Electrodissociation of clathrate-like structures

In the present work, we develop molecular dynamics (MD) simulations in the NPT (isobaric–isothermic) ensemble to analyse the effect of an external electrostatic field over a cubic methane hydrate crystallite. The amplitude of the field is in the range 0.5–3.0 V/nm. For the simulations, we used the SPC/E rigid water model and a single-site model for methane at a temperature of 248 K and a pressure of 20 bar. When the external electrostatic field is applied, the water dipoles are oriented in such a way that the methane molecules can diffuse far away from the water cages, hence the clathrate dissociation takes place. This last phenomenon was observed for intensities above 1.5 V/nm. Taking the final configuration of each run as input, we develop a new set of MD simulations, and we observe that the stable clathrate is not recovered immediately when the external electrostatic field is turned off due to limitations in the simulation time.     

Cutoff size does strongly influence molecular dynamics results on solvated polypeptides.

The behavior of a 17-residue model peptide is analyzed by means of molecular dynamics simulations including explicitly more than a thousand water molecules. On the basis of the charge-group concept, Coulomb interactions are truncated for three values of the cutoff radius: 0.6, 1.0, and 1.4 nm. It is found that the stability of an alpha-helix, which acts as a common starting configuration, is a function of the cutoff size. While the overall stability of the helix is conserved in a simulation using a cutoff of 1.0 nm, it is lost within a very short period of 100 ps when the cutoff is increased to 1.4 nm. This demonstrates that the commonly used cutoff size of 1.0 nm is inappropriate because it does not ensure the convergence of Coulomb interactions. In order to permit an independent judgment, we have performed a 225-ps simulation using the Ewald summation technique, which is more elaborate but circumvents the problem to find an appropriate cutoff value. In contrast to the 1.4-nm cutoff trajectory, the Ewald technique simulation conserves the helical character of the peptide conformation. This demonstrates that even 1.4 nm is too short a cutoff. Due to the fundamental uncertainty introduced by the use of a simple cutoff, this truncation scheme seems questionable for molecular dynamics simulations of solvated biomolecules.     

Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

Eight molecular dynamics simulations of a ubiquitin crystal unit cell were performed to investigate the effect of different schemes to treat the long-range electrostatic interactions as well as the need to include counter ions. A crystal system was chosen as the test system, because the higher charge density compared with a protein in solution makes it more sensitive to the way of treating the electrostatic interactions. Three different schemes of treating the long-range interactions were compared: straight cutoff, reaction-field approximation, and a lattice-sum method (P3M). For each of these schemes, two simulations were performed, one with and one without the counter ions. Two additional simulations with a reaction-field force and different initial placements of the counter ions were performed to examine the effect of the initial positions of the ions. The inclusion of long-range electrostatic interactions using either a reaction-field or a lattice-sum method proved to be necessary for the simulation of crystals. These two schemes did not differ much in their ability to reproduce the crystallographic structure. The inclusion of counter ions, on the other hand, seems not necessary for obtaining a stable simulation. The initial positions of the ions have a visible but small effect on the simulation.     

Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study

Abstract

An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods—residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used.     

Long-range electrostatic interactions in molecular dynamics: an endothelin-1 case study

An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods--residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used.     

Improvement of radio frequency (RF) heating-assisted alkaline pretreatment on four categories of lignocellulosic biomass

Pretreatment plays an important role in making the cellulose accessible for enzyme hydrolysis and subsequent conversion because it destroys more or less resistance and recalcitrance of biomass. Radio frequency (RF)-assisted dielectric heating was utilized in the alkaline pretreatment on agricultural residues (corn stover), herbaceous crops (switchgrass), hardwood (sweetgum) and softwood (loblolly pine). Pretreatment was performed at 90 °C with either RF or traditional water bath (WB) heating for 1 h after overnight soaking in NaOH solution (0.2 g NaOH/g Biomass). Pretreated materials were characterized by chemical compositional analysis, enzyme hydrolysis, scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The glucan yields of RF-heated four categories of hydrolysates were 89.6, 72.6, 21.7, and 9.9 %. Interestingly, RF heating raised glucan yield on switchgrass and sweetgum but not on corn stover or loblolly pine. The SEM images and FTIR spectra agreed with results of composition analysis and hydrolysis. GC–MS detected some compounds only from RF-heated switchgrass. These compounds were found by other researchers only in high-temperature (150–600 °C) and high-pressure pyrolysis processes.     

Biosynthesis of fluorescent gold nanoparticles using an edible freshwater red alga,Lemanea fluviatilis (L.) C.Ag. and antioxidant activity of biomatrix loaded nanoparticles

Biosynthesis of gold nanoparticles has been accomplished via reduction of an aqueous chloroauric acid solution with the dried biomass of an edible freshwater epilithic red alga, Lemanea fluviatilis (L.) C.Ag., as both reductant and stabilizer. The synthesized nanoparticles were characterized by UV–visible, powder X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared (FT-IR), and dynamic light scattering (DLS) studies. The UV–visible spectrum of the synthesized gold nanoparticles showed the surface plasmon resonance (SPR) at around 530 nm. The powder XRD pattern furnished evidence for the formation of face-centered cubic structure of gold having average crystallite size 5.9 nm. The TEM images showed the nanoparticles to be polydispersed, nearly spherical in shape and have sizes in the range 5–15 nm. The photoluminescence spectrum of the gold nanoparticles excited at 300 nm showed blue emission at around 440 nm. Gold nanoparticles loaded within the biomatrix studied using a modified 2,2-diphenyl-1-picrylhydrazyl (DPPH) method exhibited pronounced antioxidant activity.     

Cryopreservation of conditionally dormant orthodox seeds of Betula pendula

To evaluate the feasibility of long-term cryopreservation of Polish provenances of silver birch (Betula pendula), the sensitivity of conditionally dormant seeds to extreme desiccation and/or the ultra-low temperature of liquid nitrogen (LN; ?196°C) was evaluated. The critical water content (WC) of desiccated seeds and the high-moisture freezing limit of seeds desiccated or moistened to various WCs and frozen for 24 h or for 2 years in LN was also determined. Germination tests revealed no critical WC for seeds [to 0.02 g H₂O g^?1 dry mass (g g^?1)]. Seeds tolerated freezing in LN within specific safe range of WC 0.02–0.23 g g^?1 (nuts). Seeds desiccated to the safe WC and stored in LN for 2 years had similar or higher germination as seeds stored at ?3°C for 2 years, depending on provenance. Therefore, long-term cryopreservation of B. pendula seeds in gene banks is feasible.     

The effects of truncating long-range forces on protein dynamics

This paper considers the effects of truncating long-range forces on protein dynamics. Six methods of truncation that we investigate as a function of cutoff criterion of the long-range potentials are (1) a shifted potential; (2) a switching function; (3) simple atom-atom truncation based on distance; (4) simple atom-atom truncation based on a list which is updated periodically (every 25 steps); (5) simple group-group truncation based on distance; and (6) simple group-group truncation based on a list which is updated periodically (every 25 steps). Based on 70 calculations of carboxymyoglobin we show that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. Evaluation of the different methods is based on comparison of a simulation's rms fluctuation about the average coordinates, the rms deviation from the average coordinates of a no cutoff simulation and from the X-ray structure of the protein. The simulations in which long-range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 A, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function are investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5-9 A range gives reasonable results for a distance-dependent dielectric, but not using a constant dielectric. Both the atom-atom and group-group truncation methods based on distance shows large rms deviation and fluctuation for short cutoff distances, while for cutoff distances of 11 A or greater, reasonable results are achieved. Although comparison of these to distance-based truncation methods show surprisingly larger rms deviations for the group-group truncation, contrary to simulation studies of aqueous ionic solutions. The results of atom-atom or group-group list-based simulations generally appear to be less stable than the distance-based simulations, and require more frequent velocity scaling or stronger coupling to a heat bath.     

Cardenolide estimation in callus-mediated regenerants of Digitalis lamarckii Ivanina (dwarf foxglove)

Digitalis cardenolides can regulate heart rhythms and are effective agents in cancer chemotherapy, in particular, for treating prostate and breast cancer. In this study, an optimized and efficient plant tissue culture protocol was established using callus cultures of Digitalis lamarckii Ivanina, commonly known as dwarf foxglove. Lamina explants developed callus when cultured on Linsmaier and Skoog (LS) medium containing different concentrations of 6-benzyladenine (BA; 4.4, 13.3, or 22.2 μM) and α-naphthalene acetic acid (NAA; 2.7, 5.4, or 10.8 μM). The highest incidence of callus formation (100%) was achieved on LS medium containing 13.3 μM BA and 10.8 μM NAA. Indirect shoot regeneration was achieved when the callus explants were cultured on LS medium supplemented with varying concentrations of BA (0.4, 1.1, or 2.2 μM) and/or gibberellic acid (0.7 or 1.4 μM) for 8 wk. Following the rooting of shoots on LS medium supplemented with either indole-3-acetic acid (ranging from 1.4 to 5.7 μM) or NAA (1.3 to 5.2 μM), lamina and petiole tissues of the 4-mo-old regenerated plants were compared for their cardenolide contents. Lamina extracts showed nearly three times higher cardenolide accumulation than petiole extracts. Of the cardenolides analyzed by reverse-phase high-performance liquid chromatography, neo-odorobioside G and glucogitoroside were abundant in lamina extracts (170.3 and 143.9 mg/kg dry weight, respectively). The regeneration protocol described in this study can be used for the in vitro production of certain cardenolides from D. lamarckii.     

Systematic overestimation of Salicaceae seed survival using radicle emergence in response to drying and storage: implications for ex situ seed banking

Biodiversity conservation programmes are underpinned by seed banking following drying to low water contents (WC), and supported by both the assessment and prediction of seed viability over time. The means of judging viability is thus crucial to the comprehension of seed vigour. We selected seeds of three species and one hybrid in the Salicaceae likely to have variation in tolerance to drying, processing and storage, including in relation to cryobanking, and compared survival growth as radicle emergence (germination) and normal seedling production. With three seed lots of Salix gracilistyla, air-drying to 8–10 % WC enhanced seed survival after 40 days’ storage at 5 °C as compared with non-treated seeds at 14–20 % WC. Four seed lots of Populus alba × P. glandulosa showed equally high germination (88–100 %) and proportions of normal seedlings (81–99 %) when stored at 5 °C for 7–10 weeks. Among seven seed lots of S. gracilistyla, two groups with different storage behaviour could be statistically distinguished with normal seedling production ranging from 0 to 45 % after storage at 5 °C for 13 weeks. Seed tolerance to WC manipulation and cryopreservation was very variable among species and seed lots. Seed lots of S. hallaisanensis and S. gracilistyla with ~80 % germination survived cryopreservation at 10 % WC, but were sensitive to lower WCs. In contrast, Populus seeds had greater desiccation tolerance combined with cryopreservation capability. With seed lots of all species and hybrids, cryopreservation had little effect on viability unless the high moisture freezing limit had been exceeded (~10–20 % WC, depending on seed lot). However, under all conditions of handling (drying, rehydration, storage at 5 °C or cryopreservation) using germination as the only indicator of viability over-estimated survival compared with normal seedling production.     

New nonbonded interactions calculation strategy for rectangular systems. I. Preliminary molecular dynamics study of solvated Na(+) ion

A new molecular nonbonded interactions treatment strategy is proposed in the context of rectangular periodic boundary conditions simulations. Several molecular dynamics simulations are performed on a sodium ion in aqueous solution. Box sizes are modified from a cubic to a rectangular shape. The results are compared with those found using a classical spherical cutoff. This new method yields ion-oxygen radial distribution functions in good agreement with experimental results, thus showing its reliability. Severe perturbations in the structural orientation of water molecules in the first shell with the increase of the box length are observed under the classical cutoff method. However, these distorting effects are reduced with the present nonbonded interactions treatment.     

Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.     

Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells

Eight molecular dynamics simulations of a double crystal unit cell of ubiquitin were performed to investigate the effects of simulating at constant pressure and of simulating two unit cells compared to a single unit cell. To examine the influence of different simulation conditions, the constant-pressure and constant-volume simulations were each performed with and without counterions and using two different treatments of the long-range electrostatic interactions (lattice-sum and reaction-field methods). The constant-pressure simulations were analyzed in terms of unit cell deformation and accompanying protein deformations. Energetic and structural properties of the proteins in the simulations of the double unit cell were compared to the results of previously reported one-unit-cell simulations. Correlation between the two unit cells was also investigated based on relative translational and rotational movements of the proteins and on dipole fluctuations. The box in the constant-pressure simulations is found to deform slowly to reach convergence only after 5-10 ns. This deformation does not result from a distortion in the structure of the proteins but rather from changes in protein packing within the unit cell. The results of the double-unit-cell simulations are closely similar to the results of the single-unit-cell simulations, and little motional correlation is found between the two unit cells.     

Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method

The particle-mesh Ewald (PME) method is considered to be both efficient and accurate for the evaluation of long-range electrostatic interactions in large macromolecular systems being studied by molecular dynamics simulations. This method assumes "infinite" periodic boundary conditions resembling the symmetry of a crystal environment. Can such a "solid-state" method accurately portray a macromolecular solute such as DNA in solution? To address this issue, we have performed three 1500-ps PME molecular dynamics (MD) simulations, each with a different box size, on the d(CGCGA6CG)-(CGT6CGCG) DNA dodecamer. The smallest box had the DNA solvated by a layer of water molecules of at least 5 A along each orthogonal direction. The intermediate size box and the largest box had the DNA solvated by a layer of water molecules of at least 10 A and 15 A, respectively, along each orthogonal direction. The intermediate size box in the present study is similar to the box size currently chosen by most workers in the field. Based on a comparison of RMSDs and curvature for this single DNA dodecamer sequence, the larger two box sizes do not appear to afford any extra benefit over the smallest box. The implications of this finding are briefly discussed.     

On the truncation of long-range electrostatic interactions in DNA

Long-range interactions are known to play an important role in highly polar biomolecules like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate treatment of the long-range interactions are crucial for achieving stable nanosecond trajectories. In this report, we evaluate the structural and dynamic effects on a highly charged oligonucleotide in aqueous solution from different long-range truncation methods. Two group-based truncation methods, one with a switching function and one with a force-switching function were found to fail to give accurate stable trajectories close to the crystal structure. For these group-based truncation methods, large root mean square (rms) deviations from the initial structure were obtained and severe distortions of the oligonucleotide were observed. Another group-based truncation scheme, which used an abrupt truncation at 8. 0 A or at 12.0 A was also investigated. For the short cutoff distance, the conformations deviated far away from the initial structure and were significantly distorted. However, for the longer cutoff, where all necessary electrostatic interactions were included, the trajectory was quite stable. For the particle mesh Ewald (PME) truncation method, a stable DNA simulation with a heavy atom rms deviation of 1.5 A was obtained. The atom-based truncation methods also resulted in stable trajectories, according to the rms deviation from the initial B-DNA structure, of between 1.5 and 1.7 A for the heavy atoms. In these stable simulations, the heavy atom rms deviations were approximately 0.6-1.0 A lower for the bases than for the backbone. An increase of the cutoff radius from 8 to 12 A decreased the rms deviation by approximately 0.2 A for the atom-based truncation method with a force-shifting function, but increased the computational time by a factor of 2. Increasing the cutoff from 12 to 18 A for the atom-based truncation method with a force-shifting function requires 2-3 times more computational time, but did not significantly change the rms deviation. Similar rms deviations from the initial structure were found for the atom-based method with a force-shifting function and for the PME method. The computational cost was longer for the PME method with a cutoff of 12. 0 A for the direct space nonbonded calculations than for the atom-based truncation method with a force-shifting function and a cutoff of 12.0 A. If a nonperiodic boundary, e.g., a spherical boundary, was used, a considerable speedup could be achieved. From the rms fluctuations, the terminal nucleotides and especially the cytidines were found to be more flexible than the nonterminal nucleotides. The B-DNA form of the oligonucleotide was maintained throughout the simulations and is judged to depend on the parameters of the energy function and not on the truncation method used to handle the long-range electrostatic interactions. To perform accurate and stable simulations of highly charged biological macromolecules, we recommend that the atom-based force-shift method or the PME method should be used for the long-range electrostatics interactions.     

Thermodynamics of pyrope–majorite,Mg3Al2Si3O12–Mg4Si4O12, solid solution from atomistic model calculations

Static lattice energy calculations, based on empirical pair potentials have been performed for a large set of different structures with compositions between pyrope and majorite, and with different states of order of octahedral cations. The energies have been cluster expanded using pair and quaternary terms. The derived ordering constants have been used to constrain Monte–Carlo simulations of temperature-dependent properties in the ranges of 1073–3673 K and 0–20 GPa. The free energies of mixing have been calculated using the method of thermodynamic integration. At zero pressure the cubic/tetragonal transition is predicted for pure majorite at 3300 K. The transition temperature decreases with the increase of the pyrope mole fraction. A miscibility gap associated with the transition starts to develop at about 2000 K and x _maj = 0.8, and widens with the decrease in temperature and the increase in pressure. Activity–composition relations in the range of 0–20 GPa and 1073–2673 K are described with the help of a high-order Redlich–Kister polynomial.     

Curcumin specifically binds to the human calcium–calmodulin-dependent protein kinase IV: fluorescence and molecular dynamics simulation studies

Calcium–calmodulin-dependent protein kinase IV (CAMK4) plays significant role in the regulation of calcium-dependent gene expression, and thus, it is involved in varieties of cellular functions such as cell signaling and neuronal survival. On the other hand, curcumin, a naturally occurring yellow bioactive component of turmeric possesses wide spectrum of biological actions, and it is widely used to treat atherosclerosis, diabetes, cancer, and inflammation. It also acts as an antioxidant. Here, we studied the interaction of curcumin with human CAMK4 at pH 7.4 using molecular docking, molecular dynamics (MD) simulations, fluorescence binding, and surface plasmon resonance (SPR) methods. We performed MD simulations for both neutral and anionic forms of CAMK4-curcumin complexes for a reasonably long time (150 ns) to see the overall stability of the protein–ligand complex. Molecular docking studies revealed that the curcumin binds in the large hydrophobic cavity of kinase domain of CAMK4 through several hydrophobic and hydrogen-bonded interactions. Additionally, MD simulations studies contributed in understanding the stability of protein–ligand complex system in aqueous solution and conformational changes in the CAMK4 upon binding of curcumin. A significant increase in the fluorescence intensity at 495 nm was observed (λ_exc = 425 nm), suggesting a strong interaction of curcumin to the CAMK4. A high binding affinity (K_D = 3.7 × 10^?8 ± .03 M) of curcumin for the CAMK4 was measured by SPR further indicating curcumin as a potential ligand for the CAMK4. This study will provide insights into designing a new inspired curcumin derivatives as therapeutic agents against many life-threatening diseases.     

Optimal Waist Circumference for Prediction of Metabolic Syndrome in Young Korean Women With Polycystic Ovary Syndrome

The International Diabetes Federation consensus proposed an ethnically specific criteria of waist circumference (WC) for central obesity, but, the nationwide definition is still debated in Korea. For the detection of the optimal WC cutoff value, the nonadipose components of the metabolic syndrome (MS) were defined by modification of revised 2003 Rotterdam consensus as having two or more risk factors such as hypertension, hyperglycemia, and dyslipidemia without consideration of abdominal obesity. By using receiver‐operating characteristic (ROC) curve analysis, cutoff points of WC and visceral fat area (VFA) for prediction of MS were 80 cm and 53.1 cm². WC cutoff points corresponding to VFA >53.1 and 100 cm² were 73.3 and 77.8 cm. The sensitivity and specificity of currently used value of WC 88 cm were 41.9 and 91.5%, suggesting that it could be too high in Korean population. Central obesity defined as WC >80 cm was significantly associated with nonadipose components of MS after adjustment for age, BMI, cholesterol, triglycerides, fasting insulin, and free testosterone levels. Central obesity with WC of >80 cm predicted the presence of nonadipose MS (odds ratio 16.6; 95% confidence interval (CI) 6.5–42.6). It was also significant (odds ratio 14.7; 95% CI 3.4–64.3) when we applied the WC value of 70 cm instead of 80 cm. In conclusion, WC of 80 and 70 cm could be appropriate cutoff points to identify the MS and visceral adiposity in Korean women with polycystic ovary syndrome (PCOS), respectively. Therefore, PCOS women with a WC over 70 cm should be closely monitored for the development of MS.