Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondar

Structural analysis of nickel doped cobalt ferrite nanoparticles prepared by coprecipitation route

Magnetic nanoparticles of nickel substituted cobalt ferrite (NixCo1-xFe2O4:0 <= x <= 1) have been synthesized by co-precipitation route. Particles size as estimated by the full width half maximum (FWHM) of the strongest X-ray diffraction (XRD) peak and transmission electron microscopy (TEM) techniques was found in the range 18-28 +/- 4 nm. Energy dispersive X-ray (EDX) analysis confirms the presence of Co, Ni, Fe and oxygen as well as the desired phases in the prepared nanoparticles. The selective area electron diffraction (SAED) analysis confirms the crystalline nature of the prepared nanoparticles. Data collected from the magnetization hysteresis loops of the samples show that the prepared nanoparticles are highly magnetic at room temperature. Both coercivity and saturation magnetization of the samples were found to decrease linearly with increasing Ni-concentration in cobalt ferrite. Superparamagnetic blocking temperature as determined from the zero field cooled (ZFC) magnetization curve shows a decreasing trend with increasing Ni-concentration in cobalt ferrite nanoparticles. (C) 2009 Elsevier B.V. All rights reserved.

Structural analysis of monoterpene glycosides extracted from Paeonia lactiflora Pall. using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and high-performance liquid chromatography/electrospray ionization tandem mass spectrometry

Paeoniflorin standard was first investigated by electrospray ionization Fourier transform ion cyclotron resonance tandem mass spectrometry (ESI-FTICR-MS/MS) using a sustained off-resonance irradiation (SORI) collision-induced dissociation (CID) method at high mass resolution. The experimental results demonstrated that the unambiguous elemental composition of product ions can be obtained at high mass resolution. Comparing MS/MS spectra and the experimental methods of hydrogen and deuterium exchange, the logical fragmentation pathways of paeoniflorin have been proposed. Then, the extracts of the traditional Chinese medicine Paeonia lactiflora Pall. were analyzed by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). By comparison with the ESI-FTICR-MS/MS data of paeoniflorin, the isomers paeoniflorin and albiflorin in Paeonia lactiflora Pall. have been identified using HPLC/MS with CID in an ion trap and in-source CID. Furthermore, using the characteristic fragmentation pathways, the retention times (t(R)) in HPLC and MS/MS spectra, the structures of three other kinds of monoterpene glycoside compounds have been identified on-line without time-consuming isolation.

Structural analysis of selected characteristic flavones by electrospray tandem mass spectrometry

Seven structure analogical flavonoid aglycones have been analyzed using electrospray ionization tandem mass spectrometry (ESI-MSn) in the negative-ion mode. The spectra obtained ESI-MSn allowed us to propose plausible schemes for their fragmentation mechanism. By analyzing the product ions spectra of deprotonated molecule ions [M-H](-), some neutral diagnostic losses and specific retro Diels-Alder fragments were obtained. By using all of these characteristic fragment ions we can specially differentiate the flavone isomer.

Structural analysis of PEKEKK(T/I) using WAXD, imaging plates and SAXS

Structures and crystal form transition of the novel aryl ether ketone polymer containing meta-phenylene linkage: PEKEKK(T/I) were investigated by wide angle X-ray diffraction (WAXD), imaging plates (IPs) and small angle X-ray scattering (SAXS). The energy of activation of the decomposition reaction and degree of crystallinity of PEKEKK(T/I) were determined by WAXD and thermo-gravimetric analysis (TGA), respectively. Results obtained from WAXD and IPs show that crystal forms I and II coexist in the PEKEKK(T/I) samples isothermally cold crystallized in the temperature range from 180degreesC to 240degreesC and only form I occurs in PEKEKK(T/I) samples isothermally cold crystallized at 270degreesC. The radius of gyration (Rg), thickness of microregions with electron-density fluctuations (E) and distribution of particle sizes were investigated by SAXS.

Structural analysis of saponins from medicinal herbs using electrospray ionization tandem mass spectrometry

The underivatized saponins from Tribulus terrestris and Panax ginseng have been investigated by electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn). In ESI-MS spectra, a predominant [M + Na](+) ion in positive mode and [M - H](-) ion in negative mode were observed for molecular mass information. Multi-stage tandem mass spectrometry of the molecular ions was used for detailed structural analysis. Fragment ions from glycoside cleavage can provide information on the mass of aglycone and the primary sequence and branching of oligosaccharide chains in terms of classes of monosaccharides. Fragment ions from cross-ring cleavages of sugar residues can give some information about the linkages between sugar residues. It was found that different alkali metal-cationized adducts with saponins have different degrees of fragmentation, which may originate from the different affinity of a saponin with each alkali metal in the gas phase. ESI-MSn has been proven to be an effective tool for rapid determination of native saponins in extract mixtures, thus avoiding tedious derivatization and separation steps.

Crystal growth and structural analysis of PrMnO3 and TbMnO3

Single crystals of PrMnO3 and TbMnO3 were grown by floating zone method and the crystal structure was determined by single crystal X-ray diffractometry. The structure of these compounds belongs to the orthorhombic system (space group is Pnma, No. 62) with the lattice parameters alpha approximate to root (.) - a(p), b approximate to 2 (.) a(p) , c approximate to root 2.a(p) and Z = 4, where a(p) is ideal cubic perovskite cell parameter.

Metal ion adducts in the structural analysis of ginsenosides by electrospray ionization with multi-stage mass spectrometry

The effect of metal (Li+, Na+, K+, Ag+) cationization on collision-induced dissociation of ginsenosides was investigated by electrospray ionization mass spectrometry combined with multi-stage mass spectrometry (ESI-MSn). The fragments of sodiated and lithiated molecules give valuable structural information regarding the nature of the aglycone and the sequence and linkage information of sugar moieties. However, the number and relative abundances of fragment ions from lithiated ginsenosides are significantly greater than for the sodiated species, The K+ adducts undergo glycosidic cleavages and very limited cross-ring reactions. The silver ion adducts fragment mainly through glycosidic cleavages. Copyright (C) 2001 John Wiley & Sons, Ltd.

Application of acetone and dimethyl ether chemical ionization reagent gases to structural analysis

Acetone and dimethyl ether( DME) have been shown to be reagent gases of exceptional utitlity and versatility for the characterization of a variety of class of organic compounds. The fragmentation mechanisms of the adduct product ions, formed by ion/molceule reaction of the substrate with the ionized gases, have been studied and substantiated by experiments with acetone-d(6) and DME-d(6).

Structural analysis of nonlinearities of Ca4ReO(BO3)(3) (Re = La, Nd, Sm, Gd, Er, Y)

From the chemical bond viewpoint, second-order nonlinear optical (NLO) tensor coefficients of the family of new oxoborates Ca4ReO(BO3)(3) (CReOB, Re = La, Nd, Sm, Gd, Er, and Y) have been theoretically predicted. The d(11) tensor coefficient of CReOB is predicted to be -11 d(36)(KDP), which is the largest d(ij) tensor that has been found in borate crystals. From the structural characteristic of CReOB, we find the isolated BO33- clusters play a dominant role in contributions to the total nonlinearity, and the largest d(11) tensor of CReOB-type crystals is also ascribed to these BO33- clusters. We also find the NLO property of this family does not change dramatically for different rare-earth elements. The details of the calculation of CGdOB only are presented.

Structural analysis of peptides of PSII light-harvesting complexes in siphonous green algae, Codium fragile

peptide composition and arrangement of 4 major light-harvesting complexes LHCP1-3 and LHCP3, isolated from siphonous green algae (Codium fragile (Sur.) Hariot.) were investigated. LHCP1 showed five main peptides, 34.4, 31.5, 29.5, 28.2 and 26.5 kD in SDS-PAGE, the 34.4 and 31.5 kD peptides were never found in higher plants. LHCP3 contained the other four kinds of LHCP1 peptides except 34.4 kD, while LHCP3, consisted of only 28.2 and 26.5 kD peptides. We found that 34.4, 28.2 and 26.5 kD peptides were easy to decompose from LHCP1 when subjected to SDS-PACE without pretreatment. They might be located at the exterior of LHCP1, while the 31.5 and 29.5 kD peptides were at the central part. The 28.2 and 26.5 kD peptides often occurred in CPa, the center complex of PS II. They are possibly the LHC II peptides tightly associated with CC II. According to the results described above, a peptide map of LHCP1 was sketched.