Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies.

We have performed full atomistic molecular dynamics (MD) simulations to investigate structure and stability of bilayer membrane systems consisting of monomeric or polymeric 10,12-pentacosadiynoic acid (PCDA) units connected with lysine groups by amide bonds. The PCDA monomer molecules show a twisted three-rod-domain structure with two kinks but upon polymerization, they possess more elongated conformation. The resulting polydiacetylene (PDA) membrane systems have stable membrane structures at room temperature, which is similar to biological lipid bilayer membranes and maintain their gel-like membrane integrity even up to as high as 370 K. Structural properties such as area per monomer, membrane thickness, density profile, 2D pair distribution function, and orientational correlation function are also calculated to understand the membrane structure and check its stability upon thermal fluctuation with atomistic resolution. This study is expected to provide the understanding about PDA membrane systems in atomistic details as well as significant insights into designing new novel PDA sensors.

Inhibition mechanism of testis-expressed gene 14 (TEX14) in cytokinetic abscission: Well-tempered metadynamics simulation studies.

Cytokinesis requires a apoptosis-linked gene 2 interacting protein X (ALIX) and a 55 kDa midbody centrosomal protein (CEP55) to activate the cell abscission in somatic cells. However, in germ cells, CEP55 forms intercellular bridges with testis-expressed gene 14 (TEX14), which blocks the cell abscission. These intercellular bridges play important roles in the synchronization of the germ cells and facilitate the coordinated passage of organelles and molecules between germ cells. If TEX14 is intentionally removed, intercellular bridges are disrupted, leading to sterility. Hence, a deeper understanding regarding the roles of TEX14 can provide significant insights into the inactivation of abscission and the inhibition of proliferation in cancer cells. Previous experimental studies have shown that the high affinity and low dissociation rate of TEX14 for CEP55 prevent ALIX from binding CEP55 and inactivate the germ cell abscission. However, detailed information about how TEX14 interacts with CEP55 to prevent the cell abscission is still lacking. To gain more specific insights into the interactions between CEP55 and TEX14 and the difference in reactivity between TEX14 and ALIX, we performed well-tempered metadynamics simulations of these protein complexes using atomistic models of CEP55, TEX14, and ALIX. We identified the major binding residues of TEX14 and ALIX with CEP55 by using 2D Gibbs free energy evaluations, the results of which are consistent with previous experimental studies. Our results may help design synthetic TEX14 mimicking peptides, which can bind CEP55 and facilitate the inactivation of abscission in abnormal cells, including cancer cells.

Interstitially Mixed Self-Assembled Monolayers Enhance Electrical Stability of Molecular Junctions.

Electrical breakdown is a critical problem in electronics. In molecular electronics, it becomes more problematic because ultrathin molecular monolayers have delicate and defective structures and exhibit intrinsically low breakdown voltages, which limit device performances. Here, we show that interstitially mixed self-assembled monolayers (imSAMs) remarkably enhance electrical stability of molecular-scale electronic devices without deteriorating function and reliability. The SAM of the sterically bulky matrix (SC11BIPY rectifier) molecule is diluted with a skinny reinforcement (SCn) molecule via the new approach, so-called repeated surface exchange of molecules (ReSEM). Combined experiments and simulations reveal that the ReSEM yields imSAMs wherein interstices between the matrix molecules are filled with the reinforcement molecules and leads to significantly enhanced breakdown voltage inaccessible by traditional pure or mixed SAMs. Thanks to this, bias-driven disappearance and inversion of rectification is unprecedentedly observed. Our work may help to overcome the shortcoming of SAM's instability and expand the functionalities.

Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils.

RATIONALE: Molecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains. METHODS: In this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values. RESULTS: The CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered. CONCLUSIONS: The data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.

A motor neuron strategy to save time and energy in neurodegeneration: adaptive protein stoichiometry.

Neurofilament proteins (Nf) are a biomarker of disease progression in amyotrophic lateral sclerosis (ALS). This study investigated whether there are major differences in expression from in vivo measurements of neurofilament isoforms, from the light chain, NfL (68 kDa), compared with larger proteins, the medium chain (NfM, 150 kDa) and the heavy (NfH, 200-210 kDa) chains in ALS patients and healthy controls. New immunological methods were combined with Nf subunit stoichiometry calculations and Monte Carlo simulations of a coarse-grained Nf brush model. Based on a physiological Nf subunit stoichiometry of 7 : 3 : 2 (NfL:NfM:NfH), we found an 'adaptive' Nf subunit stoichiometry of 24 : 2.4 : 1.6 in ALS. Adaptive Nf stoichiometry preserved NfL gyration radius in the Nf brush model. The energy and time requirements for Nf translation were 56 ± 27k ATP (5.6 h) in control subjects compared to 123 ± 102k (12.3 h) in ALS with 'adaptive' (24:2.4:1.6) Nf stoichiometry (not significant) and increased significantly to 355 ± 330k (35.5 h) with 'luxury' (7:3:2) Nf subunit stoichiometry (p < 0.0001 for each comparison). Longitudinal disease progression-related energy consumption was highest with a 'luxury' (7:3:2) Nf stoichiometry. Therefore, an energy and time-saving option for motor neurons is to shift protein expression from larger to smaller (cheaper) subunits, at little or no costs on a protein structural level, to compensate for increased energy demands.

Structural and biochemical insights into the role of testis-expressed gene 14 (TEX14) in forming the stable intercellular bridges of germ cells.

Intercellular bridges are a conserved feature of spermatogenesis in mammalian germ cells and derive from arresting cell abscission at the final stage of cytokinesis. However, it remains to be fully understood how germ cell abscission is arrested in the presence of general cytokinesis components. The TEX14 (testis-expressed gene 14) protein is recruited to the midbody and plays a key role in the inactivation of germ cell abscission. To gain insights into the structural organization of TEX14 at the midbody, we have determined the crystal structures of the EABR [endosomal sorting complex required for transport (ESCRT) and ALIX-binding region] of CEP55 bound to the TEX14 peptide (or its chimeric peptides) and performed functional characterization of the CEP55-TEX14 interaction by multiexperiment analyses. We show that TEX14 interacts with CEP55-EABR via its AxGPPx3Y (Ala793, Gly795, Pro796, Pro797, and Tyr801) and PP (Pro803 and Pro804) sequences, which together form the AxGPPx3YxPP motif. TEX14 competitively binds to CEP55-EABR to prevent the recruitment of ALIX, which is a component of the ESCRT machinery with the AxGPPx3Y motif. We also demonstrate that a high affinity and a low dissociation rate of TEX14 to CEP55, and an increase in the local concentration of TEX14, cooperatively prevent ALIX from recruiting ESCRT complexes to the midbody. The action mechanism of TEX14 suggests a scheme of how to inactivate the abscission of abnormal cells, including cancer cells.

Structural insights into the efficient CO2-reducing activity of an NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA.

CO2 fixation is thought to be one of the key factors in mitigating global warming. Of the various methods for removing CO2, the NAD-dependent formate dehydrogenase from Candida boidinii (CbFDH) has been widely used in various biological CO2-reduction systems; however, practical applications of CbFDH have often been impeded owing to its low CO2-reducing activity. It has recently been demonstrated that the NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA (TsFDH) has a higher CO2-reducing activity compared with CbFDH. The crystal structure of TsFDH revealed that the biological unit in the asymmetric unit has two conformations, i.e. open (NAD(+)-unbound) and closed (NAD(+)-bound) forms. Three major differences are observed in the crystal structures of TsFDH and CbFDH. Firstly, hole 2 in TsFDH is blocked by helix α20, whereas it is not blocked in CbFDH. Secondly, the sizes of holes 1 and 2 are larger in TsFDH than in CbFDH. Thirdly, Lys287 in TsFDH, which is crucial for the capture of formate and its subsequent delivery to the active site, is an alanine in CbFDH. A computational simulation suggested that the higher CO2-reducing activity of TsFDH is owing to its lower free-energy barrier to CO2 reduction than in CbFDH.

Systems-level modeling with molecular resolution elucidates the rate-limiting mechanisms of cellulose decomposition by cellobiohydrolases.

Interprotein and enzyme-substrate couplings in interfacial biocatalysis induce spatial correlations beyond the capabilities of classical mass-action principles in modeling reaction kinetics. To understand the impact of spatial constraints on enzyme kinetics, we developed a computational scheme to simulate the reaction network of enzymes with the structures of individual proteins and substrate molecules explicitly resolved in the three-dimensional space. This methodology was applied to elucidate the rate-limiting mechanisms of crystalline cellulose decomposition by cellobiohydrolases. We illustrate that the primary bottlenecks are slow complexation of glucan chains into the enzyme active site and excessive enzyme jamming along the crowded substrate. Jamming could be alleviated by increasing the decomplexation rate constant but at the expense of reduced processivity. We demonstrate that enhancing the apparent reaction rate required a subtle balance between accelerating the complexation driving force and simultaneously avoiding enzyme jamming. Via a spatiotemporal systems analysis, we developed a unified mechanistic framework that delineates the experimental conditions under which different sets of rate-limiting behaviors emerge. We found that optimization of the complexation-exchange kinetics is critical for overcoming the barriers imposed by interfacial confinement and accelerating the apparent rate of enzymatic cellulose decomposition.

Expansion of neurofilament medium C terminus increases axonal diameter independent of increases in conduction velocity or myelin thickness.

Maturation of the peripheral nervous system requires specification of axonal diameter, which, in turn, has a significant influence on nerve conduction velocity. Radial axonal growth initiates with myelination, and is dependent upon the C terminus of neurofilament medium (NF-M). Molecular phylogenetic analysis in mammals suggested that expanded NF-M C termini correlated with larger-diameter axons. We used gene targeting and computational modeling to test this new hypothesis. Increasing the length of NF-M C terminus in mice increased diameter of motor axons without altering neurofilament subunit stoichiometry. Computational modeling predicted that an expanded NF-M C terminus extended farther from the neurofilament core independent of lysine-serine-proline (KSP) phosphorylation. However, expansion of NF-M C terminus did not affect the distance between adjacent neurofilaments. Increased axonal diameter did not increase conduction velocity, possibly due to a failure to increase myelin thickness by the same proportion. Failure of myelin to compensate for larger axonal diameters suggested a lack of plasticity during the processes of myelination and radial axonal growth.

Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation.

The present study examines the effects of the model dependence, ionic strength, divalent ions, and hydrophobic interaction on the structural organization of the human neurofilament (NF) brush, using canonical ensemble Monte Carlo (MC) simulations of a coarse-grained model with the amino-acid resolution. The model simplifies the interactions between the NF core and the sidearm or between the sidearms by the sum of excluded volume, electrostatic, and hydrophobic interactions, where both monovalent salt ions and solvents are implicitly incorporated into the electrostatic interaction potential. Several important observations are made from the MC simulations of the coarse-grained model NF systems. First, the mean-field type description of monovalent salt ions works reasonably well in the NF system. Second, the manner by which the NF sidearms are arranged on the surface of the NF backbone core has little influence on the lateral extension of NF sidearms. Third, the lateral extension of the NF sidearms is highly affected by the ionic strength of the system: at low ionic strength, NF-M is most extended but at high ionic strength, NF-H is more stretched out because of the effective screening of the electrostatic interaction. Fourth, the presence of Ca(2+) ions induces the attraction between negatively charged residues, which leads to the contraction of the overall NF extension. Finally, the introduction of hydrophobic interaction does not change the general structural organization of the NF sidearms except that the overall extension is contracted.

Conformational properties of interacting neurofilaments: Monte Carlo simulations of cylindrically grafted apposing neurofilament brushes.

Neurofilaments are essential cytoskeletal filaments that impart mechanical stability to axons. They are mostly assembled from three neurofilament proteins that form the core of the filament and its sidearms. Adjacent neurofilaments interact with each other through their apposing sidearms and attain unique conformations depending on the ionic condition, phosphorylation state, and interfilament separations. To understand the conformational properties of apposing sidearms under various conditions and gain insight into interfilament interactions, we performed Monte Carlo simulations of neurofilament pairs. We employed a sequence-based coarse-grained model of apposing NF sidearms that are end-tethered to cylindrical geometries according to the stoichiometry of the three neurofilament subunits. Monte Carlo simulations were conducted under different conditions such as phosphorylation state, ionic condition, and interfilament separations. Under salt-free conditions, apposing sidearms are found to adopt mutually excluding stretched but bent away conformations that are reminiscent of a repulsive type of interaction. Under physiological conditions, apposing sidearms are found to be in a coiled conformation, suggesting a short-range steric repulsive type of interaction. Increased sidearm mutual interpenetration and a simultaneous decrease in the individual brush heights were observed as the interfilament separation was reduced from 60 to 40 nm. The observed conformations suggest entropic interaction as a likely mechanism for sidearm-mediated interfilament interactions under physiological conditions.

Attitudinal analysis of vaccination effects to lead endemic phases.

To achieve endemic phases, repeated vaccinations are necessary. However, individuals may grapple with whether to get vaccinated due to potential side effects. When an individual is already immune due to previous infections or vaccinations, the perceived risk from vaccination is often less than the risk of infection. Yet, repeated rounds of vaccination can lead to avoidance, impeding the establishment of endemic phases. We explore this phenomenon using an individual-based Monte Carlo simulation, validating our findings with game theory. The Nash equilibrium encapsulates individuals' non-cooperative behavior, while the system's optimal value represents the societal benefits of altruistic cooperation. We define the difference between these as the price of anarchy. Our simulations reveal that the price of anarchy must fall below a threshold of 12.47 for endemic phases to be achieved in a steady state. This suggests that for a basic reproduction number of 10, a consistent vaccination rate greater than 89% is required. These findings offer new insights into vaccination-related decision-making and can inform effective strategies to tackle infectious diseases.

DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model.

We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 µm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 µm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.

Clioquinol as an inhibitor of JmjC-histone demethylase exhibits common and unique histone methylome and transcriptome between clioquinol and hypoxia.

Clioquinol (CQ) is a hypoxic mimicker to activate hypoxia-inducible factor-1α (HIF-1α) by inhibiting HIF-1α specific asparaginyl hypoxylase (FIH-1). The structural similarity of the Jumonji C (JmjC) domain between FIH-1 and JmjC domain-containing histone lysine demethylases (JmjC-KDMs) led us to investigate whether CQ could inhibit the catalytic activities of JmjC-KDMs. Herein, we showed that CQ inhibits KDM4A/C, KDM5A/B, and KDM6B and affects H3K4me3, H3K9me3, and H3K27me3 marks, respectively. An integrative analysis of the histone methylome and transcriptome data revealed that CQ-mediated JmjC-KDM inhibition altered the transcription of target genes through differential combinations of KDMs and transcription factors. Notably, functional enrichment of target genes showed that CQ and hypoxia commonly affected the response to hypoxia, VEGF signaling, and glycolysis, whereas CQ uniquely altered apoptosis/autophagy and cytoskeleton/extracellular matrix organization. Our results suggest that CQ can be used as a JmjC-KDM inhibitor, HIF-α activator, and an alternative therapeutic agent in hypoxia-based diseases.

Chlorosulfolipid (Danicalipin A) Membrane Structure: Hybrid Molecular Dynamics Simulation Studies.

Chlorosulfolipids (CSLs) are major components of flagellar membranes in sea algae. Unlike typical biological lipids, CSLs contain hydrophilic sulfate and chloride groups in the hydrocarbon tail; this has deterred the prediction of the CSL membrane structure since 1960. In this study, we combine coarse-grained (CG) and atomistic molecular dynamics (MD) simulations to gain significant insights into the membrane structure of Danicalipin A, which is one of the typical CSLs. It is observed from the CG MD that Danicalipin A lipids form a stable monolayer membrane structure wherein the hydrocarbon moieties are sandwiched by hydrophilic sulfate and chloride groups in both the head and tail regions. On the basis of the mesoscopic structure, we built the corresponding atomistic model to investigate the integrity of the CSL monolayer membrane structure. The monolayer membrane comprising bent lipids shows high thermal stability up to 313 K. The gel-liquid crystalline phase transition is observed around 300 K.

Swelling of polymers in porous media.

The swelling of polymers in random matrices is studied using computer simulations and percolation theory. The model system consists of freely jointed hard sphere chains in a matrix of hard spheres fixed in space. The average size of the polymer is a nonmonotonic function of the matrix volume fraction, phi(m). For low values of phi(m) the polymer size decreases as phi(m) is increased but beyond a certain value of phi(m) the polymer size increases as phi(m) is increased. The qualitative behavior is similar for three different types of matrices. In order to study the relationship between the polymer swelling and pore percolation, we use the Voronoi tessellation and a percolation theory to map the matrix onto an irregular lattice, with bonds being considered connected if a particle can pass directly between the two vertices they connect. The simulations confirm the scaling relation R(G) approximately (p-p(c))(delta(0))N(nu), where R(G) is the radius of gyration, N is the polymer degree of polymerization, p is the number of connected bonds, and p(c) is the value of p at the percolation threshold, with universal exponents delta(0)(approximately = -0.126+/-0.005) and nu(approximately = 0.6+/-0.01). The values of the exponents are consistent with predictions of scaling theory.

Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle.

This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide consisting of the first 25 residues from surfactant protein B. The nanoparticle model with a chemical formula C188H53 was generated using a computational code for combustion conditions. The nanoparticle has a carbon cage structure reminiscent of the buckyballs with open ends. A series of molecular-scale structural and dynamical properties of the surfactant film in the absence and presence of nanoparticle are analyzed, including radial distribution functions, mean-square displacements of lipids and nanoparticle, chain tilt angle, and the surfactant protein B peptide helix tilt angle. The results show that the nanoparticle affects the structure and packing of the lipids and peptide in the film, and it appears that the nanoparticle and peptide repel each other. The ability of the nanoparticle to translocate the surfactant film is one of the most important predictions of this study. The potential of mean force for dragging the particle through the film provides such information. The reported potential of mean force suggests that the nanoparticle can easily penetrate the monolayer but further translocation to the water phase is energetically prohibitive. The implication is that nanoparticles can interact with the lung surfactant, as supported by recent experimental data by Bakshi et al.

On-Demand Modulation of Bacterial Cell Fates on Multifunctional Dynamic Substrates.

This paper reports unprecedented dynamic surfaces based on zwitterionic low-density self-assembled monolayers (LDSAMs) of alkanethiolates on gold, which integrate three interconvertible states-bacteria-adherable, bactericidal, and nonfouling states-through electrical modulations. The conformations of alkanethiolates were electrically modulated to generate zwitterionic, anionic, and cationic surfaces, which responded differently to bacteria and determined the fate of bacteria. Furthermore, the reversible switching of multifunctions of the surface was realized for killing bacteria and subsequently releasing dead bacteria from the surface. For practical application of our strategy, we examined the selective antibacterial effect of our surface for eradication of mycoplasma contaminants in contaminated mammalian cell cultures.

Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations.

Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.

Insights into the effect of combustion-generated carbon nanoparticles on biological membranes: a computer simulation study.

Classical molecular dynamics simulations of atomistic models of combustion-generated carbon nanoparticles and lipid bilayers have been performed to explore their possible structural, dynamical, and thermodynamic effects on biological membranes. The DREIDING generic force field is used for the carbonaceous nanoparticles of different morphologies, as produced from combustion sources, and the united atom model was employed for the dimyristoylphosphatidylcholine (DMPC) bilayer. It is observed that particle shape and structure have significant effects on solvation, mobility, adsorption, and permeation behavior of the particles. While combustion-generated carbon nanoparticles with an aspect ratio close to unity prefer to stay near the membrane center, precursors with other shapes mostly reside within the hydrocarbon tail region of the membrane. Carbon nanoparticles are not trapped in a local region even inside the membranes but move freely with a speed depending on their molecular weight. The adsorption of the particles on the surface of the biological membrane is comparable to thermal fluctuations because the weak segregation effect by water molecules is the main driving force to the adsorption behavior. The bigger the precursors are, the stronger they are bound to the membrane surface. The presence of combustion-generated nanoparticles inside the membrane perturbs local lipid density by pushing the neighboring lipid molecules away from the nanoparticles. This, coupled with thermal fluctuations, can induce an instantaneous membrane pore to allow water protrusion. From the umbrella sampling method, the potential of mean force for the permeation of carbona nanoparticles into the bilayer was also obtained. Surprisingly, elongated particles have a free energy barrier an order of magnitude smaller compared with more round ones. In addition, the round carbon nanoparticles showed strong hysteresis due to the local trapping of water molecules. Although the carbon soot precursors studied in this work are not the well-known carbon nanoparticles such as fullerenes or carbon nanotubes, the qualitative features of this study may be applicable to them as well.