanotube channels that are capable of selectively transporting molecules through the membrane in response to changes in the local environment.

Comparative study of predictive computational models for nanoparticle-induced cytotoxicity

With the increasing use of nanomaterials incorporated into consumer products, there is a need for developing approaches to establish "quantitative structure-activity relationships" (QSARs). These relationships could be used to predict various biological responses after exposure to nanomaterials for the purposes of risk analysis. This risk analysis is applicable to manufacturers of nanomaterials in an effort to determine potential hazards. Because metal oxide materials are some of the most widely applicable and studied nanoparticle types for incorporation into cosmetics, food packaging, and paints and coatings, we focused on comparing different approaches for establishing QSARs for this class of materials. Metal oxide nanoparticles are believed, by some, to cause alterations in cellular function due to their size and/or surface area. Others have said that these nanomaterials, because of the oxidized state of the metal, do not induce stress in biological tests systems. This controversy highlights the need to systematically develop structure-activity relationships (i.e., the relationship between physicochemical features to the cellular responses) and tools for predicting potential biological effects after a metal oxide nanomaterial exposure. Here, we attempt to identify a set of properties of two specific metal oxide nanomaterials-TiO(2) and ZnO-that could be used to characterize and predict the induced cellular membrane damage of immortalized human lung epithelial cells. We adopt a mathematical modeling approach that uses the engineered nanomaterial size characterized as a dry nanopowder and the nanomaterial behavior in ultrapure water, phosphate buffer, and cell culture media to predict nanomaterial-induced cellular membrane damage (via lactate dehydrogenase release). Results of these studies provide insights on how engineered nanomaterial features influence cellular responses and thereby outline possible approaches for developing and applying predictive computational models for biological responses caused by exposure to nanomaterials.

Synthetic chloride-selective carbon nanotubes examined by using molecular and stochastic dynamics

Synthetic channels, such as nanotubes, offer the possibility of ion-selective nanoscale pores which can broadly mimic the functions of various biological ion channels, and may one day be used as antimicrobial agents, or for treatment of cystic fibrosis. We have designed a carbon nanotube that is selectively permeable to anions. The virtual nanotubes are constructed from a hexagonal array of carbon atoms (graphene) rolled up to form a tubular structure, with an effective radius of 4.53 Å and length of 34 Å. The pore ends are terminated with polar carbonyl groups. The nanotube thus formed is embedded in a lipid bilayer and a reservoir containing ionic solutions is added at each end of the pore. The conductance properties of these synthetic channels are then examined with molecular and stochastic dynamics simulations. Profiles of the potential of mean force at 0 mM reveal that a cation moving across the pore encounters an insurmountable free energy barrier of ∼25 kT in height. In contrast, for anions, there are two energy wells of ∼12 kT near each end of the tube, separated by a central free energy barrier of 4 kT. The conductance of the pore, with symmetrical 500 mM solutions in the reservoirs, is 72 pS at 100 mV. The current saturates with an increasing ionic concentration, obeying a Michaelis-Menten relationship. The pore is normally occupied by two ions, and the rate-limiting step in conduction is the time taken for the resident ion near the exit gate to move out of the energy well.

Molecular Dynamics Studies of the Interactions Between Carbon Nanotubes and Biomembranes

Molecular simulations can be used to explore possible of bionanotechnology applications of biomembranes. In this chapter we review the use of both atomistic and coarse grained simulations to explore interactions between carbon nanotubes (CNTs) and model biomembranes. Issues of parameterization of CNTs for simulations are of especial importance, and are likely to be an area of future methodological refinement. Simulations have been used to characterize the interactions of CNTs with detergent and lipid molecules, and with model lipid bilayers. Once embedded within a bilayer, CNTs may form transbilayer pores. Simulations have been used to explore the behaviour of water and ions in CNT pores, and to explore their potential as ‘nanosyringes' for injection across cell membranes.

Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer

The conformations of model transmembrane peptides are studied to understand the structural and dynamical aspects of tetrameric bundles using a series of coarse grain (CG) molecular dynamics (MD) simulations since membrane proteins play a crucial role in cell function. In this work, two different amphipathic models have been constructed using similar hydrophobic/hydrophilic characteristics with two structurally distinct morphologies to evaluate the effect of roughness and hydrophilic topology on the structure of tetrameric bundles, one class that forms an ion-channel and one class that does not. Free energy calculations of typical amphipathic peptide topologies show that using a relatively smooth surface morphology allows for a stable conformation of the tetramer bundle in a diamond formation. However, the model with side chains attached to the core in order to roughen the surface has a stable square tetramer bundle which is consistent with experimental data and all-atom (AA) MD simulations. Comparisons of the CG simulations with AA MD simulations are in reasonable agreement with the formation of tetrameric homo-oligomers, partitioning within the lipid bilayer and tilt angle with respect to the bilayer normal. We concluded that a square or diamond shape tetrameric homo-oligomers could be stabilized by rational design of the peptide morphology and topology of the surface, thus allowing us to tune the permeability of the bundle or channel.

Peptide nanopores and lipid bilayers: interactions by coarse-grained molecular-dynamics simulations

A set of 49 protein nanopore-lipid bilayer systems was explored by means of coarse-grained molecular-dynamics simulations to study the interactions between nanopores and the lipid bilayers in which they are embedded. The seven nanopore species investigated represent the two main structural classes of membrane proteins (alpha-helical and beta-barrel), and the seven different bilayer systems range in thickness from approximately 28 to approximately 43 A. The study focuses on the local effects of hydrophobic mismatch between the nanopore and the lipid bilayer. The effects of nanopore insertion on lipid bilayer thickness, the dependence between hydrophobic thickness and the observed nanopore tilt angle, and the local distribution of lipid types around a nanopore in mixed-lipid bilayers are all analyzed. Different behavior for nanopores of similar hydrophobic length but different geometry is observed. The local lipid bilayer perturbation caused by the inserted nanopores suggests possible mechanisms for both lipid bilayer-induced protein sorting and protein-induced lipid sorting. A correlation between smaller lipid bilayer thickness (larger hydrophobic mismatch) and larger nanopore tilt angle is observed and, in the case of larger hydrophobic mismatches, the simulated tilt angle distribution seems to broaden. Furthermore, both nanopore size and key residue types (e.g., tryptophan) seem to influence the level of protein tilt, emphasizing the reciprocal nature of nanopore-lipid bilayer interactions.

Carbon nanotube based artificial water channel protein: membrane perturbation and water transportation

We functionalized double-walled carbon nanotubes (DWCNTs) as artificial water channel proteins. For the first time, molecular dynamics simulations show that the bilayer structure of DWCNTs is advantageous for carbon nanotube based transmembrane channels. The shielding of the amphiphilic outer layer could guarantee biocompatibility of the synthetic channel and protect the inner tube (functional part) from disturbance of the membrane environment. This novel design could promote more sophisticated nanobiodevices which could function in a bioenvironment with high biocompatibility.

Modeling Transport Through Synthetic Nanopores

Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article.

Orientation of the monomeric porin OmpG in planar lipid bilayers

Outer membrane protein G (OmpG) is a non-selective porin from Escherichia coli. OmpG is a monomer, which makes it unusual among porins, and suggests that it may be useful in biotechnology. In planar lipid bilayers, individual OmpG pores reconstituted by insertion from detergent exhibit pronounced asymmetry in current-voltage relationships and voltage-dependent gating. Here, this asymmetry is used to deduce the orientation of OmpG in the bilayers. We introduced two cysteines into the extracellular loops of OmpG. Cleavage of the disulfide bond formed by these residues significantly increases spontaneous gating of the pore. By adding DTT to one side of the bilayer or the other, we demonstrated that pores showing a quiet trace at negative potentials have a "trans" conformation (extracellular loops on the trans side of the bilayer), while pores showing a quiet trace at positive potentials have a "cis" conformation (extracellular loops on the cis side). With this knowledge, we examined the binding of a cyclodextrin to OmpG. When the cyclodextrin was presented to the extracellular face of the pore, transient multisite interactions were observed. In contrast, when the cyclodextrin was presented to the periplasmic face, a more stable single-site interaction occurred. Because the cyclodextrin can act as a molecular adapter by binding analytes, this information serves to advance the use of OmpG as a biosensor.

Coarse-grained simulation studies of peptide-induced pore formation

We investigate the interactions between lipid bilayers and amphiphilic peptides using a solvent-free coarse-grained simulation technique. In our model, each lipid is represented by one hydrophilic and three hydrophobic beads. The amphiphilic peptide is modeled as a hydrophobic-hydrophilic cylinder with hydrophilic caps. We find that with increasing peptide-lipid attraction the preferred state of the peptide changes from desorbed, to adsorbed, to inserted. A single peptide with weak attraction binds on the bilayer surface, while one with strong attraction spontaneously inserts into the bilayer. We show how several peptides, which individually bind only to the bilayer surface, cooperatively insert. Furthermore, hydrophilic strips along the peptide cylinder induce the formation of multipeptide pores, whose size and morphology depend on the peptides' overall hydrophilicity, the distribution of hydrophilic residues, and the peptide-peptide interactions. Strongly hydrophilic peptides insert less readily, but prove to be more destructive to bilayer integrity.

Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study

Carbon nanotubes (CNTs) are possible nanoinjectors for the introduction of therapeutic agents into cells. To explore their interactions with a lipid bilayer membrane and to model the nanoinjection process, we used coarse-grained molecular dynamics to simulate the penetration of dipalmitoylphosphatidylcholine (DPPC) bilayers by single-walled CNTs. Lipids are extracted from a bilayer during CNT penetration and reside on both the inner and the outer tube surfaces. Lipids that interact with the CNT interior wall spread out and hence can "block" the tube. However, the degree of lipid lining of the inner surface is strongly dependent upon the tube penetration velocity, with fewer lipids extracted from the bilayer at higher rates. There is no apparent effect on bilayer integrity after CNT penetration, with the bilayer able to self-seal. Our findings reveal some of the complexities of the interactions of lipids with CNT nanoinjectors and suggest a need to further characterize the influence of, for example, CNT functionalization and cargo on lipid blocking of CNTs.

Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes

The study of interactions between carbon nanotubes and cellular components, such as membranes and biomolecules, is fundamental for the rational design of nanodevices interfacing with biological systems. In this work, we use molecular dynamics simulations to study the electrophoretic transport of RNA through carbon nanotubes embedded in membranes. Decorated and naked carbon nanotubes are inserted into a dodecane membrane and a dimyristoylphosphatidylcholine lipid bilayer, and the system is subjected to electrostatic potential differences. The transport properties of this artificial pore are determined by the structural modifications of the membrane in the vicinity of the nanotube openings and they are quantified by the nonuniform electrostatic potential maps at the entrance and inside the nanotube. The pore is used to transport electrophoretically a short RNA segment and we find that the speed of translocation exhibits an exponential dependence on the applied potential differences. The RNA is transported while undergoing a repeated stacking and unstacking process, affected by steric interactions with the membrane headgroups and by hydrophobic interaction with the walls of the nanotube. The RNA is structurally reorganized inside the nanotube, with its backbone solvated by water molecules near the axis of the tube and its bases aligned with the nanotube walls. Upon exiting the pore, the RNA interacts with the membrane headgroups and remains attached to the dodecane membrane while it is expelled into the solvent in the case of the lipid bilayer. The results of the simulations detail processes of molecular transport into cellular compartments through manufactured nanopores and they are discussed in the context of applications in biotechnology and nanomedicine.

Computer modeling in biotechnology: a partner in development

Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.

Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers

We have previously demonstrated that some poly(alkylthiophenes) (PATs) are able to increase the electrical conductance of unsupported phospholipid bilayers and have hypothesized that this effect is due to the ability of some PAT side chains to permit stable insertion into the bilayer. We have further proposed the development of long-term intracellular electrodes based on that phenomenon. In this article, we apply molecular dynamics techniques to study the insertion of two model PATs into a patch of a lipid bilayer. Steered molecular dynamics is used to obtain potential trajectories of insertion, followed by umbrella sampling to determine the free-energy change upon insertion. Our results indicate that both branched-side-chain poly(3-(2-ethylhexyl)thiophene) (EHPT) and straight-side-chain poly(3-hexylthiophene) (HPT) are able to enter the bilayer but only EHPT can cross the center of the membrane and establish an electrical bridge. HPT penetrates the head groups but is not able to enter the alkyl tail phase. These findings support the feasibility of our electrode concept and raise questions regarding the mechanisms by which branched side chains grant PATs greater solubility in a lipid bilayer environment. The parameters and methods used in this study establish a novel framework for studying these and similar systems, and the results hold promise for the use of EHPT in biosensing and neural interfacing.

An algorithm for three-dimensional Voronoi S-network

The paper presents an algorithm for calculating the three-dimensional Voronoi-Delaunay tessellation for an ensemble of spheres of different radii (additively-weighted Voronoi diagram). Data structure and output of the algorithm is oriented toward the exploration of the voids between the spheres. The main geometric construct that we develop is the Voronoi S-network (the network of vertices and edges of the Voronoi regions determined in relation to the surfaces of the spheres). General scheme of the algorithm and the key points of its realization are discussed. The principle of the algorithm is that for each determined site of the network we find its neighbor sites. Thus, starting from a known site of the network, we sequentially find the whole network. The starting site of the network is easily determined based on certain considerations. Geometric properties of ensembles of spheres of different radii are discussed, the conditions of applicability and limitations of the algorithm are indicated. The algorithm is capable of working with a wide variety of physical models, which may be represented as sets of spheres, including computer models of complex molecular systems. Emphasis was placed on the issue of increasing the efficiency of algorithm to work with large models (tens of thousands of atoms). It was demonstrated that the experimental CPU time increases linearly with the number of atoms in the system, O(n).

Coarse grained protein-lipid model with application to lipoprotein particles

A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins. In the framework of such models pioneered by Klein, atoms are described group-wise by beads, with the interactions between beads governed by effective potentials. The extension developed here is based on a coarse-grained lipid model developed previously by Marrink et al., although future versions will reconcile the approach taken with the systematic approach of Klein and other authors. Each amino acid of the protein is represented by two coarse-grained beads, one for the backbone (identical for all residues) and one for the side-chain (which differs depending on the residue type). The coarse-graining reduces the system size about 10-fold and allows integration time steps of 25-50 fs. The model is applied to simulations of discoidal high-density lipoprotein particles involving water, lipids, and two primarily helical proteins. These particles are an ideal test system for the extension of coarse-grained models. Our model proved to be reliable in maintaining the shape of preassembled particles and in reproducing the overall structural features of high-density lipoproteins accurately. Microsecond simulations of lipoprotein assembly revealed the formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer.

Vstx1, a modifier of Kv channel gating, localizes to the interfacial region of lipid bilayers

VSTx1 is a tarantula venom toxin which binds to the archaebacterial voltage-gated potassium channel KvAP. VSTx1 is thought to access the voltage sensor domain of the channel via the lipid bilayer phase. In order to understand its mode of action and implications for the mechanism of channel activation, it is important to characterize the interactions of VSTx1 with lipid bilayers. Molecular dynamics (MD) simulations (for a total simulation time in excess of 0.2 micros) have been used to explore VSTx1 localization and interactions with zwitterionic (POPC) and with anionic (POPE/POPG) lipid bilayers. In particular, three series of MD simulations have been used to explore the net drift of VSTx1 relative to the center of a bilayer, starting from different locations of the toxin. The preferred location of the toxin is at the membrane/water interface. Although there are differences between POPC and POPE/POPG bilayers, in both cases the toxin forms favorable interactions at the interface, maximizing H-bonding to lipid headgroups and to water molecules while retaining interactions with the hydrophobic core of the bilayer. A 30 ns unrestrained simulation reveals dynamic partitioning of VSTx1 into the interface of a POPC bilayer. The preferential location of VSTx1 at the interface is discussed in the context of Kv channel gating models and provides support for a mode of action in which the toxin interacts with the Kv voltage sensor "paddle" formed by the S3 and S4 helices.

Molecular Dynamics Simulations of PAMAM Dendrimer-Induced Pore Formation in DPPC Bilayers with a Coarse-Grained Model

We have performed 0.5-micros-long molecular dynamics (MD) simulations of 0%, 50%, and 100% acetylated third- (G3) and fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in dipalmitoylphosphatidylcholine (DPPC) bilayers with explicit water using the coarse-grained (CG) model developed by Marrink et al. (J.Phys. Chem. B 2004, 108, 750-760), but with long-range electrostatic interactions included. Radii of gyration of the CG G5 dendrimers are 1.99-2.32 nm, close to those measured in the experiments by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and atomistic simulations by Lee et al. (J. Phys. Chem. B 2006, 110, 4014-4019). Starting with the dendrimer initially positioned near the bilayer, we find that positively charged un-acetylated G3 and 50%-acetylated and un-acetylated G5 dendrimers insert themselves into the bilayer, and only un-acetylated G5 dendrimer induces hole formation at 310 K, but not at 277 K, which agrees qualitatively with experimental observations of Hong et al. (Bioconj. Chem. 2004, 15, 774-782) and Mecke et al. (Langmuir 2005, 21, 10348-10354). At higher salt concentration (approximately 500 mM NaCl), un-acetylated G5 dendrimer does not insert into the bilayer. The results suggest that with inclusion of long-range electrostatic interactions into coarse-grained models, realistic MD simulation of membrane-disrupting effects of nanoparticles at the microsecond time scale is now possible.

MD Simulations of Mistic: Conformational Stability in Detergent Micelles and Water

Mistic is an unusual membrane protein from Bacillus subtilis. It appears to fold and insert autonomously into a lipid bilayer and has been suggested as a tool that aids the targeting of eukaryotic membrane proteins to bacterial membranes. The NMR structure of Mistic in detergent (LDAO) micelles has revealed it to be a four alpha-helix bundle. From a structural perspective, Mistic does not resemble other membrane proteins. Its external surface is not very hydrophobic, and standard methods do not predict any of its helices to be in the transmembrane orientation. Molecular dynamics simulations (simulation times approximately 30 ns) in water and in detergent micelles have been used to explore the conformational stability of Mistic as a function of its environment. In water, the protein is stable, exhibiting no significant change in fold on a 30 ns time scale. In contrast, in three simulations in detergent micelles, the partial unfolding of Mistic occurred, whereby the H4 helix drifted away from the H1-H3 core. This was due to the penetration of detergent molecules between H4 and the remainder of the protein. This is unlike the behavior of several other membrane proteins, both alpha-helix bundles and beta-barrels, in comparable detergent micelle simulations. The unfolding of H4 from the H1-H3 core of Mistic could be partially reversed by a simulation in which the detergent molecules were removed, and the unfolded protein was simulated in water. These results suggest that Mistic may not be a stable integrated membrane protein but rather that it may undergo a conformational change upon interaction with a membrane or membrane-like environment.

Coarse-Grained Transmembrane Proteins: Hydrophobic Matching, Aggregation, and Their Effect on Fusion

Molecular transport between organelles is predominantly governed by vesicle fission and fusion. Unlike experimental vesicles, the fused vesicles in molecular dynamics simulations do not become spherical readily, because the lipid and water distribution is inappropriate for the fused state and spontaneous amendment is slow. Here, we study the hypothesis that enhanced transport across the membrane of water, lipids, or both is required to produce spherical vesicles. This is done by adding several kinds of model proteins to fusing vesicles. The results show that equilibration of both water and lipid content is a requirement for spherical vesicles. In addition, the effect of these transmembrane proteins is studied in bilayers and vesicles, including investigations into hydrophobic matching and aggregation. Our simulations show that the level of aggregation does not only depend on hydrophobic mismatch, but also on protein shape. Additionally, one of the proteins promotes fusion by inducing pore formation. Incorporation of these proteins allows even flat membranes to fuse spontaneously. Moreover, we encountered a novel spontaneous vesicle enlargement mechanism we call the engulfing lobe, which may explain how lipids added to a vesicle solution are quickly incorporated into the inner monolayer.

Synthetic ion channels and pores (2004-2005)

This critical review covers synthetic ion channels and pores created between January 2004 and December 2005 comprehensively. The discussion of a rich collection of structural motifs may particularly appeal to organic, biological, supramolecular and polymer chemists. Functions addressed include ion selectivity and molecular recognition, as well as responsiveness to light, heat, voltage and membrane composition. The practical applications involved concern certain topics in medicinal chemistry (antibiotics, drug delivery), catalysis and sensing. An introduction to principles and methods is provided for the non-specialist; some new sources of inspiration from fields beyond chemistry are highlighted.

Modelling of proteins in membranes

This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins.