The structure of the gas-phase tyrosine–glycine dipeptide

The structural preferences of the neutral dipeptide Tyr–Gly have been investigated using a hierarchical selection scheme. This scheme consists of a hierarchy of increasingly more accurate electronic structure methods (single-point HF/3-21G* energy calculation, HF/3-21G* geometry optimization, B3LYP/6-31+G* geometry optimization, MP2/6-31+G* single-point energy calculation, and MP2/6-31+G* geometry optimization). The conformers are sorted according to their single-point or optimized energy, and only the most stable conformers according to one level are taken through to the next level of calculation. The defining structural characteristics in the 20 most stable Tyr–Gly conformers are the presence or absence of a folded arrangement of the peptide backbone (‘book’) and an OH···O hydrogen bond between the C-terminal hydroxyl group and the carbonyl oxygen of tyrosine (‘OHO’). The most stable conformer is of the book/OHO type. MP2 geometry optimization significantly alters the structure of the book-type conformers, increasing their degree of foldedness. Thus, care has to be taken when applying standard density functionals like B3LYP in structural studies of peptides with aromatic side chains.     

光动力蛋白C-PC中脱辅蛋白的空间结构研究

本文利用拉曼光谱分析技术,对纯化后的螺旋藻C藻蓝蛋白(CPC)分子,在0075mol/L盐溶液中的空间结构进行了分析。本文认为CPC的脱辅蛋白空间构象在此溶液和10℃条件下是α螺旋与β回转结构。“暴露的”酪氨酸占44%;色氨酸也处于部份“暴露”状态;β111的半胱氨酸不参与硫醚键的形成,有自由的CS单键伸缩振动模;谱中没有二硫键的存在。     

片层硅酸盐用于热固性PU/PLS复合可能性探讨

高岭土(Kaolinite)和蒙脱土(Montromollite)等粘土,被广泛用作添加剂来改善聚合物的耐热性能。文章用各种先进技术对高岭土与蒙脱土的形态、组成和结构进行表征比较。电子透射电镜及电子探针(TEM/EDX)结果显示高岭土较蒙脱土有较大的粒径和较小的硅铝比,TEM还显示出这些粘土是由片层粒子堆积而成。热重分析(TGA)的结果表明蒙脱土由于失去吸附水从60 ℃升温至90 ℃失重明显(约7%),而高岭土在此温度下几乎不失水。高岭土脱除结构羟基官能团脱水失重的温度大约在510 ℃,低于蒙脱土的670 ℃。室温下光声傅里叶变换(PAS-FTIR)红外光谱显示蒙脱土在羟基吸收区有较强的吸附水的吸收,1 650 cm-1处孤立的弱吸收谱带可给予左证。变温红外和TGA的结果显示,片层硅酸盐表面的结构羟基从100～500 ℃非常稳定,它可以和异氰酸酯基团(NCO)封端的预聚物反应形成热固性PU/PLS复合聚合物。     

Transition of the hydration state of a surfactant accompanying structural transitions of self-assembled aggregates

What role does water play in the self-assembly of soft materials? To understand the correlation between the hydration state and the various self-assembled structures of a nonionic surfactant, terahertz time-domain spectroscopy has been performed for a C(12)E(5) solution with complementary use of small-angle x-ray scattering. Precise observations of the hydration state show clearly that transitions of the hydration state are accompanied by structural phase transitions of the surfactant from hexagonal to micelle to lamellae. These transitions of hydration state suggest that water is not a homogeneous solvent, and the interaction between water and the soft material is important for self-assembly.     

Studies in the vibrational splitting of the giant dipole resonance (II). Ni and Ni

The total photoneutron cross sections for ⁵⁸Ni and ⁶⁰Ni have been measured with bremsstrahlung from threshold to 24 MeV. Although their magnitudes are greatly different, the two cross sections show similar structure over the giant dipole resonance region. The structural features of both are in only fair agreement with the dynamic collective model calculations of Huber, and of Seaborn, Drechsel, Arenhövel and Greiner. However the agreement of the ⁶⁰Ni cross section and the collective correlations calculation of Seaborn et al. is far better, and thus indicates the importance of shell-model aspects.     

SOLEIL shining on the solution‐state structure of biomacromolecules by synchrotron X‐ray footprinting at the Metrology beamline

Synchrotron X‐ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small‐angle X‐ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X‐ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X‐ray footprinting of biomolecules performed for the first time at the X‐ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped‐flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X‐ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid‐associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high‐resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent‐exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X‐ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X‐ray footprinting of biomolecules.     

Temperature and hydration dependence of proton MAS NMR spectra in MCM-41: Model based on motion induced chemical shift averaging

The proton MAS NMR spectra in MCM-41 at low hydration levels (less than hydration amounting to one water molecule per surface hydroxyl group) show complex proton resonance peak structures, with hydroxyl proton resonances seen in dry MCM-41 disappearing as water is introduced into the pores and new peaks appearing, representing water and hydrated silanol groups. Surface hydroxyl group–water molecule chemical exchange and chemical shift averaging brought about by a water molecule visiting different surface hydrogen bonding sites have been proposed as possible causes for the observed spectral changes. In this report a simple model based on chemical shift averaging, due to the making and breaking of hydrogen bonds as water molecules move on the MCM-41 surface, is shown to fully reproduce the NMR spectra, both as a function of hydration and temperature. Surface proton–water proton chemical exchange is not required in this model at low hydration levels.     

The structure of the interface in the solvent-mediated interaction of dipolar surfaces

Summary Interaction of two dipolar surfaces separated by a polar medium is considered within the framework of nonlocal electrostatics. The dipolar-surface layers are modelled as regular lattices with fixed orientation of dipoles which are immersed into the solvent; solvent response is characterized by nonlocal dielectric function. The model is elaborated in order to reveal the role of the dipolar-layer discreteness in the electric field produced by one surface and the interaction between two surfaces (which gives rise to the so-called ?hydration? or ?structural? force acting between mineral surfaces and phospholipid bilayers). The discreteness effects are present only for commensurate lattices. Their special mutual arrangement then may lead to considerable reduction of structural forces,viz. the usual repulsion regime may change at short distances to attraction. Conditions are considered when repulsion is entirely replaced by attraction,i.e. the ?hydration barrier? disappears. In appended note we discuss the role of solvation of surface dipolar groups. We propose an explanation of why two modes of decay (one with oscillative fine structure) may be present in the dependence of the force upon distance, if the surface dipolar groups are immersed deep enough in the solvent, and how the long-range oscillative mode disappears when the surface is but weakly solvated. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

Solution structure of the histidine-containing phosphocarrier protein fromStaphylococcus carnosus

The solution structure of histidine-containing phosphocarrier protein fromStaphylococcus carnosus was determined by two- and three-dimensional nuclear magnetic resonance (NMR) spectroscopy on uniformly¹⁵N-enriched protein. The main structural element is an antiparallel β-pleated sheet with four strands A, B, C, and D arranged with the topology A-D-B-C. Strand A comprises residues 2 to 8, strand B residues 32 to 37, strand C reidues 40 to 43, and strand D residues 59 to 66. Three right-handed helices are arranged on top of the β-pleated sheet. Helix a reaches from residue 16 to 29, helix b from residue 48 to 53, and helix c from residue 72 to 83. Strands B and C of the β-pleated sheet are connected by a type II turn. The hydroxyl proton of Ser-31 is exchanging with the solvent so slowly that cross peaks can be detected in two-dimensional NMR spectra based on homonuclearJ-couplings. The imidazole ring of the active-center His-15, which is partly charged in the structure determined at pH 7.2, is located above the N-terminal end of helix a, perpendicular to its axis. The N^δ1 atom of His-15, accepting the phosphoryl from enzyme I, is exposed to the solvent.     

On the fluorescence of C_60 at room temperature

The fluorescence properties of C 60 in different organic solvents have been investigated at room temperature. Three fluorescence emission centers are discovered and ascribed to different aggregations of C 60 in solvent. A series of blue fluorescence peaks centered at 440 nm derive from C 60 nanoparticles; a distinctive yellow-green fluorescence band in 575 nm region arises from the aggregates of C 60 nanoparticles; a more informative salmon fluorescence band around 700 nm originates from C 60 microcrystals....     

Nmr and Mass Spectroscopic Studies of the Competitive-Angiotensin II Antagonist “Sarmesin”

Fast atom bombardment mass spectrometry (FAB-MS) and high resolution (400 Mz) proton nuclear magnetic resonance (NMR spectroscopy) on the competitive angiotensin II antagonist, |Sar¹, Tyr(Me)⁴ (ANGII (Sarmesin) and its he-ptapeptide homolog, [Tyr(Me)³ |ANGIII, yield spectra which provide confirmation of structure and molecular weight. The characteristics of the spectra are discussed and compared with the spectra of natural ANG II, ANG III and |Sar¹|ANG II. The NMR data are suggestive of interactions in angiotensin between: 1) the phenolic hydroxyl group and the imidazole ring, and 2) the N-terminal amino group and the Tyrring. These interactions may be important for the formation of the proposed charge transfer system in angiotensin II involving the phenoxyl and α-carboxylate groups.     

Peptide backbone-copper ring structure: A molecular insight into copper-induced amyloid toxicity

Copper ions can promote amyloid diseases that are associated with amyloid peptides, such as type 2 diabetes (T2D), Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). However, the underlying molecular mechanism remains obscure. Here we present that Cu²⁺ is able to specifically bind to the backbone of T2D-related human islet amyloid polypeptide (hIAPP) by forming a ring structure, which causes the reduction of Cu²⁺ to Cu⁺ to produce reactive oxygen species (ROS) and the modulation of hIAPP aggregation. Nuclear magnetic resonance spectroscopy showed that Cu²⁺ bound to the backbone of a turn region, His18—Ser21, which is critical for hIAPP aggregation. Ab initio calculations and x-ray absorption fine structure analyses revealed that Cu²⁺ simultaneously bound with both the amide nitrogen and carbonyl oxygen on the peptide backbone, resulting in a ring structure, and causing the reduction of Cu²⁺ to Cu⁺ to form a hIAPP-Cu⁺ complex. 2',7'-dichlorodihydrofluorescin diacetate fluorescence measurements further indicated that this complex led to enhanced ROS levels in rat insulinoma cells. Additionally, thioflavin T fluorescence and atomic force microscopy measurements denoted that the backbone-Cu ring structure largely modulated hIAPP aggregation, including the inhibition of hIAPP fibrillation and the promotion of peptide oligomerization. These findings shed new light on the molecular mechanism of Cu²⁺-induced amyloid toxicity involving both the enhancement of ROS and the modulation of hIAPP aggregation.     

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with ?386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.     

A molecular dynamics study of uranyl hydration

Molecular dynamics calculations were carried out in order to investigate the hydration structure of uranyl in aqueous solution. The CF1 model of flexible water molecules is used. This model allows one to investigate a hydrolysis reaction for water molecules in the first uranyl hydration shell. Charge redistribution effects on hydrolysis products are also taken into account. We found five ligands in uranyl hydration shell, which is of bipyramidal pentacoordinated structure. The charge redistribution effects resulted in ligands of four water molecules and one hydroxyl, which was found closer to uranium than the other ligands.     

Geometric stability and adsorption property of hydroxyl group on graphene sheets

The stable geometrics and adsorption behaviors of hydroxyl (OH) groups on graphene sheets are investigated using the first-principles calculations. The single hydroxyl adatom has small adsorption energy and diffusion barrier on pristine graphene. The binding strength of the hydroxyl group increases with the coverage, and the aggregations of the hydroxyl groups reduce the structural bucking of graphene sheet. On the graphene with single vacancy (SV-graphene), the large trapping zones mean the adsorbed OH would be easily trapped at the vacancy site. The hydroxyl groups prefer to aggregate on graphene surfaces and form the water molecule, leaving the epoxy group on pristine graphene or oxygen dopant in SV-graphene, which is used to constitute the structural model of oxidized graphene. These results would provide us a useful reference to understand the atomic structure and adsorption property of functional groups on graphene sheets.     

Effects of hydroxyl groups and hydrogen passivation on the structure,electrical and optical properties of silicon carbide nanowires

The effects of hydrogen and hydroxyl passivation on the structure, electrical and optical properties of SiCNWs were investigated. The passivation performance of different atoms (groups) were discussed by analyzing the distribution of electronic states and the polarity of chemical bonds. The results show that passivation can improve the stability of SiCNWs structure, and the effect of hydroxyl is better than hydrogen passivation. And hydrogen and hydroxyl passivation both increase the band gap of SiCNWs, and the changing trend of band gap is relevant to the polarity of the covalent bond formed by the passivation of surface atoms. Moreover, passivation enhances the stability of the optical properties of SiCNWs, resulting in narrowing of light absorption, photoconductivity and other spectra, and the response peak shifts to the deep ultraviolet region, which means that hydrogen or hydroxyl passivation of SiCNWs is likely to be a candidate material for deep ultraviolet micro-nano optoelectronic devices.     

Fluorescence of a Histidine-Modified Enhanced Green Fluorescent Protein (EGFP) Effectively Quenched by Copper(II) Ions

Two histidines were introduced by site-directed mutagenesis into the structure of Enhanced Green Fluorescent Protein, replacing the serine at position 202 and the glutamine at position 204 for increasing the sensitivity of the protein towards different metal ions by creating possible metal binding sites near the chromophore group. There is no appreciable difference between the absorbance and fluorescence spectra of the two proteins (wild type and the double-histidine mutant) indicating that the mutation does not change the environment of the fluorophore. Fluorescence quenching was measured at different pH (6.5–8) and temperatures (20–45 °C) varying the concentration of metal ions. Under optimal conditions (pH?=?7.5, 20 °C) the mutant’s K_d is 16 nM, it binds copper more than 200fold stronger than the wild type EGFP.     

Is the hydration number of a non-electrolyte additive with length and constituents of the solute molecule?

Sound velocity and density were measured at 298.15 K in a number of very diluted aqueous solutions of simple non-electrolytes: alcohols, amines and acids. From these data the adiabatic compressibilities were calculated, and further the hydration numbers of solutes using the Passynski formula. It was found that all the homologous series under investigation exhibit linear concentration dependence of compressibility – and, consequently, that of the hydration numbers – up to concentrations of ca. 0.01 mole fraction or more. The slopes of these dependences are decreasing and n_h's are increasing with the molecular mass of the solute. This observation suggests that hydration numbers n_h are additive with the constituents of the molecule. Moreover, it would also imply the conclusion that local loss in compressibility of water solvent caused by hydration is very short in distance. To test the above assumption the hydration numbers were calculated using partial hydration numbers (i.e. those assigned to specific functional groups of the solute molecules), the latter are fitted parameters. The obtained values of partial n_h's are ca. 0.5 for –OH group, ca. 1.15 for –COOH and –NH₂ and from 0.5 to ca. 1.3 for hydrocarbon elements of the hydrophobic chain (–CH₂– and –CH₃ groups). The obtained total n_h's are surprisingly close to the experimentally obtained hydration numbers. There are, however, systems where differences between calculated and experimental n_h's are exceeding the experimental uncertainty; they are amino acids and diols, particularly α, ω-diols. The reasons are, most possibly, interaction of the hydration shells of the hydroxyl groups in the latter case and formation of two charged sites in the zwitterionic form of the former ones.