Molecular dynamics study on the stabilization of dehydrated lipid bilayers with glucose and trehalose

In this study, we use molecular dynamics simulations to investigate and compare the interactions of DPPC bilayers with and without saccharides (glucose or trehalose) under dehydrated conditions. Results from the simulations indicate that unilamellar bilayers lose their structural integrity under dehydrated conditions in the absence of saccharides; however, in the presence of either glucose or trehalose, the bilayers maintain their stability. Hydrogen bond analysis shows that the saccharide molecules displace a significant amount of water surrounding the lipid headgroups. At the same time, the additional hydrogen bonds formed between water and saccharide molecules help to maintain a hydration layer on the lipid bilayer interface. On the basis of the hydrogen bond distributions, trehalose forms more hydrogen bonds with the lipids than glucose, and it is less likely to interact with neighboring saccharide molecules. These results suggest that the interaction between the saccharide and lipid molecules through hydrogen bonds is an essential component of the mechanism for the stabilization of lipid bilayers.     

Molecular dynamics simulation study of the interaction of trehalose with lipid membranes

The interactions of the cryoprotective agent trehalose with a lipid membrane made of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine at 323 K were studied by means of molecular dynamics simulations. It was observed that trehalose binds to the phospholipid headgroups with its main axis parallel to the membrane normal. Trehalose establishes hydrogen bonds with the carbonyl and phosphate groups and replaces water molecules from the lipid headgroup. Notably, the number of hydrogen bonds (HBs) that the membrane made with its environment was conserved after trehalose binding. The HBs between lipid and trehalose have a longer lifetime than those established between lipid and water. The binding of the sugar does not produce changes either in the lipid area or in the lipid order parameter. The effect of trehalose on the dipole potential is in agreement with experimental results. The contribution of the different components to the membrane dipole potential was analyzed. It was observed that the binding of trehalose produces changes in the different components and the sugar itself contributes to the surface potential due to the polarization of its hydroxyl in the interface.     

Solvent effect on the excited-state dynamics of analogues of the photoactive yellow protein chromophore

We previously reported that two analogues of the Photoactive Yellow Protein chromophore, trans-p-hydroxycinnamic acid (pCA(2-)) and its amide derivative (pCM-) in their deprotonated forms, undergo a trans-cis photoisomerization whereas the thioester derivative, trans-p-hydroxythiophenyl cinnamate (pCT-), does not. pCT- is also the only one to exhibit a short-lived intermediate on its excited-state deactivation pathway. We here further stress the existence of two different relaxation mechanisms for these molecules and examine the reaction coordinates involved. We looked at the effect of the solvent properties (viscosity, polarity, solvation dynamics) on their excited-state relaxation dynamics, probed by ultrafast transient absorption spectroscopy. Sensitivity to the solvent properties is found to be larger for pCT- than for pCA(2-) and pCM-. This difference is considered to reveal that either the relaxation pathway or the reaction coordinate is different for these two classes of analogues. It is also found to be correlated to the electron donor-acceptor character of the molecule. We attribute the excited-state deactivation of analogues bearing a weaker acceptor group, pCA(2-) and pCM-, to a stilbene-like photoisomerization mechanism with the concerted rotation of the ethylenic bond and one adjacent single bond. For pCT-, which contains a stronger acceptor group, we consider a photoisomerization mechanism mainly involving the single torsion of the ethylenic bond. The excited-state deactivation of pCT- would lead to the formation of a ground-state intermediate at the "perp" geometry, which would return to the initial trans conformation without net isomerization.     

Predicting internal protein dynamics from structures using coupled networks of hindered rotators

Internal motions in proteins, such as oscillations of internuclear vectors u(N(i)H(i) (N)) of amide bonds about their equilibrium position, can be characterized by a local order parameter. This dynamic parameter can be determined experimentally by measuring the longitudinal and transverse relaxation rates of (15)N(i) nuclei by suitable NMR methods. In this paper, it is shown that local variations of order parameters S(ii) (2) can be predicted from the knowledge of the structure. To this effect, the diffusive motion of the internuclear vector u(N(i)H(i) (N)) is described in a potential that takes into account the deviations of the angles theta(ij) between u(N(i)H(i) (N)) and neighboring vectors u(N(j)H(j) (N)) from their average value and similarly of deviations of the angles subtended between u(N(i)H(i) (N)) and u(X(j)Y(j)), where X(j) and Y(j) are heavy atoms in the vicinity of the u(N(i)H(i) (N)) vector under investigation. It is shown how the concept of vicinity can be defined by a simple cutoff threshold, i.e., by neglecting vectors u(X(j)Y(j)) with distances d(N(i),X(j))>7.5 A. The local order parameters S(ii) (2) can be predicted from the structure using a limited set of coordinates of heavy atoms. The inclusion of a larger number of heavy atoms does not improve the predictions. Applications to calmodulin, calbindin, and interleukin 4 illustrate the success and limitations of the predictions.     

The effect of fiber coating on the tensile properties of ionomer-based composites

Asbestos fibers, of the chrysotile variety, were coated with a thin polyamide film by an in situ polycondensation technique. Ionomer-based composites were prepared containing the so-modified asbestos fibers in a random in-plane orientation; results of testing the tensile properties of these asbestos/polyamide/ionomer composites are presented. Parameters investigated comprise the asbestos content in the composite and the polyamide content deposited on asbestos. A significant improvement in the tensile performance was established, especially at the intermediate polyamide content of 3.4 phr. The behavior is discussed in terms of possible interactions between the phases present in the composite material.     

The influence of macromolecular crowding on HIV-1 protease internal dynamics

High macromolecular concentrations, or crowded conditions, have been shown to affect a wide variety of molecular processes, including diffusion, association and dissociation, and protein folding and stability. Here, we model the effect of macromolecular crowding on the internal dynamics of a protein, HIV-1 protease, using Brownian dynamics simulations. HIV-1 protease possesses a pair of flaps which are postulated to open in the early stages of its catalytic mechanism. Compared to low concentrations, close-packed concentrations of repulsive crowding agents are found to significantly reduce the fraction of time that the protease flaps are open. Macromolecular crowding is likely to have a major effect on in vivo enzyme activity, and may play an important regulatory role in the viral life cycle.     

The effect of tungsten coating on the properties of diamond thick films

According to the physical properties of pure tungsten and tantalum and their carbides, a layer of tungsten thin films coating three tantalum filaments at a current of 750 A was prepared by us for the first time and called tungsten coating. Diamond thick films were deposited in a hot filament chemical vapor deposition (HFCVD) reactor using tantalum filaments before and after tungsten coating, respectively. The success of tungsten coating is verified by scanning electron microscopy examination of these filaments. The remarkable discrepancies in thermal conductivity, colors of diamond thick films, and electron dispersion spectroscopy of the films substantiate the success of tungsten coating, too. The effects of tungsten coating on the quality of diamond films were finally evaluated by Raman spectra. The text was submitted by the authors in English.     

The effect of coating on the stiffness and toughness of encapsulated fiber composites

The effect of the coating of the fiber on the stiffness and toughness of composite materials is presented in this paper. The type of composite material considered is of a macroscopically isotropic composite medium containing coated fibers. The models used to simulate such materials consists of: the cylindrical fiber, a cylindrical annulus of the coating, an annulus of the matrix enveloped by an infinite region of an equivalent composite consisting of a transversely isotropic material and representing the real composite with dispersed coated fibers. Solutions for the longitudinal, transverse and shear elastic moduli in the four-phase model were established assuming linear elastic conditions. The results were found to depend on the extent and the mechanical properties of the coating. The stiffness and toughness of the composite were evaluated in models representing plane-stress equatorial sections of the representative volume element of the real material according to the Hashin-Rosen model. The stiffness of the fiber composites was studied by varying the rigidity and the extent of the fiber-coating in the model and evaluating its influence on the overall mechanical behavior of the model. On the other hand, the toughness of the composite was evaluated by the method of caustics in models made of composite PMMA plates with PMMA inclusions coated with a ductile annulus. Interesting results were derived concerning the influence of the soft annulus on the mechanical behavior of the composite.     

Photodissociation dynamics of the methyl radical at 212.5 nm: effect of parent internal excitation

Photodissociation dynamics of the CH3 radical at 212.5 nm has been investigated using the H atom Rydberg tagging time-of-flight method with a pure CH3 radical source generated by the photolysis of CH3I at 266 nm. Time-of-flight spectra of the H atom products from the photolysis of both cold and hot methyl radicals have been measured at different photolysis polarizations. Experimental results indicate that the photodissociation of the methyl radical in its ground vibrational state at 212.5 nm excitation occurs on a very fast time scale in comparison with its rotational period, indicating the CH3 dissociation at 212.5 nm occurs on the excited 3s Rydberg state surface. Experimental evidence also shows that the photodissociation of the methyl radical in the nu2 = 1 state of the umbrella mode at 212.5 nm excitation is characteristically different from that in the ground vibrational state.     

Modulating membrane properties: the effect of trehalose and cholesterol on a phospholipid bilayer

The protective properties of trehalose on cholesterol-containing lipid dipalmitoylphosphatidylcholine (DPPC) bilayers are studied through molecular simulations. The ability of the disaccharide to interact with the phospholipid headgroups and stabilize the membrane persists even at high cholesterol concentrations and restricts some of the changes to the structure that would otherwise be imposed by cholesterol molecules. Predictions of bilayer properties such as area per lipid, tail ordering, and chain conformation support the notion that the disaccharide decreases the main melting transition in these multicomponent model membranes, which correspond more closely to common biological systems than pure bilayers. Molecular simulations indicate that the membrane dynamics are slowed considerably by the presence of trehalose, indicating that high sugar concentrations would serve to avert possible phase separations that could arise in mixed phospholipid systems. Various time correlation functions suggest that the character of the modifications in lipid dynamics induced by trehalose and cholesterol is different in the hydrophilic and hydrophobic regions of the membrane.     

Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.     

The effect of a polypyrrole coating on the thermal stability of microporous polyethylene membranes

Microporous polyethylene (PE) membranes were coated on both sides with a polypyrrole (PPy) overlayer. PPy was deposited also on the walls of pores. Thermodeformation measurements indicate that the hard framework produced by rigid-chain PPy controls the mechanical properties of composite membranes. FTIR spectroscopy was used to detect oxidative processes in both polymer components above 200 °C. Elemental analysis showed that the nitrogen content remains at high level, even after the treatment of membranes in air at 300 °C, indicating that the decomposition involved mainly PE while PPy was much more stable. The changes in surface relief after annealing were assessed with electron microscopy. No oxidative processes were identified in the FTIR spectra of composites after annealing in vacuum, even after treatment at 300 °C.     

The effect of environment on local dynamics of macromolecules

The role of local environment on mobility of chain molecules is illustrated by considering the case of a miscible mixture of two polymers. The historical background, observed dynamic responses to mixing, and theoretical explanations for these responses are outlined. Two miscible blend systems: poly(isoprene) [PI]/poly(vinyl ethylene) [PVE] and poly(ethylene oxide) [PEO]/poly(methyl methacrylate) [PMMA] are reviewed in detail, with available data consolidated in a set of figures. Unusual features of the PEO/PMMA blend are discussed.     

Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations

Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents from AHBC simulations and experimental results, we observed based on the presented simulations that the two ends of the peptide may simultaneously take part in the formation of the helical structure at the early stage of folding and finally merge to form a helix with lowest backbone RMSD of about 0.9 A? in 40% 2,2,2-trifluoroethanol solution. However, in pure water, the folding may start at the center of the peptide sequence instead of at the two opposite ends. The analysis of the free energy landscape indicates that the solvent may determine the folding clusters of E6ap, which subsequently leads to the different final folded structure. The current study demonstrates new insight to the role of solvent in the determination of protein structure and folding dynamics.     

The effect of internal lipids on the water sorption kinetics of keratinised tissues

Water has a large influence on the properties of keratinised tissues. The water diffusion properties of keratinised tissues are known to be governed by the cell membrane complex, which is mainly composed of internal lipids. The main aim of this work was to characterise the differences in the water sorption and desorption behaviour of human hair and stratum corneum (SC) both with and without internal lipids. Absorption and desorption curves were obtained using a thermogravimetric balance equipped with a controlled humidity chamber. The results demonstrate that the role of the intercellular lipids in the SC is more marked than in hair, which is likely due to the greater amount of lipids present in its structure. Therefore, lipid structures in the SC are essential both to prevent changes in the water-holding capacity of the skin and to maintain the water permeability of the SC.     

The effect of organic additives on the local dynamics of polyelectrolyte-surfactant complexes

The effect of organic additives on the local dynamics of complexes of poly(N-ethyl-4-vinylpyridinium bromide) with sodium dodecyl sulfate is studied with the use of the solubilization of butanol and Triton X-100 as an example. It is shown that, irrespective of the chemical nature of the solubilizate, the addition of organic compounds gives rise to an increase in the local mobility of the micellar phase. In this case, the segmental mobility of the polyelectrolyte in complexes remains unchanged.     

The effect of interfacial viscosity on the droplet dynamics under flow field

The effects of interfacial viscosity on the droplet dynamics in simple shear flow and planar hyperbolic flow are investigated by numerical simulation with diffuse interface model. The change of interfacial viscosity results in an apparent slip of interfacial velocity. Interfacial viscosity has been found to have different influence on droplet deformation and coalescence. Smaller interfacial viscosity can stabilize droplet shape in flow field, while larger interfacial viscosity will increase droplet deformation, or even make droplet breakup faster. Different behavior is found in droplet coalescence, where smaller interfacial viscosity speeds up film drainage and droplet coalescence, but larger interfacial viscosity postpones the film drainage process. This is due to the change of film shape from flat‐like for smaller interfacial viscosity to dimple‐like for larger interfacial viscosity. The film drainage time still scales as Ca⁰ at smaller capillary number (Ca), and Ca^1.5 at higher capillary number when the interfacial viscosity changes. The interfacial viscosity only affects the transition between these limiting scaling relationships. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1505–1514, 2008     

Water dynamics at protein interfaces: ultrafast optical Kerr effect study

The behavior of water molecules surrounding a protein can have an important bearing on its structure and function. Consequently, a great deal of attention has been focused on changes in the relaxation dynamics of water when it is located at the protein surface. Here we use the ultrafast optical Kerr effect to study the H-bond structure and dynamics of aqueous solutions of proteins. Measurements are made for three proteins as a function of concentration. We find that the water dynamics in the first solvation layer of the proteins are slowed by up to a factor of 8 in comparison to those in bulk water. The most marked slowdown was observed for the most hydrophilic protein studied, bovine serum albumin, whereas the most hydrophobic protein, trypsin, had a slightly smaller effect. The terahertz Raman spectra of these protein solutions resemble those of pure water up to 5 wt % of protein, above which a new feature appears at ~80 cm(-1), which is assigned to a bending of the protein amide chain.     

The combined effect of cations and anions on the dynamics of water

We studied the orientational relaxation of the OD-stretch vibration of HDO molecules in concentrated solutions of alkali-halide salts (NaCl, NaI, CsCl and KI) in isotopically diluted water (4% D(2)O in H(2)O), using polarization-resolved femtosecond infrared pump-probe spectroscopy (fs-IR). We were able to distinguish the orientational dynamics of the water molecules solvating the halide ions from the dynamics of the bulk water and the water solvating the cations. We found that the reorientation of the halide-bound molecules shows two strongly different components (2.0 ± 0.3 ps and 9 ± 1 ps), related to a wiggling motion of the OD group hydrogen-bonded to the anion, and rotational diffusion of the molecule over the charged anion surface, respectively. The relative amplitudes of the two components are dependent on the nature of both the anion and cation, and on the concentration. These results show that cations can have a profound effect on the solvation shell dynamics of their counter-ions.     

Role of hydrogen bonds in the fast dynamics of binary glasses of trehalose and glycerol: a molecular dynamics simulation study

Trehalose-glycerol mixtures are known to be effective in the long time preservation of proteins. However, the microscopic mechanism of their effective preservation abilities remains unclear. In this article we present a molecular dynamics simulation study of the short time, less than 1 ns, dynamics of four trehalose-glycerol mixtures at temperatures below the glass transition temperature. We found that a mixture of 5% glycerol and 95% trehalose has the most suppressed short time dynamics (fast dynamics). This result agrees with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured via neutron scattering, and correlates with the experimentally observed enhancement of the stability of some enzymes at this particular concentration. Our microscopic analysis suggests that the formation of a robust intermolecular hydrogen bonding network is most effective at this concentration and is the main mechanism for the suppression of the fast dynamics.