Dynamic mechanism of fatty acid transport across cellular membranes through FadL: molecular dynamics simulations

FadL is an important member of the family of fatty acid transport proteins within membranes. In this study, 11 conventional molecular dynamics (CMD) and 25 steered molecular dynamics (SMD) simulations were performed to investigate the dynamic mechanism of transport of long-chain fatty acids (LCFAs) across FadL. The CMD simulations addressed the intrinsically dynamic behavior of FadL. Both the CMD and SMD simulations revealed that a fatty acid molecule can move diffusively to a high-affinity site (HAS) from a low-affinity site (LAS). During this process, the swing motion of the L3 segment and the hydrophobic interaction between the fatty acid and FadL could play important roles. Furthermore, 22 of the SMD simulations revealed that fatty acids can pass through the gap between the hatch domain and the transmembrane domain (TMD) by different pathways. SMD simulations identified nine possible pathways for dodecanoic acid (DA) threading the barrel of FadL. The binding free energy profiles between DA and FadL along the MD trajectories indicate that all of the possible pathways are energetically favorable for the transport of fatty acids; however, one pathway (path VI) might be the most probable pathway for DA transport. The reasonability and reliability of this study were further demonstrated by correlating the MD simulation results with the available mutagenesis results. On the basis of the simulations, a mechanism for the full-length transport process of DA from the extracellular side to the periplasmic space mediated by FadL is proposed.     

Probing the neutral graphene-ionic liquid interface: insights from molecular dynamics simulations

We study basic mechanisms of the interfacial layer formation at the neutral graphite monolayer (graphene)-ionic liquid (1,3-dimethylimidazolium chloride, [dmim][Cl]) interface by fully atomistic molecular dynamics simulations. We probe the interface area by a spherical probe varying the charge (-1e, 0, +1e) as well as the size of the probe (diameter 0.50 nm and 0.38 nm). The molecular modelling results suggest that: there is a significant enrichment of ionic liquid cations at the surface. This cationic layer attracts Cl(-) anions that leads to the formation of several distinct ionic liquid layers at the surface. There is strong asymmetry in cationic/anionic probe interactions with the graphene wall due to the preferential adsorption of the ionic liquid cations at the graphene surface. The high density of ionic liquid cations at the interface adds an additional high energy barrier for the cationic probe to come to the wall compared to the anionic probe. Qualitatively the results from probes with diameter 0.50 nm and 0.38 nm are similar although the smaller probe can approach closer to the wall. We discuss the simulation results in light of available experimental data on the interfacial structure in ionic liquids.     

Reaction mechanism of soluble epoxide hydrolase: insights from molecular dynamics simulations

Molecular dynamics simulations have been performed to gain insights into the catalytic mechanism of the hydrolysis of epoxides to vicinal diols by soluble epoxide hydrolase (sEH). The binding of a substrate, 1S,2S-trans-methylstyrene oxide, was studied in two conformations in the active site of the enzyme. It was found that only one is likely to be found in the active enzyme. In the preferred conformation the phenyl group of the substrate is pi-sandwiched between two aromatic residues, Tyr381 and His523, whereas the other conformation is pi-stacked with only one aromatic residue, Trp334. Two simulations were carried out to 1 ns for each conformation to evaluate the protonation state of active site residue His523. It was found that a protonated histidine is essential for keeping the active site from being disrupted. Long time scale, 4 ns, molecular dynamics simulation was done for the structure with the most likely combination of binding conformation and protonation state of His523. Near Attack Conformers (NACs) are present 5.3% of the time and nucleophilic attack on either epoxide carbon atom, approximately 75% on C(1) and approximately 25% on C(2), is found. A maximum of one hydrogen bond between the epoxide oxygen and either of the active site tyrosines, Tyr465 and Tyr381, is present, in agreement with experimental mutagenesis results that reveal a slight loss in activity if one tyrosine is mutated and essential loss of all activity upon double mutation of the two tyrosines in question. It was found that a hydrogen bond from Tyr465 to the substrate oxygen is essential for controlling the regioselectivity of the reaction. Furthermore, a relationship between the presence of this hydrogen bond and the separation of reactants was found. Two groups of amino acid segments were identified each as moving collectively. Furthermore, an overall anti-correlation was found between the movements of these two individually collectively moving groups, made up by parts of the cap-region, including the two tyrosines, and the site of the catalytic triad, respectively. This overall anti-correlated collective domain motion is, perhaps, involved in the conversion of E.NAC to E.TS.     

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations

We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five third-generation peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.     

How natural materials remove heavy metals from water: mechanistic insights from molecular dynamics simulations

Water pollution by heavy metals is of increasing concern due to its devastating effects on the environment and on human health. For the removal of heavy metals from water sources, natural materials, such as spent-coffee-grains or orange/banana/chestnut peels, appear to offer a potential cheap alternative to more sophisticated and costly technologies currently in use. However, in order to employ them effectively, it is necessary to gain a deeper understanding – at the molecular level – of the heavy metals-bioorganic-water system and exploit the power of computer simulations. As a step in this direction, we investigate via atomistic simulations the capture of lead ions from water by hemicellulose – the latter being representative of the polysaccharides that are common components of vegetables and fruit peels − as well as the reverse process. A series of independent molecular dynamics simulations, both classical and ab initio, reveals a coherent scenario which is consistent with what one would expect of an efficient capture, i.e. that it be fast and irreversible: (i) binding of the metal ions via adsorption is found to happen spontaneously on both carboxylate and hydroxide functional groups; (ii) in contrast, metal ion desorption, leading to solvation in water, involves sizable free-energy barriers.

We investigate via atomistic simulations the capture of lead ions from water by hemicellulose – as representative of the polysaccharides that are common components of vegetables and fruit peels – and the reverse process.     

Nanoporous carbon membranes for separation of nitrogen and oxygen: Insight from molecular simulations

Here we summarize some of our recent work on using molecular simulations to understand the key mechanism that result in large differences in the reported permeation rates of O₂ and N₂ in nanoporous carbon membranes. Two different representation of the amorphous nanoporous membrane structure are used; the hypothetical C₁₆₈ Schwarzite and a single wall carbon nanotube with a constriction. By comparing the results obtained from empirical planar graphite potential and an ab initio-based potential, the effect of carbon curvature and the presence of non-hexagonal carbon rings in C₁₆₈ Schwarzite is also investigated. It is found using either force field, that the energetic effect alone cannot explain the experimental observations. However, simulations performed using carbon nanotube with a constriction show that the size or entropic effect can be dominant. In particular, it is shown that an appropriate size constriction can result in large transport resistance to nitrogen while letting oxygen to pass through at a much higher rate, even though these gases have very similar molecular sizes and interaction energetics.     

Hydration of methane intercalated in Na-smectites with distinct layer charge: insights from molecular simulations

Molecular dynamic simulations have been carried out to investigate the behavior of methane hydration in Na-smectite interlayers with different layer-charge distributions and water contents under certain pressure-temperature (P-T) conditions, which is analogous to the methane hydrate-bearing marine sediments. It was found that sufficient interlayer water is necessary for coordinating with methane and forming hydrate-like structures. Methane molecules are solvated by nearly 12-13 water molecules and coordinated with six oxygen atoms from the clay surface in the interlayer of nontronite as well as in montmorillonite. The mobility of the interlayer water of smectite, which is determined by the layer-charge amount and distribution of smectite, also influences the stability of hydrate methane complexes. The tetrahedral negative charge site is closer to the surface than the octahedral charge site and is more effective in confining water than methane water molecules.     

Selective ablation of Xe from silicon surfaces: molecular dynamics simulations and experimental laser patterning

The mechanism of laser-induced removal of Xe overlayers from a Si substrate has been investigated employing MD simulations and evaluated by buffer layer assisted laser patterning experiments. Two distinct regimes of overlayer removal are identified in the simulations of a uniform heating of the Si substrate by a 5 ns laser pulse: The intensive evaporation from the surface of the Xe overlayer and the detachment of the entire Xe overlayer driven by explosive boiling in the vicinity of the hot substrate. Simulations of selective heating of only a fraction of the silicon substrate suggest that the lateral heat transfer and bonding to the unheated, colder regions of the Xe overlayer is very efficient and suppresses the separation of a fraction of the overlayer from the substrate. Interaction with surrounding cold Xe is responsible for significant increase in the substrate temperature required for achieving the spatially selective ablation of the overlayer. The predictions of the MD simulations are found to be in a qualitative agreement with the results of experimental measurements of the threshold laser power required for the removal of Xe overlayers of different thickness and the shapes of metallic stripes generated by buffer-assisted laser patterning.     

A simple and tailor‐made fabrication of porous silicon carbide from functionalized kraft pulp paper

Porous silicon carbide (SiC) materials were fabricated using the polymer‐derived ceramics method with kraft pulp papers (KPP) and a commercial polycarbosilane, the allylhydridopolycarbosilane (AHPCS), as starting materials. For this, KPP, propargylated KPP, or phosphorylated KPP were used to be impregnated by the AHPCS, with or without Karstedt catalyst. The pyrolysed materials were characterized at different stages, by using thermogravimetric analysis (TGA) coupled with mass spectrometry, X‐ray diffraction (XRD), and scanning electron microscopy (SEM). Depending on the nature of the initial template, various architectured SiC ceramics were successfully obtained with adjustable porosities. The key role of the previous functionalization of the papers was highlighted in terms of interactions at the interface between the polymer and the lignocellulosic handsheets. It led to either replica or sacrificial template methods. Thus, it was possible to tune the open porosity of the porous carbon and β‐SiC materials between 14.8% and 92.9%, with ceramic yields varying from 12% to 71%.     

Mechanical properties of surfactant bilayer membranes from atomistic and coarse-grained molecular dynamics simulations

We use simulations to predict the stability and mechanical properties of two amphiphilic bilayer membranes. We carry out atomistic MD simulations and investigate whether it is possible to use an existing coarse-grained (CG) surfactant model to map the membrane properties. We find that certain membranes can be represented well by the CG model, whereas others cannot. Atomistic MD simulations of the erucate membrane yield a headgroup area per surfactant a(0) of 0.26 nm(2), an elastic modulus K(A) of 1.7 N/m, and a bending rigidity kappa of 5 k(B)T. We find that the CG model, with the right choice for the size and potential well depth of the head, correctly reproduces a(0), kappa, as well as the fluctuation spectrum over the whole range of q values. Atomistic MD simulations of EHAC, on the other hand, suggest that this membrane is unstable. This is indicated by the fact that kappa is of the order of k(B)T, which means that the interface is extremely flexible and diffuse, and K(A) is close to zero, which means that the surface tension is zero. We argue that the CG model can be used if the headgroups are uncharged, dipolar, or effectively dipolar due to headgroup charge screening induced by counterion condensation.     

A novel sacrificial interlayer-based method for the preparation of silicon carbide membranes

A novel method is presented based on the use of sacrificial interlayers for the preparation of nanoporous silicon carbide membranes. It involves periodic and alternate coatings of polystyrene sacrificial interlayers and silicon carbide pre-ceramic layers on the top of slip-casted tubular silicon carbide supports. Membranes prepared by this technique exhibit single gas ideal separation factors of helium and hydrogen over argon in the ranges 176–465 and 101–258, respectively, with permeances that are typically two to three times higher than those of silicon carbide membranes prepared previously by the more conventional techniques. Mixed-gas experiments with the same membranes indicate separation factors as high as 117 for an equimolar H₂/CH₄ mixture. We speculate that the improved membrane characteristics are due to the sacrificial interlayers filling the pores in the underlying structure and preventing their blockage by the pre-ceramic polymer. The new method has good promise for application to the preparation of a variety of other inorganic microporous membranes.     

Direct synthesis of aligned silicon carbide nanowires from the silicon substrates

Aligned silicon carbide nanowires were synthesized directly from the silicon substrates via a novel catalytic reaction with a methane-hydrogen mixture at 1,100 degrees C, with a mean diameter of 40 nm and length of 500 microm; they consist of a single-crystalline zinc blende structure crystal in the [111] growth direction; X-ray diffraction, Raman, and infrared spectroscopy confirm the synthesis of high-purity silicon carbide nanowires.     

Voltammetric insights in the transfer of ionizable drugs across biomimetic membranes: recent achievements

The latest results of voltammetric research on the ionic transfer process of ionisable drugs across bare and lipid-modified liquid-liquid interfaces are reviewed. In recent years, two voltammetric methods have been extensively applied to this purpose, i.e. the classical four electrode voltammetry at the interface between two immiscible electrolyte solutions, and the "three-phase electrode." Thus, a brief background of the methodologies and some successful examples of their application are highlighted in this work. Particular attention is given to the ionic transfer kinetics and to the electrochemical characterization of the drug-membrane interactions between the ionized drugs and lipid-modified interfaces. Future trends in this area are also mentioned in connection with high-throughput assessment of ADMET properties of drugs.     

Effects of temperature and salt concentration on the structural stability of human lymphotactin: insights from molecular simulations

Extensive molecular dynamics (MD) simulations ( approximately 70 ns total) with explicit solvent molecules and salt ions are carried out to probe the effects of temperature and salt concentration on the structural stability of the human Lymphotactin (hLtn). The distribution of ions near the protein surface and the stability of various structural motifs are observed to exhibit interesting dependence on the local sequence and structure. Whereas chloride association to the protein is overall enhanced as the temperature increases, the sodium distribution in the C-terminal helical region and, to a smaller degree, the chloride distribution in the same region are found higher at the lower temperature. The similar trend is also observed in nonlinear Poisson-Boltzmann calculations with a temperature-dependent water dielectric constant, once conformational averaging over a series of MD snapshots is done. The unexpected temperature dependence in the ion distribution is explained on the basis of the cancellation of association entropy for ion-side chain pairs of opposite-charge and like-charge characters, which have positive and negative contributions, respectively. The C-terminal helix is observed to partially melt whereas a short beta strand forms at the higher temperature with little salt dependence. The N-terminal region, by contrast, develops partial helical structure at a higher salt concentration. These observed behaviors are consistent with solvent and salt screening playing an important role in stabilizing the canonical chemokine fold of hLtn.     

Selective monocationic inhibitors of neuronal nitric oxide synthase. Binding mode insights from molecular dynamics simulations

The reduction of pathophysiologic levels of nitric oxide through inhibition of neuronal nitric oxide synthase (nNOS) has the potential to be therapeutically beneficial in various neurodegenerative diseases. We have developed a series of pyrrolidine-based nNOS inhibitors that exhibit excellent potencies and isoform selectivities (J. Am. Chem. Soc. 2010, 132, 5437). However, there are still important challenges, such as how to decrease the multiple positive charges derived from basic amino groups, which contribute to poor bioavailability, without losing potency and/or selectivity. Here we present an interdisciplinary study combining molecular docking, crystallography, molecular dynamics simulations, synthesis, and enzymology to explore potential pharmacophoric features of nNOS inhibitors and to design potent and selective monocationic nNOS inhibitors. The simulation results indicate that different hydrogen bond patterns, electrostatic interactions, hydrophobic interactions, and a water molecule bridge are key factors for stabilizing ligands and controlling ligand orientation. We find that a heteroatom in the aromatic head or linker chain of the ligand provides additional stability and blocks the substrate binding pocket. Finally, the computational insights are experimentally validated with double-headed pyridine analogues. The compounds reported here are among the most potent and selective monocationic pyrrolidine-based nNOS inhibitors reported to date, and 10 shows improved membrane permeability.     

Gas sorption and barrier properties of polymeric membranes from molecular dynamics and Monte Carlo simulations

It is important for many industrial processes to design new materials with improved selective permeability properties. Besides diffusion, the molecule's solubility contributes largely to the overall permeation process. This study presents a method to calculate solubility coefficients of gases such as O2, H2O (vapor), N2, and CO2 in polymeric matrices from simulation methods (Molecular Dynamics and Monte Carlo) using first principle predictions. The generation and equilibration (annealing) of five polymer models (polypropylene, polyvinyl alcohol, polyvinyl dichloride, polyvinyl chloride-trifluoroethylene, and polyethylene terephtalate) are extensively described. For each polymer, the average density and Hansen solubilities over a set of ten samples compare well with experimental data. For polyethylene terephtalate, the average properties between a small (n = 10) and a large (n = 100) set are compared. Boltzmann averages and probability density distributions of binding and strain energies indicate that the smaller set is biased in sampling configurations with higher energies. However, the sample with the lowest cohesive energy density from the smaller set is representative of the average of the larger set. Density-wise, low molecular weight polymers tend to have on average lower densities. Infinite molecular weight samples do however provide a very good representation of the experimental density. Solubility constants calculated with two ensembles (grand canonical and Henry's constant) are equivalent within 20%. For each polymer sample, the solubility constant is then calculated using the faster (10x) Henry's constant ensemble (HCE) from 150 ps of NPT dynamics of the polymer matrix. The influence of various factors (bad contact fraction, number of iterations) on the accuracy of Henry's constant is discussed. To validate the calculations against experimental results, the solubilities of nitrogen and carbon dioxide in polypropylene are examined over a range of temperatures between 250 and 650 K. The magnitudes of the calculated solubilities agree well with experimental results, and the trends with temperature are predicted correctly. The HCE method is used to predict the solubility constants at 298 K of water vapor and oxygen. The water vapor solubilities follow more closely the experimental trend of permeabilities, both ranging over 4 orders of magnitude. For oxygen, the calculated values do not follow entirely the experimental trend of permeabilities, most probably because at this temperature some of the polymers are in the glassy regime and thus are diffusion dominated. Our study also concludes large confidence limits are associated with the calculated Henry's constants. By investigating several factors (terminal ends of the polymer chains, void distribution, etc.), we conclude that the large confidence limits are intimately related to the polymer's conformational changes caused by thermal fluctuations and have to be regarded--at least at microscale--as a characteristic of each polymer and the nature of its interaction with the solute. Reducing the mobility of the polymer matrix as well as controlling the distribution of the free (occupiable) volume would act as mechanisms toward lowering both the gas solubility and the diffusion coefficients.     

Nature of water transport and electro-osmosis in nafion: insights from first-principles molecular dynamics simulations under an electric field

The effects of water content on water transport and electro-osmosis in a representative polymer electrolyte membrane, Nafion, are investigated in detail by means of first-principles molecular dynamics (MD) simulations in the presence of a homogeneous electric field. We have directly evaluated electro-osmotic drag coefficients (the number of water molecules cotransported with proton conduction) from the trajectories of the first-principles MD simulations and also explicitly evaluated factors that contribute to the electro-osmotic drag coefficients. In agreement with previously reported experiments, our calculations show virtually constant values ( approximately 1) of the electro-osmotic drag coefficients for both low and high water content states. Detailed comparisons of each factor contributing to the drag coefficient reveal that an increase in water content increases the occurrence of the Grotthuss-like effective proton transport process, whose contribution results in a decrease in the electro-osmotic drag coefficient. At the same time, an environment that is favorable for the Grotthuss-like effective proton transport process is also favorable for the transport of water arising from water transport occurring beyond the hydration shell around the protons, whose contribution results in an increase in the electro-osmotic drag coefficient. Conversely, an environment that is not favorable for proton conduction is also not favorable for water transport. As a result, the electro-osmotic drag coefficient shows virtually identical values with respect to change in the water content.     

Cholate-derived amphiphilic molecular baskets as glucose transporters across lipid membranes

With introverted polar groups and hydrophobic exteriors, cholate-derived amphiphilic molecular baskets were efficient transporters of glucose across lipid membranes.