Hydration of β-cyclodextrin: A molecular dynamics simulation study

We study by molecular dynamics simulations the hydration of -cyclodextrin. Our simulations show that within these barrel-shaped molecules hydrophobicity dominates, while at the top and bottom sides of the barrel interactions with water are mostly hydrophilic in nature. These results agree with crystallographic data at 120 K and, in particular, with the spontaneous hydration process of a cyclodextrin crystal in wet atmosphere. The predicted structure of the hydration shells is discussed and compared with previous molecular mechanics calculations which report an overall hydrophobic behavior. Moreover, the temperature dependence of the hydration process is discussed.     

A molecular dynamics study of the thermal response of crystalline cellulose Iβ

Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose Iβ. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose Iβ at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475–500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30° and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.     

Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization

N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.     

Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study

The interaction of OH(-) with the sugar β-d-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH(-) abstracts a proton from the sugar in a barrier-less process, yielding H(2)O and a Deprotonated beta-d-Galactose anion, (Dep-beta-d-G)(-). (2) This reaction can be reversed when two additional H(2)O molecules are present in the sugar. (3) At 500 K, a ring-opening reaction occurs in (Dep-beta-d-G)(-) within a timescale of 10 ps. The (neutral) sugar itself is stable over this timescale, and well beyond. This indicates that OH(-) can catalyze the degradation of β-d-galactose. Implications of this process are briefly discussed.     

Amyloid peptide Aβ40 inhibits aggregation of Aβ42: evidence from molecular dynamics simulations

Effects of amyloid beta (Aβ) peptide Aβ(40) on secondary structures of Aβ(42) are studied by all-atom simulations using the GROMOS96 43a1 force field with explicit water. It is shown that in the presence of Aβ(40) the beta-content of monomer Aβ(42) is reduced. Since the fibril-prone conformation N? of full-length Aβ peptides has the shape of beta strand-loop-beta strand this result suggests that Aβ(40) decreases the probability of observing N? of Aβ(42) in monomer state. Based on this and the hypothesis that the higher is the population of N? the higher fibril formation rates, one can expect that, in agreement with the recent experiment, Aβ(40) inhibit fibril formation of Aβ(42). It is shown that the presence of Aβ(40) makes the salt bridge D23-K28 and fragment 18-33 of Aβ(42) more flexible providing additional support for this experimental fact. Our estimation of the binding free energy by the molecular mechanics-Poisson-Boltzmann surface area method reveals the inhibition mechanism that Aβ(40) binds to Aβ(42) modifying its morphology.     

Stabilizing effect of cholesterol on the state of β2-adrenergic receptor with a broken ionic lock: a molecular dynamics study

A molecular dynamics simulation of the β₂-adrenergic receptor (β₂AR) embedded in a hydrated lipid bilayer showed that the state with a broken ionic lock (salt bridge) between the arginine residue Arg131 and the glutamic acid residue Glu268 is stabilized in the presence of cholesterol molecules. This should be considered as a transient state to the active state of the receptor.     

Identify promising IKK-β inhibitors: A docking-based 3D-QSAR study combining molecular design and molecular dynamics simulation

Inhibitor of nuclear factor kappa B kinase subunit beta (IKK-β), a specific regulator of nuclear factor-κB (NF-κB), is considered a valid target to design novel drugs to treat rheumatoid arthritis, glomerulonephritis and various cancers. In this study, in order to design and then identify promising compounds targeting IKK-β, a series of reported IKK-β inhibitors were used to develop 3D-QSAR models. Docking-based and minimization-based poses were generated for model construction. CoMSIA model #8 based on docking poses was selected due to its satisfactory internal and external validation results and the sufficient information delivery capability. After a contour map analysis, 41 new designs were depicted based on a graphical design scheme and 25 of them were assessed as eligible for screening. Compound 21MX007 has aroused our attention for its both competitive QSAR-prediction and docking-scoring result. Detailed docking interactions of 21MX007-protein complex were investigated via a deep analysis of docking results and a comparative molecular dynamics simulation. Strong interactions and an extra hydrogen bond which echoes the H-bond requirements of substituent acquired from the design scheme were observed. From MD analysis, 21MX007-protein system was tested. The system was proved to have good stability in terms of a downward trend of RMSD and Rg values and a continuous and stable H-bond interaction and a lower average binding free energy. Thus, compound 21MX007 was successfully identified as a promising IKK-β inhibitor.     

Effect of concentration on surfactant micelle shapes —A molecular dynamics study

Many aspects of the behavior of surfactants have not been well understood due to the coupling of many different mechanisms. Computer simulation is, therefore, attractive in the sense that it can explore the effect of different mechanisms separately. In this paper, the shapes, structures and sizes of sodium dodecylbenzenesulfonate (SDBS) micelles under different concentrations in an oil/water mixture were studied via molecular dynamics (MD) simulations using a simplified atomistic model which basically maintains the hydrophile and lipophile properties of the surfactant molecules. Above the critical micellar concentration (cmc), surfactant molecules aggregate spontaneously to form a wide variety of assemblies, from spherical to rodlike, wormlike and bilayer micelles. Changes in their ratios of the principle moments of inertia (g₁/g₃, g₂/g₃) indicated the transition of micelle shapes at different concentrations. The aggregation number of micelle is found to have a power-law dependence on surfactant concentration.     

Role of alkylated residues in the tetrapeptide self-assembly—A molecular dynamics study

Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.     

Effect of concentration on surfactant micelle shapes——A molecular dynamics study

Above the critical micellar concentration (cmc), micelles with a wide variety of structures and shapes are formed with the increase of surfactant concentra-tion in surfactant-water or surfactant-water-oil systems, such as spherical micelles, rodlike micelles, and bilay-ers. The viewpoint that micelle should be in spheres of constant size was first proposed by Hartley[1]. Later experiments by light scatter indicated that most mi-celles were indeed spherical, and their aggregation numbers were c…     

Structure and molecular dynamics of host–guest complexes of TEMPO with cucurbituryl: An ESR and DFT study

Host–guest complexes are of interest as promising nanodevices for molecular recognition and chemosensors. In this work, the structure and molecular dynamics of complexes of the nitroxyl radical TEMPO (I), as models of indicator and analyte, with cucurbituril CB[7] in solution and in the solid phase have been studied by ESR and DFT methods. The kinetic accessibility of the NO group of I for water-soluble reagents has been determined. By simulation of the ESR spectra of the complex, the rotational diffusion coefficients and the anisotropy of its rotation have been determined. To study the rotational mobility of the guest in the CB[7] cavity, solid solutions of I@CB[7] in the CB[7] matrix have been obtained. The ESR spectra indicate rapid jump-like rotation of I about an axis oriented along the normal to the CB[7] portals. The formation energy and the spatial structure of the complex have been calculated by the DFT method; a change in the spin density on the NO group with changing the orientation of I in the CB[7] cavity has been found.     

What determines MALDI ion yields? A molecular dynamics study of ion loss mechanisms

Ion recombination in matrix-assisted laser desorption/ionization (MALDI) is as important as any ion formation process in determining the quantity of ions observed but has received comparatively little attention. Molecular dynamics simulations are used here to investigate some models for recombination, including a Langevin-type model, a soft threshold model and a tunneling model. The latter was found to be superior due to its foundations in a widespread physical phenomenon, and its lack of excessive sensitivity to parameter choice. Tunneling recombination in the Marcus inverted region may be a major reason why MALDI is a viable analytical method, by allowing ion formation to exceed ion loss on the time scale of the plume expansion. Ion velocities, photoacoustic transients and pump-probe measurements might be used to investigate the role of recombination in different MALDI matrices, and to select new matrices.     

Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's Aβ42 peptide

The growth of amyloid fibrils is studied by replica exchange molecular dynamics in an implicit solvent. Our data indicate that extremely long simulation times (at least a few hundred ns) are necessary to study the thermodynamics of fibril elongation in detail. However some aspects of the aggregation process are already accessible on the time scales available in the present study. A peak in the specific heat indicates a docking temperature of T(dock) ≈ 320 K. Irreversible locking requires lower temperatures with the locking temperature estimated as T(lock) ≈ 280 K. In our simulation the fibril grows from both sides with the C-terminal of the incoming monomer attaching to the C-terminal of the peptides in the fibril forming a β-sheet on the fibril edge. Our simulation indicates that the C-terminal is crucial for aggregation.     

Stochastic kinetic study of protein aggregation and molecular crowding effects of Aβ40 and Aβ42

Two isoforms of β-amyloid peptides, Aβ40 and Aβ42, differ from each other only in the last two amino acids, IA, at the end of Aβ42. They, however, differ significantly in their ability in inducing Alzheimer's disease (AD). The rate curves of fibril growth of Aβ40 and Aβ42 and the effects of molecular crowding have been measured in in vitro experiments. These experimental curves, on the other hand, have been fitted in terms of rate constants for elementary reaction steps using rate equation approaches. Several sets of such rate parameters have been reported in the literature. Employing a recently developed stochastic kinetic method, implemented in a browser-based simulator, popsim, we study to reveal the differences in the kinetic behaviors implied by these sets of rate parameters. In particular, the stochastic method is used to distinguish the kinetic behaviors between Aβ40 and Aβ42 isoforms. As a result, we make general comments on the usefulness of these sets of rate parameters.     

Host–guest complexation of a nitroheterocyclic compound with cyclodextrins: a spectrofluorimetric and molecular modeling study

Nitroheterocyclic compounds (NC) were candidate drugs proposed for Chagas disease chemotherapy. In this study, we investigated the complexation of hydroxymethylnitrofurazone (NFOH), a potential antichagasic compound, with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD), Hydroxypropyl-β-cyclodextrin (HP-β-CD), Dimethyl-β-cyclodextrin (DM-β-CD) and γ-cyclodextrin (γ-CD) by fluorescence spectroscopy and molecular modeling studies. Hildebrand–Benesi equation was used to calculate the formation constants of NFOH with cyclodextrins based on the fluorescence differences in the CDs solution. The complexing capacity of NFOH with different CDs was compared through the results of association constant according to the following order: DM-β-CD > β-CD > α-CD > HP-β-CD > γ-CD. Molecular modeling studies give support for the experimental assignments, in favor of the formation of an inclusion complex between cyclodextrins with NFOH. This is an important study to investigate the effects of different kinds of cyclodextrins on the inclusion complex formation with NFOH and to better characterize a potential formulations to be used as therapeutic options for the oral treatment of Chagas disease.     

Is the alignment of nematics on a polymer slab always along the rubbing direction? A molecular dynamics study

ABSTRACT

We have studied the alignment and molecular organisation within a thin film of the popular nematic 5CB sandwiched between two flat polymer slabs, examining the effect of polymer chemical nature and morphology with atomistic molecular dynamics simulations. We have chosen two common polymers: polystyrene (PS) and polymethylmethacrylate (PMMA), either with their chains in random coil conformation (disordered) or with chains unidirectionally stretched (ordered). We found that, independently on the arrangement of the chains, both surfaces align planarly the liquid crystal, in accord with experimental observation. Moreover, while 5CB molecules align along the chains stretching direction of the PMMA ordered surface, on the combed PS surface they arrange on average perpendicularly to the stretching direction. This behaviour is attributed to the chemically specific interactions between the respective aromatic moieties of PS and 5CB.     

The damage of the Watson–Crick base pairs by nickel nanoparticles: A first-principles molecular dynamics study

The nickel nanoparticles are harmful atmospheric pollutants, and the damage caused by them in humans has become a topic of great relevance. In this study we investigate the interaction of the Ni₂ and Ni₃ clusters with the AT and GC Watson–Crick base pairs in an aqueous medium. Molecular dynamics in combination with density functional theory are employed. A novel method is implemented to create realistic thermodynamic conditions (NVT) in the simulations. The energies, the charges of the interacting compounds, the temperature changes, and the geometric rearrangements are reported. The results show the formation of stable organometallic compounds of the nickel nanoparticles with the DNA nucleic acid bases. In this respect, the biological processes where the DNA is implicated may be altered by the formation of such super-structures.     

Accumulation of host—guest ion complexes with different counterions at the water—supercritical CO2 interface: a molecular dynamics study

The behavior of ion complexes at the water—supercritical carbon dioxide interface was considered by molecular dynamics simulations. The following complexes were studied: Cs⁺calix[4]crown-6, K⁺222 cryptate with chloride or dicarbollide (CCD^–) counterions, the Sr²⁺18C6 complex with the picrate (Pic^–) or perfluorooctanoate (PFO^–) counterions, and the Cl^–Tet ⁴⁺ complex with chloride counterions (Tet ⁴⁺ is a tetrahedral tetraammonium cation). The simulations demonstrate the analogy between aqueous interfaces with organic immiscible liquids and the CO₂ phase. Water and supercritical CO₂ are poorly miscible and form an interface. Most of the complexes are accumulated at the interface, instead of diffusing into the organic phase in which they should be more soluble. In addition, marked counterion effects are observed. The CCD^–, Pic^–, and PFO^– anions are surface active and are concentrated at the interface, but show different relationships with the complexes. The formation of ion pairs is precluded by the very hydrophobic CCD^– anions, which promote the extraction of cryptates as separated ion pairs to the CO₂ phase. Conversely, the extraction of the Sr²⁺ ions with 18C6 proceeds via a co-complexation mechanism, including the formation of the Sr18C6(PFO)₂, complex having a CO₂ affinity. The mechanism of assisted ion transfer to the CO₂ phase is discussed.     

Poly(oxyethylene)–cation interactions in aqueous solution: a molecular dynamics study

We have performed molecular dynamics simulations of a poly(oxyethylene) (POE) chain with 15 ethylene oxide units in an aqueous solution in the presence of potassium cations for 1 ns. The effect of the potassium ions on the POE aqueous solution characteristics are examined for the energetics, the hydration, the chain conformation and dynamics, and the solvent structure in comparison to those in the absence of cations. The POE's helical conformation is considerably distorted by complex formations with K⁺, and a significant perturbation of the POE hydration by K⁺ is observed. The competition between the K⁺–water and the K⁺–POE associations is found to be heavily shifted toward the latter. Furthermore, the POE–water pair interaction energy drastically decreases upon addition of K⁺. The observations, along with the decreased chain flexibility, point to the salting-out of POE salt aqueous solutions.