Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

天然无序蛋白质:序列-结构-功能的新关系

天然无序蛋白质是一类新发现的蛋白质,它们在天然条件下没有确定的三维结构,却具有正常的生物学功能,广泛参与信号传递、DNA转录、细胞分裂和蛋白质聚集等重要的生理与病理过程.无序蛋白质的发现是对传统的蛋白质"序列-结构-功能"范式的挑战.在这篇综述里,我们首先回顾了蛋白质的传统范式以及无序蛋白质的发现过程,然后介绍无序蛋白质在结构、序列、功能等方面的特征与相互作用,并以分子识别过程为例,进一步阐述目前国际上对无序蛋白质所具有优势的一些认识与观点.我们还分析了无序蛋白质研究在生命科学和医学等领域的应用前景,并介绍了国内在无序蛋白质领域的研究现状.     

接枝微球PMAA-HEMA/NVP对溶菌酶的吸附行为与吸附机理

采用反相悬浮聚合法制备了甲基丙烯酸羟乙酯(HEMA)与N-乙烯基吡咯烷酮(NVP)的交联共聚微球HEMA/NVP,然后采用"接出"法,实施了甲基丙烯酸(MAA)在交联微球表面的接枝聚合,制得了接枝微球PMAA-HEMA/NVP.以溶菌酶(LYZ)为模型碱性蛋白,深入研究了接枝微球PMAA-HEMA/NVP对碱性蛋白的吸附性能与吸附机理.测定了微球PMAA-HEMA/NVP的zeta电位,考察了PMAA接枝度、介质pH值及离子强度等因素对体系吸附性能的影响.结果表明,在较大的pH范围内,接枝微球PMAA-HEMA/NVP的zeta电位为绝对值较大的负值,即其表面携带有高密度的负电荷.在强静电相互作用的驱动下,接枝微球PMAA-HEMA/NVP对溶菌酶表现出很强的吸附能力.随介质pH值的增高,接枝微球对溶菌酶的吸附容量呈现先增大后减小的变化趋势,在与溶菌酶等电点接近的pH值处(pH=9),具有最大的吸附容量(90mg.g-1);离子强度对接枝微球的吸附能力也有较大的影响,当pH9时,溶菌酶吸附容量随NaCl浓度的增高而减小;当pH9时,吸附容量随NaCl浓度的增高而增大.     

Heterogeneous versus bulk nucleation of lysozyme crystals

Heterogeneous (on‐glass) protein crystal nucleation was separated from the bulk one in systems of thin protein solution layers, confined between two glass plates of custom made quasi two‐dimensional all‐glass cells, as well as by applying forced protein solution flow. Two commercial samples of hen‐egg‐white lysozyme, Seikagaku and Sigma were used as model proteins. Applying the classical technique of separation in time of nucleation and growth stages with protein solution layers of thickness 0.05 cm we found that the on‐glass crystal nucleation prevailed highly with Seikagaku HEWL, while on the opposite, bulk nucleated crystals represented the main crystal fraction in Sigma solution. Also using 0.05 cm solution layers nucleation rates were measured separately for the on‐glass and bulk protein crystals. The process was investigated by varying solution layer thicknesses as well, from 0.05 down to 0.01, 0.0065 and 0.002 cm. Studying the influence of the forced protein solution flow on HEWL crystal nucleation the classical double‐pulse technique was modified by separating the nucleation and growth stages not only in time, but simultaneously also in place. In this case we found that the ratio of on‐glass formed crystal nuclei to bulk nuclei depended on the flow velocity, but in different manner with Seikagaku HEWL and Sigma HEWL. A plausible explanation of our experimental results is that the bulk crystal nucleation occurs on foreign surfaces as well, e.g. on rests of source biomaterial, which are always present in the protein solutions. Moreover, biomaterial seems to be more active nucleant than glass. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The global version of the gyrokinetic turbulence code GENE

The understanding and prediction of transport due to plasma microturbulence is a key open problem in modern plasma physics, and a grand challenge for fusion energy research. Ab initio simulations of such small-scale, low-frequency turbulence are to be based on the gyrokinetic equations, a set of nonlinear integro-differential equations in reduced (five-dimensional) phase space. In the present paper, the extension of the well-established and widely used gyrokinetic code GENE [F. Jenko, W. Dorland, M. Kotschenreuther, B.N. Rogers, Electron temperature gradient driven turbulence, Phys. Plasmas 7 (2000) 1904–1910] from a radially local to a radially global (nonlocal) version is described. The necessary modifications of both the basic equations and the employed numerical methods are detailed, including, e.g., the change from spectral methods to finite difference and interpolation techniques in the radial direction and the implementation of sources and sinks. In addition, code verification studies and benchmarks are presented.     

Theoretical study of new acceptor and donor molecules based on polycyclic aromatic hydrocarbons

Functionalized polycyclic aromatic hydrocarbons (PAHs) are an interesting class of molecules in which the electronic state of the graphene-like hydrocarbon part is tuned by the functional group. Searching for new types of donor and acceptor molecules, a set of new PAHs has recently been investigated experimentally using ultraviolet photoelectron spectroscopy (UPS). In this work, the electronic structure of the PAHs is studied theoretically with the help of B3LYP hybrid density functionals. Using the ΔSCF method, electron binding energies have been determined which affirm, specify and complement the UPS data. Symmetry properties of molecular orbitals are analyzed for a categorization and an estimate of the related signal strength. While σ-like orbitals are difficult to detect in UPS spectra of condensed film, calculation provides a detailed insight into the hidden parts of the electronic structure of donor and acceptor molecules. In addition, a diffuse basis set (6-311++G**) was used to calculate electron affinity and LUMO eigenvalues. The calculated electron affinity (EA) provides a classification of the donor/acceptor properties of the studied molecules. Coronene-hexaone shows a high EA, comparable to TCNQ, which is a well-known classical acceptor. Calculated HOMO-LUMO gaps using the related eigenvalues have a good agreement with the experimental lowest excitation energies. TD-DFT also accurately predicts the measured optical gap.     

Applications of vertically oriented TiO2 micro-pillars array on the electrode of dye-sensitized solar cell

In this research, dye-sensitized solar cells based on TiO₂ micro-pillars fabricated by inductive couple plasma etcher were investigated by analyses of X-ray diffraction (XRD), scanning electron microscopy (SEM), contact angle, ultraviolet-visible absorption spectra (UV-vis), and current-voltage characteristics. X-ray diffraction patterns show that the TiO₂ anatase phase forms while sintering at 450 °C for 30 min. The SEM images reveal that the diameter and height of TiO₂ micro-pillars are about 3 and 0.8 μm, respectively. The measurements of contact angle between TiO₂ micro-pillars and deionized water (DI water) reveal that the TiO₂ micro-pillars is super-hydrophilic while annealed at 450 °C for 30 min.The absorption spectrum of TiO₂ micro-pillars is better than TiO₂ thin film and can be widely improved in visible region with N3 dye adsorbed. The results of current-voltage (I-V) characteristics analysis reveal that dye-sensitized solar cell with TiO₂ micro-pillars electrode has better I-V characteristics and efficiency than TiO₂ film electrodes. This result may be due to the annealed TiO₂ micro-pillars applied on the electrode of dye-sensitized solar cell can increase the contact area between TiO₂ and dye, resulting in the enhancement of I-V characteristics and efficiency for dye-sensitized solar cell.     

Effect of annealing on structural and electrical properties of the Li–Mn–O thin films, prepared by high frequency RF magnetron sputtering

Li–Mn–O thin film cathode materials are prepared by high frequency (27.12 MHz) RF magnetron sputtering. The high RF frequency gives higher deposition rates without compromising on the quality of the films. This investigation focuses on the effects of post-annealing on the micro-structural, morphological and electrical properties of Li–Mn–O films. It is observed that with the increase of annealing temperature the crystallinity as well as the electrical conductivity of the films increases. The films annealed at 600–700 °C are found to have high structural perfection and good electrical properties.     

Thermodynamic equilibrium for nitrogen species discharge: Comparison with global model

The equilibrium process of plasma nitrogen species by chemical kinetic reactions along various pressures is successfully investigated. The equilibrium process is required in industrial application to obtain the stable condition when heating up the material for having homogenous reaction. Nitrogen species densities is modeled by a continuity equation and extended Arrhenius form. These equations are used to integrate the change of density over the time. The integration is to acquire density and the reaction rate of each reaction where temperature and time dependence are imposed. A comparison is made with global model within pressure range of 1-100 mTorr and the temperature of electron is set to be higher than other nitrogen species. The results show that the chemical kinetic model only agrees for high pressure because of no power imposed; while the global model considers the external power along the pressure range then the electron and nitrogen species give highly quantity densities by factor of 3-5.     

A comparative study of dispersion relation of EM waves in ternary one-dimensional plasma photonic crystals having two different structures

In this paper, a rigorous theoretical analysis has been made to study the dispersion relation of EM waves in periodic ternary one-dimensional photonic crystal having two different structures. In one case we have chosen glass-plasma and ZnS in one unit cell and in other case we have considered glass-plasma and M_gF₂ in one unit cell. Using Kronig-Penney model the dispersion relation for proposed structures has been obtained and numerical results are presented in the form of dispersion curves. The dependence of photonic band gap (PBG) characteristics on plasma frequency, plasma width and the width of dielectric media are discussed in the light of frequency gap and cutoffs of binary one-dimensional plasma photonic crystal. An attempt has been made to show how the PBG characteristic of a particular structure changes when the dielectric materials of its unit cell is changed by the other dielectric material. It is found that the structure having glass-plasma-ZnS in unit cell is more useful for broad band filtering and other plasma functioning devices compared to the structure having glass-plasma-MgF₂ in one unit cell.