An automated method for the analysis of stable isotope labeling data in proteomics

An algorithm is presented for the generation of a reliable peptide component peak table from liquid chromatography-mass spectrometry (LC-MS) and subsequent quantitative analysis of stable isotope coded peptide samples. The method uses chemical noise filtering, charge state fitting, and deisotoping toward improved analysis of complex peptide samples. Overlapping peptide signals in mass spectra were deconvoluted by correlation with modeled peptide isotopic peak profiles. Isotopic peak profiles for peptides were generated in silico from a protein database producing reference model distributions. Doublets of heavy and light labeled peak clusters were identified and compared to provide differential quantification of pairs of stable isotope coded peptides. Algorithms were evaluated using peptides from digests of a single protein and a seven-protein mixture that had been differentially coded with stable isotope labeling agents and mixed in known ratios. The experimental results correlated well with known mixing ratios.     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

Two-particle dynamics on an electrode in ac electric fields

The relative motion between pairs of negatively charged latex particles 9.7 microm in diameter and deposited on an electrode was measured by optical microscopy and image analysis. At an rms field of approximately 30 V cm(-1), the two particles moved toward each other at frequencies below 500 Hz, but they separated at 1000 Hz. In the cases of aggregation, there are several interesting characteristics. First, when the center-to-center separation of a pair was initially 6 particle radii or more apart, a transient 'incubation' period of tens of seconds was observed before the particles began to move toward each other. Second, the two particles never came into contact, rather at long times the pair maintained a stationary gap between them equal to approximately one-half the particle radius. This stationary gap between particles was also observed for the aggregation of clusters of three or more particles. Finally, the rate of approach for a pair of particles decreased as the frequency increased. Larger fields are required to move particles together in ac compared to dc fields; at 30 Hz the ac field must be 130 times greater than the dc field to achieve the same rate of approach. Taking advantage of the qualitative and quantitative differences of the cooperative motion of particles in dc vs. ac fields, one should be able to re-position particles by alternating between these two modes. We demonstrated that the same pair of particles can be brought together at low frequency (100 or 200 Hz) and then separated at high frequency (1000 Hz).     

A crystallite packing model for pseudoboehmite formed during the hydrolysis of trisecbutoxyaluminium to explain the peptizability

A model for pseudoboehmite crystallite packing formed during the hydrolysis of trisecbutoxyaluminium is postulated. The model describes platelike crystallites of pseudoboehmite stacked in a sharing edges only configuration. With this type of stacking, the pore sizes detected are approximately equal to the crystallite sizes of the hydrolysates. The hydrolysates age via a dissolution re-precipitation reaction. This increases the size of the crystallite size of the pseudoboehmite formed, speeding peptization by allowing nitrate ions to enter pores and access the surfaces of the crystallites. This type of model also allows an explanation for the peptization kinetics of systems containing sec-butanol formed during the hydrolysis of trisecbutoxyaluminium.     

Two-dimensional metallic chain compounds Y5M2Te2 (M = Fe, Co, Ni) that are related to Gd3MnI3. The hydride derivative Y5Ni2Te2D0.4

Y(5)M(2)Te(2) (M = Fe, Co, Ni) have been prepared by high-temperature solid-state techniques and shown to be isostructural and orthorhombic Cmcm (No. 63), Z = 4. The structure was established by single crystal X-ray methods at 23 degrees C for M = Fe, with a = 3.9594(3) A, b = 15.057(1) A, and c = 15.216(1) A. The new structure contains zigzag chains of the late transition metal sheathed by a column of yttrium atoms that are in turn condensed through trans vertices on the latter to yield 2D bimetallic layers separated by single layers of tellurium atoms. Reaction of hydrogen with Y(5)Ni(2)Te(2) causes a rumpling of the Y-Ni layers as determined by both single X-ray crystal means at 23 degrees C and neutron powder diffraction at -259 degrees C for Y(5)Ni(2)Te(2)D(0.41(1)), Pnma (No. 62), Z = 4. Lattice constants from the former study are a = 14.3678(7) A, b = 4.0173(2) A, and c = 15.8787(7) A. The hydrogen is accommodated in tetrahedral yttrium cavities generated by bending the formerly flat sheets at the trans Y vertices. A higher hydride version also exists. Band structure calculations confirm the 2D metal-bonded character of the compounds and also help illustrate the bonding/matrix changes that accompany the bonding of hydrogen. The ternary structures for both Y(5)M(2)Te(2) and Sc(5)Ni(2)Te(2) can be derived from that of Gd(3)MnI(3), the group illustrating three different kinds of metal chain condensation.     

Coordination complexes of l-azetidine-2-carboxylic acid with platinum(II) and palladium(II)

Summary The complexes K[Pt(l-aze)Cl₂, [Pt(l-aze)₂] and [Pd(l-aze)₂] (l-aze = l-azetidine-2-carboxylate) were prepared. X-ray structures show that [Pt(l-aze)₂] and [Pd(l-aze)₂] are isomorphous, having a planar tetragonal geometry with a trans configuration around the Pt and Pd atoms. Slight puckerings of the MN(1)N(11)O(11) chelate ring (M = Pt or Pd) and the azetidine ring were observed. The circular dichroism (c.d.) spectra of the complexes in aqueous solution agree with the structures found in the solid state as far as the hexadecant rule is concerned, giving, for the trans configuration of [M(l-ia)₂] (where ia = imino acid), the profile of the c.d. signs for the three predominant d-d transitions as: +,-,-. I.r., conductivity and n.m.r. measurements are also reported and are in accord with the proposed structures.     

ICP-MS for elemental speciation studies

The use of inductively coupled plasma mass spectrometry (ICP-MS) coupled with separation techniques for the purpose of elemental speciation has recently gained a lot of attention. Much of this is due to ever improving separation capabilities of Chromatographic techniques, the high sensitivity of ICP-MS, and the continuing development of better interface techniques. Additionally, there is a growing awareness of the need to monitor various species of an analyte, rather than just total analyte concentrations, due to their often varying natures. For the sake of learning from different elemental speciation approaches, this review brings together some selected types of elemental speciation which have been recently seen in literature. These include separations using various forms of liquid chromatography, such as reversed phase, reversed phase ion pairing, micelle, ion exchange, and size exclusion. Elemental speciation employing gas Chromatographie separations and supercritical fluid separations are discussed as well as elemental speciation using capillary electrophoresis.     

Ozonolysis of tetramethylethylene: characterization of cyclic and open-chain oligoperoxidic products

The ozonolysis of tetramethylethylene (TME) in solution to high conversion in nonparticipating solvents at -60 degrees C yields predominantly oligoperoxides. For the first time, these products have been characterized using electrospray ionization mass spectrometry (ESI-MS) under soft ionization conditions. The predominant structure formed in reactions carried out in pentane (up to 2.0 M TME) is shown to be the cyclic hexamer of acetone carbonyl oxide (oligocarbonyl oxide with degree of polymerization, n = 6), but cyclic structures with n up to 19 are observed. A small proportion of the oligoperoxides formed are open-chain compounds with end groups that suggest that chain termination of oligocarbonyl oxides can occur through reaction with either water or hydrogen peroxide. Ozonolysis in dried butyl acetate similarly produces mainly cyclic oligoperoxides. However, ozonolyses carried out in undried butyl acetate yield mainly open-chain oligoperoxides, confirming that propagating carbonyl oxide chains are readily terminated by water. Relative amounts of the open-chain oligomers so-formed suggest that undried butyl acetate contains ca. 0.1% w/w water. The ozonolysis of TME in the participating solvent, methanol, at -60 degrees C yields 2-methoxyprop-2-yl hydroperoxide via reaction of acetone carbonyl oxide with methanol; no oligoperoxidic products are formed in this case.     

A re‐examination of supra­molecular aggregation in two polymorphs of acetone 2,4‐dinitro­phenyl­hydrazone

The structure of the triclinic polymorph of acetone 2,4‐dinitrophenylhydrazone, C₉H₁₀N₄O₄, has been redetermined from diffraction data collected at 120 (2) K; the mol­ecules are linked by C—H⋯O hydrogen bonds into centrosymmetric R₂²(10) dimers which are themselves linked into a chain by an aromatic π–π stacking inter­action. In the monoclinic polymorph, which crystallizes with Z′ = 2 in the space group P2₁/n, one type of mol­ecule forms dimers exactly as in the triclinic polymorph, while the other forms C(6) chains.     

Heterometallic Ln/Hg compounds with fluorinated thiolate ligands

The early lanthanide benzenefluorothiolates (Ln(SC(6)F(5))(3); Ln = La, Ce, Pr, Nd, Sm, Gd) react with Hg(SC(6)F(5))(2) in DME to form ionic heterometallic compounds with Ln cations and Hg anions. X-ray diffraction analyses of all compounds reveal an isostructural series with the general formula [(DME)(3)Ln(SC(6)F(5))(2)](2)[Hg(2)(SC(6)F(5))(6)]. In the structures, a fluorothiolate ligand has been extracted from the Ln coordination sphere that is saturated with three neutral DME donor ligands and a dative interaction between one ortho fluorine and the Ln. Distances between Ln and F do not vary simply with Ln ionic radius. There are two Ln cations with charge balanced by a Hg(2)(SC(6)F(5))(6) dianion composed of two distinctly nonideal Hg(II) tetrahedra, all connected through a series of pi-pi interactions that link cations with anions in a one-dimensional array and anions to anions in a more complex 2D network.