Conformational analysis of dipeptide‐derived polyisocyanides

The conformational properties of polymers derived from isocyanodipeptides have been investigated with a combination of model calculations, X‐ray diffraction, and circular dichroism spectroscopy. Depending on the configuration of the side chains, defined arrays of hydrogen bonds along the polymeric backbone are formed. This leads to a well‐defined conformation as, for example, expressed in the formation of lyotropic liquid‐crystalline phases and increased helical stability. Upon the disruption of the hydrogen bonds by a strong acid, a less well‐defined macromolecular conformation is observed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1725–1736, 2003     

General covariance of the non-abelian DBI-action: checks and balances

We perform three tests on our proposal to implement diffeomorphism invariance in the non-abelian D0-brane DBI action as a base-point independence constraint between matrix Riemann normal coordinate systems. First, we show that T-duality along an isometry correctly interchanges the potential and kinetic terms in the action. Second, we show that the method to impose base-point independence using an auxiliary dN²-dimensional nonlinear sigma model also works for metrics which are curved along the brane, provided a physical gauge choice is made at the end. Third, we show that without alteration this method is applicable to higher order in velocities. Testing specifically to order 4, we elucidate the range of validity of the symmetrized trace approximation to the non-abelian DBI action.     

Fluid-fluid phase separation in colloid-polymer mixtures studied with small angle light scattering and light microscopy

Mixtures of colloidal silica spheres and polydimethylsiloxane in cyclohexane with a colloid-polymer size ratio of about one were found to phase separate into two fluid phases, one which is colloid-rich and one which is colloid-poor. In this work the phase separation kinetics of this fluid-fluid phase separation is studied for different compositions of the colloid-polymer mixtures, and at several degrees of supersaturation, with small angle light scattering and with light microscopy. The small angle light scattering curve exhibits a peak that grows in intensity and that shifts to smaller wave vector with time. The characteristic length scale that is obtained from the scattering peak is of the order of a few μm, in agreement with observations by light microscopy. The domain size increases with time as , which might be an indication of coarsening by diffusion and coalescence, like in the case of binary liquid mixtures and polymer blends. For sufficiently low degrees of supersaturation the angular scattering intensity curves satisfy dynamical scaling behavior.     

Dispersion effects of laminar flow and spray chamber volume in capillary electrophoresis-inductively coupled plasma-mass spectrometry: a numerical and experimental approach

Band broadening related to laminar flow and spray chamber dead volume is a potential problem in flow injection (FI)-inductively coupled plasma-mass spectrometry (ICP-MS). We studied these two dispersion effects with a sheath flow capillary electrophoresis (CE)-ICP-MS interface. A numerical model was used to simulate advection diffusion processes in the CE-capillary and dispersion in the spray chamber. Experimental results of FI with this CE-ICP-MS interface agree well with numerical modeling results. Dispersion due to laminar flow depends strongly on capillary diameter and analyte diffusion coefficient and to a lesser extent on laminar velocity and capillary length and typically amounts to one order of magnitude peak width increase. Three spray chambers of 5, 20 and 150 ml dead volume showed an increase in band broadening and peak tailing with increasing dead volume. The use of standard Scott-type spray chambers (>90 ml volume) increases peak widths by 5-10 s regardless of injection time. The use of a low dead volume spray chamber is recommended for experiments where resolution is critical. The modeling approach can be extended to the coupling of other flow injection techniques, like micro-LC and nano-LC with ICP-MS.     

Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination

In this report, we evaluate the validity of using hydrogen/deuterium exchange in combination with collision-induced dissociation mass spectrometry (CID MS) for the detailed structural and conformational investigation of peptides and proteins. This methodology, in which partly deuterated peptide ions are subjected to collision-induced dissociation in the vacuum of a mass spectrometer, has emerged as a useful tool in structural biology. It may potentially provide quantitatively the extent of deuterium incorporation per individual amino acid in peptides and proteins, thus providing detailed structural information related to protein structure and folding. We report that this general methodology has limitations caused by the fact that the incorporated deuterium atoms migrate prior or during the CID MS analysis. Our data are focused on a variety of transmembrane peptides, incorporated in a lipid bilayer, in which the near-terminal amino acids that anchor at the lipid-water interface are systematically varied. Our findings suggest that, under the experimental conditions we use, the extent of intramolecular hydrogen scrambling is strongly influenced by experimental factors, such as the exact amino acid sequence of the peptide, the nature of the charge carrier, and therefore most likely by the gas-phase structure of the peptide ion. Moreover, the observed scrambling seems to be independent of the nature of the peptide fragment ions (i.e., protonated B and Y' ' ions, and sodiated A and Y' ions). Our results strongly suggest that scrambling may be reduced by using alkali metal cationization instead of protonation in the ionization process.     

Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics

Conventional proteomics makes use of two-dimensional gel electrophoresis followed by mass spectrometric analysis of tryptic fragments derived from in-gel digestion of proteins. Although being a very strong technique capable of separating and visualizing hundreds of proteins, 2D-gel electrophoresis has some well-documented disadvantages as well. More recently, liquid chromatographic-(tandem) mass spectrometric techniques have been developed to overcome some of the shortcomings of 2D-gel electrophoresis. In this review we have described several recent applications of liquid chromatography-(tandem) mass spectrometry in the field of proteomics and especially in the field of membrane proteomics, quantitative proteomics and in the analysis of post-translational modifications.     

Raman imaging of PLGA microsphere degradation inside macrophages

Understanding the degradation behavior of polymeric microspheres is crucial for the successful application of such devices in controlled drug delivery. The degradation mechanism of poly(lactic-co-glycolic acid) (PLGA) microspheres inside phagocytic cells is not known, but different models for degradation in aqueous solution have been proposed. We have used confocal Raman spectroscopy and imaging to study the intracellular degradation of PLGA microspheres inside individual macrophages. Our results show that ingested microspheres degrade in a heterogeneous manner, with a more rapid degradation in the center. Comparison of Raman spectra from degrading beads with those of uningested beads reveals that ester hydrolysis occurs throughout the phagocytosed microspheres, with a selective loss of glycolic acid units. Furthermore, we show that PLGA degradation is a cell-mediated process, possibly caused by the low pH of the phagosome and/or the presence of hydrolytic enzymes. In conclusion, we have demonstrated that the chemical composition of degrading polymers inside cells can be probed by Raman spectral imaging. This technique will expand the capabilities of investigating biomaterial degradation in vivo.     

A note on the 5-person traveling salesman game

LetN=1,2,...,n be a set of customers andG=(N {0},E) an undirected connected graph with non-negative edge lengths. 0 is the home location of a salesman who visits the customers inN. Each subset can invite the salesman to visit its members only. The costc(S) of coalitionS is the length of a shortest tour that starts in 0, visits each customer inS at least once and returns to 0. The cooperative cost game defined in this way is called a (symmetric) traveling salesman game (TSG).The core of a TSG can be empty when ¦N¦ 6 and it was proved that it always has a non-empty core when ¦N¦ 4. In this note we shall prove that a TSG always has a non-empty core when ¦N¦=5.     

Construction of functional porphyrin polystyrene nano-architectures by ATRP

A series of mono-functionalized metallo-porphyrin polystyrenes have been synthesized using atom transfer radical polymerization and their self-assembling behavior was studied by electron microscopy showing that the polystyrene tail-length influences the aggregate architecture.     

Cu K-edge EXAFS characterisation of copper(I) arenethiolate complexes in both the solid and liquid state: detection of Cu-Cu coordination

Herein we describe a structural characterisation with EXAFS of copper(I) arenethiolate complexes in both the solid and liquid state. Previously noted difficulties in the detection of the Cu-Cu interaction have been attributed to anti-phase behaviour of different Cu-Cu neighbour contributions. A data analysis procedure solely based on EXAFS parameters is presented which resolves these problems. A careful analysis of the individual coordination shells and the use of different k-weightings during the data analysis are shown to be an absolute necessity to obtain reliable results. During R-space fitting, the difference file technique is used to separate, examine and compare the individual contributions. Using this technique their statistical significance and correctness can be determined. Anti-phase behaviour can be detected and accounted for in this way. An additional mixed organocopper aggregate [Cu4(SAr)2(Mes)2] with different Cu sites is analysed, which proves the value of the analysis procedure described above. Moreover, this newly developed EXAFS data analysis procedure is applicable to any other EXAFS spectrum obtained. The structural analysis of these organocopper complexes with EXAFS provides information about their actual structure and dynamic behaviour in solution. The technique can now be used to obtain insights into the reactivity of these complexes and the way in which they form catalytic reaction intermediates.