Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D difference in-gel electrophoresis

Endothelial senescence contributes to endothelium dysfunctionality and is thereby linked to vascular aging. A dynamic proteomic study on human umbilical vein endothelial cells, isolated from three umbilical cords, was performed. The cells were cultured towards replicative senescence and whole cell lysates were subjected to 2-D difference gel electrophoresis (DIGE). Despite the biological variability of the three independent isolations, a set of proteins was found that showed senescence-dependent expression patterns in all isolations. We focused on those proteins that showed significant changes, with a paired analysis of variance (RM-ANOVA) p-value of < or =0.05. Thirty-five proteins were identified with LC-Fourier transform MS, and functional annotation revealed that endothelial replicative senescence is accompanied by increased cellular stress, protein biosynthesis and reduction in DNA repair and maintenance. Nuclear integrity becomes affected and cytoskeletal structure is also changed. Such important changes in the cell infrastructure might accelerate endothelium dysfunctionality. This study provides biological information that will initiate studies to further unravel endothelial senescence and gain more knowledge about the consequences of this process in the in vivo situation.     

Controlling Through‐Space and Through‐Bond Exchange Pathways in Bis‐Cobaltocenes for Molecular Spintronics

Pinching molecules via chemical strain suggests intuitive consequences, such as compression at the pinched site and clothespin‐like opening of other parts of the structure. If this opening affects two spin centers, it should result in reduced communication between them. We show that for naphthalene‐bridged biscobaltocenes with competing through‐space and through‐bond pathways, the consequences of pinching are far less intuitive: despite the known dominance of through‐space interactions, the bridge plays a much larger role for exchange spin coupling than previously assumed. Based on a combination of chemical synthesis, structural, magnetic, and redox characterization, and a newly developed theoretical pathway analysis, we can suggest a comprehensive explanation for this non‐intuitive behavior. These results are of interest for molecular spintronics, as naphthalene‐linked cobaltocenes can form wires on surfaces for potential spin‐only information transfer.     

Molecular interactions of glycopeptide antibiotics investigated by affinity capillary electrophoresis and bioaffinity electrospray ionization-mass spectrometry

Many analytical approaches are available to evaluate (bio)molecular interactions, all of which have their particular advantages and disadvantages. In recent years, two relatively new techniques have emerged that may be used by the bioanalytical community to evaluate such interactions, namely affinity capillary electrophoresis (ACE) and bioaffinity electrospray ionization-mass spectrometry (ESI-MS). In this paper, we describe and evaluate the use of both these techniques for the investigation of the interactions of glycopeptide antibiotics with peptides that mimic the bacterial cell wall binding site. We focus particularly on the effect of the sugar moieties attached to the antibiotic peptide backbone and on the noncovalent dimerization of these glycopeptide antibiotics.     

ZrIV‐ und TaV‐Komplexe mit methanoverbrückten Bis(aryloxy)‐Liganden

Zr^IV and Ta^V Complexes with Methano‐Bridged Bis(aryloxy) Ligands The bis(aryloxy) ligand precursor compounds bis(2‐trimethylsiloxy‐5‐tbutylphenyl)methane (L–SiMe₃) and its bromoderivative (2‐trimethylsiloxy‐3‐bromo‐5‐tbutylphenyl)(2′‐trimethylsiloxy‐5′‐tbutylphenyl)methane (L^Br–SiMe₃) are prepared in analogy to the corresponding calixarenes in excellent yields. X‐ray structure analysis for L^Br–SiMe₃: space group P2₁/c, a = 12.462(7), b = 10.466(6), c = 23.315(14) Å, β = 105.02(4)°, V = 2937(3) ų, Z = 4. L–SiMe₃ and L^Br–SiMe₃ react with Zr^IV and Ta^V chlorides in very good yields forming di‐ and trinuclear complexes. From the reaction of CpZrCl₃ with L^Br–SiMe₃ in the ratio of 3 : 2 a Zr₃ complex ( 7 ) is obtained, with one L^Br ligand only, which Zr atoms are bridged by a μ₃‐oxygen. The X‐ray structure analysis of 7 (space group R 3, a = 33.23(6), c = 24.47(8) Å, V = 23405(128) ų, Z = 18) additionally reveals that one phenolato oxygen atom of the L^Br ligand is terminally bound to a distorted tetragonal‐pyramidal coordinated Zr atom, while the second phenolato oxygen atom of the L^Br ligand forms a bridge to another Zr atom with a distorted octahedral coordination. The third Zr atom is also found in a distorted octahedral coordination mode. The reactions of L–SiMe₃ and L^Br–SiMe₃ with CpTaCl₄ and TaCl₅ yield dinuclear Ta complexes with a bridging bis(aryloxy) ligand. NMR spectroscopic data point out that the coordination of the bis(aryloxy) ligands in the Ta complexes very much resembles that in the Zr₃‐complex with one terminal and one bridging phenolato oxygen atom. The Zr₃ and the Ta complexes L^BrTa₂Cp₂Cl₆ and LTa₂Cl₈ were tested with respect to their catalytic properties in olefin polymerisation reactions in the presence of MAO.     

Heat-shrinking spherical and columnar supramolecular dendrimers: their interconversion and dependence of their shape on molecular taper angle

Synthesis and modes of self-assembly are described for the tapered monodendritic molecules 3,4,5-nGi-X of generation i = 1, 2, 3 (see structures below) that contain multiple (CH2)nH alkyl chains on their periphery (n = 12, 14, 16) and a polar group X at the apex (X = COOH, COONa, COOCs, CO(OCH2CH2)3OH). These monodendrons self-assemble into supramolecular cylindrical or spherical dendrimers, which in turn self-organise into p6mm columnar or Pm3n cubic thermotropic liquid crystals, respectively. The two principal ways of affecting the self-assembly of these compounds by means of their molecular architecture are: a) by changing the width of the wide (aliphatic) end, and b) by changing the volume at the apex. In the present work a) is controlled through temperature (conformational disorder) and b) is controlled by chaging the generation number i or the size of X, for example, through the choice of metal cation. The single most important geometric parameter of these dendritic building blocks is the molecular solid angle (taper angle) alpha; a high alpha leads to spherical and a low alpha to cylindrical supramolecular dendrimers. Furthermore, alpha also determines the equilibrium size of the supramolecular objects; a larger alpha results in a smaller diameter. The unusually strong negative thermal expansion coefficient of the cubic and columnar lattice is attributed to the excess of the increasingly highly tapered molecules being rejected from their parent aggregates and reassembling as new ones. Increasing alpha is also considered to be responsible for the observed thermotropic columnar-cubic transition.     

Isomorphism within the hexagonal columnar mesophase of molecular and macromolecular self- and co-assembled columns containing tapered groups

Abstract

The phase behaviour of binary mixtures of self-assembled tapering molecules based on monoesters of oligooxyethylene glycol and 3,4,5-tris[4-(n-dodecan-1-yloxy)benzyloxy]benzoic acid, their corresponding polymethacrylates, and of 4′-methyl (benzo-15-crown-5)-3,4,5-tris[4-(n-dodecan-1-yloxy)benzyloxy]benzoate within their hexagonal columnar mesophase (Φ_h) is described. The binary blends between molecular tapers co-assemble into a single supramolecular column resulting in isomorphism within their Φ_h mesophase over the entire range of composition. The binary blends between polymethacrylates containing tapered side groups co-assemble into a single Φ_h phase only when the columns of the parent polymers are of similar diameters. This results in binary mixtures which are isomorphic within the Φ_h mesophase over the entire composition range. When the diameters of the columns formed by the parent polymers are dissimilar, isomorphic mixtures are obtained only over a narrow range of composition. Binary mixtures between molecular tapers and macromolecular systems containing tapered side groups co-assemble into a single column to the extent that intercalation of the molecular taper, within the column formed by the macromolecular system containing tapered side groups, is permissible. In all systems increased intracolumnar interactions can be induced by complexation of CF₃SO₃Li by the oligooxyethylenic receptors leading to isomorphism in otherwise non-isomorphic mixtures. Ternary mixtures between molecular tapers with non-specific oligooxyethylenic receptors and specific crown ether receptors and CF₃SO₃ Na as the third component are non-isomorphic within their Φ_h phase due to preferential complexation of the alkali metal cation by the column of the crown ether containing the molecular taper. This results in two columns of dissimilar diameters, which are isomorphic in the Φ_h phase only within a limited range of composition.     

Three-branched dendritic dipolar nonlinear optical chromophores, more than three times a single-strand chromophore?

To elucidate the dependence of the nonlinear optical (NLO) response on the conformation of triply branched derivatives, a new series of D-pi-A dendrimers has been synthesized. A combined approach of experiments (UV-vis and EOA measurements) and computational predictions (semiempirical and ab initio) was applied both on the dendrimers and on the corresponding single-strand chromophores. It has been shown that depending on the surrounding media the NLO activity of a flexible dendrimer can be very different. Two limiting cases are proposed: (i) the dendrimer resembles a solution of the corresponding single-strand chromophores with about 3-fold concentration, where the hyperpolarizability is the sum of the effect of three noninteracting single-strand subunits ("independent chromophores" limit); (ii) the dendrimers show nearly parallel or helical alignments of the single-strand subunits. Because of this change of conformation the NLO activity can be enhanced up to nine times the value of the "independent chromophores" limit and, thus, are more than a single strand chromophore. Conformers of dendrimers with interacting single-strand chromophores have been identified experimentally in nonpolar solutions by the EOA spectroscopy and possible structures have been revealed by numerical calculations, which could moreover show the tendency of the effects on the hyperpolarizability due to structural changes of the flexible dendritic architecture. Implications for future research developments are given to implement the "more than three times" concept.     

Modern biomolecular mass spectrometry and its role in studying virus structure, dynamics, and assembly

Over a century since its development, the analytical technique of mass spectrometry is blooming more than ever, and applied in nearly all aspects of the natural and life sciences. In the last two decades mass spectrometry has also become amenable to the analysis of proteins and even intact protein complexes, and thus begun to make a significant impact in the field of structural biology. In this Review, we describe the emerging role of mass spectrometry, with its different technical facets, in structural biology, focusing especially on structural virology. We describe how mass spectrometry has evolved into a tool that can provide unique structural and functional information about viral-protein and protein-complex structure, conformation, assembly, and topology, extending to the direct analysis of intact virus capsids of several million Dalton in mass. Mass spectrometry is now used to address important questions in virology ranging from how viruses assemble to how they interact with their host.     

Phosphopeptide fragmentation and analysis by mass spectrometry

Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision‐induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss‐dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS³ and multistage activation (MSA), have been designed to generate more sequence‐informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron‐driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large‐scale phosphoproteomics studies. Copyright © 2009 John Wiley & Sons, Ltd.     

Quantitative analysis of the novel anticancer drug ABT-518, a matrix metalloproteinase inhibitor, plus the screening of six metabolites in human plasma using high-performance liquid chromatography coupled with electrospray tandem mass spectrometry

A liquid chromatographic/tandem mass spectrometric (LC/MS/MS) assay for the quantitative analysis of the novel anticancer drug ABT-518 and the screening of six potential metabolites in human plasma has been developed and validated to support a phase I study with the drug. ABT-518 is an inhibitor of matrix metalloproteinases, which are associated with tumor growth and development of metastasis. Plasma samples were prepared for analysis using a simple solid-phase extraction method on phenyl cartridges. LC separation was performed on a Zorbax extend C18 column (150 x 2.1 mm i.d., 5 microm particle size) using a mobile phase of methanol-aqueous 10 mM ammonium hydroxide (80:20, v/v) pumped at a flow-rate of 0.2 ml min(-1). An API2000 triple-quadrupole mass spectrometer was used for specific and sensitive detection. The best chromatographic speed (total run time 8 min) and peak shapes were obtained by employing an alkaline mobile phase (pH in aqueous phase approximately 10). Furthermore, an alkaline eluent was favored in order to obtain a better overall sensitivity for the protonated analytes. The dynamic range was from 10 to 1000 ng ml(-1) from 500 microl of plasma for ABT-518 and the metabolites were detected at levels of the same order of magnitude. Inter-assay accuracies for ABT-518 at five concentration levels were between -9.24 and 6.93% and inter-assay precisions were always <10.7%. Analyte stability was not critical during either storage or processing. This method was successfully applied in a phase I clinical study of ABT-518. The active drug, ABT-518, and all of the metabolites included in the assay could be identified in plasma from dosed patients. We believe that the method described in this paper using an alkaline mobile phase in combination with a basic stable analytical column may also be generally useful for the bioanalysis of other basic drugs.