静电作用力算法对分子动力学模拟结果的影响分析

蛋白质分子和界面之间的作用在药物输送以及生物分离等领域至关重要。利用分子动力学模拟考察蛋白质分子在界面附近的行为是最近10年研究的热点。在早期的工作中,Wang等发现同电荷离子交换介质可用于辅助蛋白质复性,但其机理不甚明确。在利用分子动力学模拟研究其分子机理时发现,不同静电作用力参数对模拟结果有直接的影响。因此,通过全原子分子动力学模拟考察不同静电参数条件对模拟结果的影响,展示此过程的构象和能量变化,分析了造成结果差异的原因。研究结果揭示了不同静电参数对模拟结果的影响,为进一步研究蛋白质在界面表面的行为奠定了一定的理论基础。     

Construction of covalently attached enzyme multilayer films based on the photoreaction of diazo-resins and glucose oxidase

A novel and facile approach to construct multilayered glucose oxidase (GOx) films on the surface of quartz or CaF₂ slides as well as gold electrodes for use as biosensing interfaces is described. Diazo-resins (DAR) as polycation and glucose oxidase as polyanion were alternately deposited into a multilayer structure using layer-by-layer self-assembly technique based on electrostatic interaction as driving force. Upon near UV irradiation, the adjacent interfaces of the multilayer reacted to form a crosslinking structure which greatly improved the stability of the enzyme films. These changes was monitored and confirmed by UV-vis and IR spectroscopy. Ellipsometric measurements reveal that the enzymes formed sub-molecule layers, and the thickness of the film shows a linear relationship with the number of assembled layers, demonstrating a spatially well-ordered manner in multilayer structure. The covalently attached enzyme multilayer film has a highly permeable structure, and can be used as biosensing interface. Electrochemical and analytical behavior of the enzyme electrodes was studied by cyclic voltammetry (CV) in the presence or absence of glucose. The sensitivity of the enzyme-modified electrodes was estimated through the analysis of voltammetric signals, which can be fine turned to the desired level by adjusting the number of attached bilayers.     

Orientation‐dependent mechanical and thermal properties of plasma‐sprayed ceramics

Due to droplet‐based assembly, microstructure anisotropy is expected in atmospheric plasma‐sprayed coatings (APS), with lamellar separations and interfaces having critical effects on properties. Quantitative determination of these anisotropic properties is difficult due to geometric test constraints. This has been overcome in the literature through a variety of indirect, local, or modeled evaluation, however direct measurement on like‐dimensioned coatings is not available. In this work, 25‐mm thick ceramic coating variants, deposited at two different feed rates, were obtained from industry and macroscopic mechanical and thermal properties were evaluated in both in‐plane and out‐of‐plane orientations using identical specimen geometries. As expected, and confirming select past work, coating anisotropy has a direct influence on measured properties. The response of each property is microstructure‐dependent, highlighting the specific interaction: for instance, the fracture toughness is 120% higher in the through‐thickness orientation versus in‐plane after thermal aging, while the thermal conductivity was 24% lower in the through‐thickness. The former benefits from the lamellar interfaces that provide obstacles to crack propagation while the latter sees these interfaces as efficient phonon scatters. The results provide insights for design through robust property measurements and into operational mechanisms in this class of highly defected ceramics.     

Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin

Cargo transport within cells is essential to healthy cells, which requires microtubules-based motors, including kinesin. The C-terminal tails (E-hooks) of alpha and beta tubulins of microtubules have been proven to play important roles in interactions between the kinesins and tubulins. Here, we implemented multi-scale computational methods in E-hook-related analyses, including flexibility investigations of E-hooks, binding force calculations at binding interfaces between kinesin and tubulins, electrostatic potential calculations on the surface of kinesin and tubulins. Our results show that E-hooks have several functions during the binding process: E-hooks utilize their own high flexibilities to increase the chances of reaching a kinesin; E-hooks help tubulins to be more attractive to kinesin. Besides, we also observed the differences between alpha and beta tubulins: beta tubulin shows a higher flexibility than alpha tubulin; beta tubulin generates stronger attractive forces (about twice the strengths) to kinesin at different distances, no matter with E-hooks in the structure or not. Those facts may indicate that compared to alpha tubulin, beta tubulin contributes more to attracting and catching a kinesin to microtubule. Overall, this work sheds the light on microtubule studies, which will also benefit the treatments of neurodegenerative diseases, cancer treatments, and preventions in the future.     

Microwave assisted HMDSO/oxygen plasma coated polyethylene terephthalate films: Effects of process parameters and uniaxial strain on gas barrier properties,surface morphology,and chemical composition

The coating structure and barrier property relation of coated PET films is of high interest for understanding the difference between predicted and actual barrier performance of coated PET films. In this work the chemical and morphological structure of HMDSO coatings generated with and without oxygen in a microwave plasma has been investigated with XPS and AFM analysis. These results were correlated with oxygen permeation measurements at different strain rates and temperatures. The results show that with a more glass‐like chemical composition the barrier property is improved. The growth of the coatings takes place in a columnar manner and the interfaces between the columns seem to be the low energy passages for the permeation, which cause the difference between predicted and actual barrier performance. When the coatings are strained the barrier fails at a strain higher than 1%. Cracks occur and with higher strain rates the number of cracks increases. Cracking takes place perpendicular to the strain direction and at the interfaces of the columns of the coating. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1485–1495, 2006     

Enhanced flocculation of colloidal dispersions by polymer mixtures

Bridging flocculation and electrolyte coagulation of negatively charged colloidal dispersions in the presence and absence, respectively, of uncharged polymers and polymer mixtures were studied. The relative coagulation and flocculation rates of particles in the presence of electrolyte and small polymer amounts were measured and the stability ratios have been calculated at various ionic strengths. Also, the structure of polymer layers formed in individual adsorption of polymers and in simultaneous competitive adsorption from binary polymer mixtures at particle/solution interfaces was investigated. The electrophoretic mobility and the diffusion coefficient of particles with and without adsorbed polymer were measured by laser Doppler-electrophoresis and photon correlation spectroscopy, respectively, and the electrophoretic and the hydrodynamic thickness of adsorbed polymer layers have been calculated. It was found that the adsorbed polymers may enhance or diminish the rate of successsful encounters between particles, even at low surface coverages, depending on the magnitude of the interparticle electrostatic repulsion. In addition, competitive adsorption of chemically different polymers for particle surfaces may result in considerable alteration in the conformation of macromolecules in the mixed adsorption layer. Close correlation was found between the effectiveness of polymers as flocculants and the thickness of adsorbed polymer layers formed at optimum polymer dosages on the particle surfaces. Binary mixtures of suitable polymers proved to be very efficient flocculants for the dispersions. The enhanced flocculating effect of some mixtures can be ascribed to extended polymer layers formed in competitive adsorption of chemically different macromolecules at particle/solution interfaces. These findings have relevance in many environmental technologies and offer a way of improving the effectiveness of solid–liquid separation processes.     

Study of interactions at water-soluble polymer/Ca(OH)2 or gibbsite interfaces by XPS

In an attempt to better understand interactions occuring at hydrated cement/organic polymer interfaces, the reaction mechanism and products formed at the interfaces between poly(acrylic acid), p(AA) or poly(acrylamide), p(AM), and Ca(OH)₂ or gibbsite, Al₂O₃·3H₂O, were explored using x-ray photoelectron spectroscopy (XPS). It was estimated that at p(AA)/Ca(OH)₂ interfaces, a Ca-complexed carboxylate interfacial reaction product was formed by an ionic reaction between the COOH in p(AA) and Ca²⁺ ions from Ca(OH)₂. A similar reaction product was formed at p(AM)/Ca(OH)₂ interfaces as a result of an inter-facial transformation of amide in p(AM) into carboxylic acid, caused by the alkali-catalyzed hydrolysis of the amide. The proton-accepting hydroxyl groups existing at the outermost surface sites of Al₂O₂·3H₂O react favorably with proton-donating COOH groups in p(AA). This acidbase interaction at the p(AA)/Al₂O₃·3H₂O joint formed hydrogen bonds. Whereas, when the p(AM) was applied on Al₂O₃·3H₂O surfaces, interfacial electrostatic bonds were formed through charge-transferring reaction mechanisms in which the charge density was transferred from the Al in Al₂O₃·3H₂O to the C=0 oxygen in p(AM).     

Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways

Proteins with similar structures may have different functions. Here, using a non-redundant two-chain protein-protein interface dataset containing 103 clusters, we show that this paradigm extends to interfaces. Whereas usually similar interfaces are obtained from globally similar chains, this is not always the case. Remarkably, in some interface clusters, although the interfaces are similar, the overall structures and functions of the chains are different. Hence, our work suggests that different folds may combinatorially assemble to yield similar local interface motifs. The preference of different folds to associate in similar ways illustrates that the paradigm is universal, whether for single chains in folding or for protein-protein association in binding. We analyze and compare the two types of clusters. Type I, with similar interfaces, similar global structures and similar functions, is better packed, less planar, has larger total and non-polar buried surface areas, better complementarity and more backbone-backbone hydrogen bonds than Type II (similar interfaces, different global structures and different functions). The dataset clusters may provide rich data for protein-protein recognition, cellular networks and drug design. In particular, they should be useful in addressing the difficult question of what the favorable ways for proteins to interact are.     

A universal approach to solvation modeling

Continuum mean-field models that have been carefully designed to address the various electrostatic and nonelectrostatic interactions that develop between a molecule and a surrounding medium are particularly efficient tools for studying the effects of condensed phases on molecular structure, energetics, properties, spectra, interaction potentials, and dynamics. The SM8 model may be combined with density functional theory or Hartree-Fock theory to describe a solute's electronic structure and its self-consistent-field polarization by a solvent. A key feature is the use of class IV charge models to obtain accurate charge distributions (either in the vapor phase or in solution), even when using small basis sets that are affordable for large systems. A second key feature is that nonelectrostatic effects due to cavity formation, dispersion interactions, and changes in solvent structure are included in terms of empirical atomic surface tensions that depend on geometry but do not require atom-type assignments by the user. Use of an analytic surface area algorithm provides very stable energy gradients that allow geometry optimization in solution. The SM8 continuum model, the culmination of a series of SMx models (x = 1-8), permits the modeling of such diverse media as aqueous and organic solvents, soils, lipid bilayers, and air-water interfaces. In addition to predicting accurate transfer free energies between gaseous and condensed phases or between two different condensed phases, SMx models have been useful for predicting the significant influence of condensed phases on processes associated with a change in molecular charge, including acid/base equilibria and oxidation/reduction processes. In this Account, we provide an overview of the algorithms associated with the computation of free energies of solvation in the SM8 model. We also compare the accuracies of the SM8 model with those of other continuum solvation models. Finally, we highlight applications of the SM8 models to compute ionic solvation free energies, oxidation and reduction potentials, and pK(a) values.     

Recycling of Poly(phenylene ether) Blends

The effects of postindustry recycling of polymer blends composed of poly(phenylene ether) (PPE) on the properties of the PPE blends were investigated by simulated recycling with multiple molding cycles. Two compositions with different concentrations of PPE were reprocessed with an injection‐molding machine. Mechanical, thermal, rheological, and morphological characterizations were carried out on as‐produced and reprocessed samples to examine the influence of the number of molding cycles on the two specific PPE blends. Efforts were made to determine the effect of each molding cycle on the specific properties of the two PPE blends, including the Elastic (E), modulus, stress at break, strain at break, multiaxial impact, and melt viscosity. The results are discussed in detail. The retention of the properties correlated well with the unperturbed morphology of the compositions before and after recycling, as observed by transmission electron microscopy analyses on fractured tensile samples. However, more in‐depth microanalyses are required to identify the effect of recycling on the individual components present in the studied compositions. In this study, we aimed to establish structure–property relations upon recycling using several characterization techniques. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011     

Hen Egg‐White Lysozyme Crystallisation: Protein Stacking and Structure Stability Enhanced by a Tellurium(VI)‐Centred Polyoxotungstate

As synchrotron radiation becomes more intense, detectors become faster and structure‐solving software becomes more elaborate, obtaining single crystals suitable for data collection is now the bottleneck in macromolecular crystallography. Hence, there is a need for novel and advanced crystallisation agents with the ability to crystallise proteins that are otherwise challenging. Here, an Anderson–Evans‐type polyoxometalate (POM), specifically Na₆[TeW₆O₂₄] ? 22 H₂O (TEW), is employed as a crystallisation additive. Its effects on protein crystallisation are demonstrated with hen egg‐white lysozyme (HEWL), which co‐crystallises with TEW in the vicinity (or within) the liquid–liquid phase separation (LLPS) region. The X‐ray structure (PDB ID: 4PHI) determination revealed that TEW molecules are part of the crystal lattice, thus demonstrating specific binding to HEWL with electrostatic interactions and hydrogen bonds. The negatively charged TEW polyoxotungstate binds to sites with a positive electrostatic potential located between two (or more) symmetry‐related protein chains. Thus, TEW facilitates the formation of protein–protein interfaces of otherwise repulsive surfaces, and thereby the realisation of a stable crystal lattice. In addition to retaining the isomorphicity of the protein structure, the anomalous scattering of the POMs was used for macromolecular phasing. The results suggest that hexatungstotellurate(VI) has great potential as a crystallisation additive to promote both protein crystallisation and structure elucidation.     

Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment

Different methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene p16/INK4A was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Cluster analyses were used to establish methylated and unmethylated groups for each method. Agreement and concordance between pyrosequencing and MS-qPCR was evaluated with Pearson’s correlation, Bland–Altman, Cohen’s kappa index and ROC curve analyses. Based on these analyses, cut-offs were derived for MS-qPCR. An acceptable correlation (Pearson’s R2 = 0.738) was found between pyrosequencing (PYRmean) and MS-qPCR (NMP; normalized methylation percentage), providing similar clinical results when categorizing data as binary using cluster analysis. Compared to pyrosequencing, MS-qPCR tended to underestimate methylation for values between 0 and 15%, while for methylation >30% overestimation was observed. The estimated cut-off for MS-qPCR data based on cluster analysis, kappa-index agreement and ROC curve analysis were much lower than that derived from pyrosequencing. In conclusion, our results indicate that independently of the approach used for estimating the cut-off, the methylation percentage obtained through MS-qPCR is lower than that calculated for pyrosequencing. These differences in data and therefore in the cut-off should be examined when using methylation biomarkers in the clinical practice.     

Isobaric vapor-liquid equilibrium of 2-propanone+2-butanol system at 101.325 kPa: Experimental and molecular dynamics simulation

Isobaric vapor-liquid equilibrium (VLE) data for binary mixtures of 2-propanone+2-butanol have been measured at 101.325 kPa. The measurements were in a modified recirculating type of Othmer equilibrium still. All the data passed the thermodynamics consistency test and no azeotropic behavior was exhibited. The experimental VLE data were correlated with the Wilson, non-random two-liquid (NRTL) and universal quasi-chemical (UNIQUAC) activity coefficient models. The correlation results showed that the experimental data were well correlated with those models. The experimental data also showed slight deviations from the predicted results using UNIFAC and modified UNIFAC (Dortmund) models. To gain more insight into the nature of interactions between 2-propanone molecule and alcohol, we analyzed the hydrogen-bonds, the electrostatic (Coulomb) interactions, and the van der Waals (Lennard- Jones) interaction energies extracted from MD simulations. In addition, the structural property of liquid phase was characterized through radial distribution function (RDF) to establish favorable interactions between 2-propanone and 2-butanol in the mixture.     

The Odd Faces of Oligomers: The Case of TRAF2-C,A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor

TNF Receptor Associated Factor 2 (TRAF2) is a trimeric protein that belongs to the TNF receptor associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding and for its interaction with other proteins involved in the TNFR signaling. The monomer-trimer equilibrium of a C- terminal domain truncated form of TRAF2 (TRAF2-C), plays also a relevant role in binding the membrane, causing inward vesiculation. In this study, we have investigated the conformational dynamics of TRAF2-C through circular dichroism, fluorescence, and dynamic light scattering, performing temperature-dependent measurements. The data indicate that the protein retains its oligomeric state and most of its secondary structure, while displaying a significative increase in the heterogeneity of the tyrosines signal, increasing the temperature from ≈15 to ≈35 °C. The peculiar crowding of tyrosine residues (12 out of 18) at the three subunit interfaces and the strong dependence on the trimer concentration indicate that such conformational changes mainly involve the contact areas between each pair of monomers, affecting the oligomeric state. Molecular dynamic simulations in this temperature range suggest that the interfaces heterogeneity is an intrinsic property of the trimer that arises from the continuous, asymmetric approaching and distancing of its subunits. Such dynamics affect the results of molecular docking on the external protein surface using receptor peptides, indicating that the TRAF2-receptor interaction in the solution might not involve three subunits at the same time, as suggested by the static analysis obtainable from the crystal structure. These findings shed new light on the role that the TRAF2 oligomeric state might have in regulating the protein binding activity in vivo.     

Electrostatic and Entropic Interactions between Parallel Interfaces Separated by a Glassy Film

A simple classical density functional model is set up to describe the electrostatic and entropic interactions between two parallel planar charged interfaces separated by a thin film of a phase (the glass) containing a distribution of charged ions. The total charge in the system is zero. Three cases are treated: (1) the two interfaces carry a fixed surface charge; (2) the first interface carries a fixed surface charge, simulating a ceramic, while the second is held at zero potential, simulating a metal; and (3) both interfaces are held at zero potential. A discretized form of the nonlinear Poisson–Boltzmann equation is derived and solved by a Newton–Raphson method. The continuum approximation is compared with a model in which the ions are only allowed to occupy discrete planes. The effect of correlation among the ions is included within the local density approximation. Inserting parameters appropriate to the copper–alumina interface, we find that the attractive image force between the ceramic and metal dominates the entropic (DLVO) repulsive force in the 1–2 nm range.     

Coatings with a self-generating hydrogel surface for antifouling

We prepared a coating by mixing a polyfunctional axiridine cross-linking agent and a self-polishing resin pre-synthesized via the polymerization of methyl methacrylate (MMA), acrylic acid (AA) and tributylsilyl methacrylate (TBSM). The coating can be easily applied on a surface to form a cross-linked polymer film by conventional brushing or spraying method. After immersing it into seawater, the film self-generates a thin soft and dynamic layer of hydrogel at the water-contacting surface because of the hydrolysis of TBSM. Such a hydrogel-formation process continues after gradual corrosion and detachment of each top hydrophilic layer. This hydrogel-formation and self-peeling property makes it ideal in various antifouling applications. In the current study, besides the synthesis and preparation of this novel kind of coatings, we focused on the correlation between the TBSM content and the antifouling property by using contact angle, water-absorption, and antifouling measurements. The results of immersing different coatings in shallow submergence for two months reveal that the addition of more TBSM leads to a more hydrophilic surface and a better antifouling property.     

Experimental correlation for pipe flow drag reduction using relaxation time of linear flexible polymers in a dilute solution

In this study, we investigate the drag reduction property of a linear flexible polymer, PEO (polyethylene oxide) in a fully turbulent pipe flow. The aim of this study is to develop a correlation to predict the drag reduction using the Weissenberg number, a dimensionless number related to the relaxation time of the polymer and the polymer concentration in dilute solutions. The physical meaning of the relaxation time of polymers and overlap concentration between the dilute and semi-dilute polymer solution are clarified. A higher polymer concentration, Reynolds number, and Weissenberg number lead to an increasing drag reduction. A semi-empirical correlation to predict the drag reduction with two dimensionless variables mentioned above is established and can predict the experimental data in this work and other previous works well. Previous correlations that use Reynolds number often require high flow velocity or large pipes in the experimental setup to predict drag reduction in large-scale industrial applications, which involves extra cost and potential safety issues. The current new correlation method uses relatively low velocities to avoid the problems mentioned above.     

棉籽蛋白/剑麻纤维复合材料加工、界面与性能

为了提高植物蛋白基绿色高分子材料的力学性能和热稳定性能,以棉籽蛋白（CP）为原料,在尿素变性、甘油增塑、双醛淀粉（DAS）交联的基础上,将其与取向排列的天然剑麻长纤维（SF）复合,经热压硫化加工制备得到具有优异性能的棉籽蛋白/剑麻纤维全绿色复合材料。微观结构形貌和性能分析测试表明,复合材料获得改善性能主要归功于：CP基体与SF增强相间形成的紧密界面结合、对剑麻长纤维的预浸渍处理、CP与SF生物大分子间的强氢键作用。考察了不同DAS含量对复合材料力学性能和热稳定性能的影响。拉伸、热重和差示量热分析表明,经20%（质量） DAS交联的复合材料具有最优的拉伸强度（断裂应力7.5 MPa）、模量（杨氏模量93 MPa）、热稳定性（最大分解温度328℃）和玻璃化转变温度（102℃）。