Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

A quantitative HPLC–MS/MS method for studying internal concentrations and toxicokinetics of 34 polar analytes in zebrafish (Danio rerio) embryos

An analytical method using high-performance liquid chromatography–tandem mass spectrometry was developed to determine internal concentrations of 34 test compounds such as pharmaceuticals and pesticides in zebrafish embryos (ZFE), among them, cimetidine, 2,4-dichlorophenoxyacetic acid, metoprolol, atropine and phenytoin. For qualification and quantification, multiple reaction monitoring mode was used. The linear range extends from 0.075 ng/mL for thiacloprid and metazachlor and 7.5 ng/mL for coniine and clofibrate to 250 ng/mL for many of the test compounds. Matrix effects were strongest for nicotine, but never exceeded ±20 % for any of the developmental stages of the ZFE. Method recoveries ranged from 90 to 110 % from an analysis of nine pooled ZFE. These findings together with the simple sample preparation mean this approach is suitable for the determination of internal concentrations from only nine individual ZFE in all life stages up to 96 h post-fertilization. Exemplarily, the time course of the internal concentrations of clofibric acid, metribuzin and benzocaine in ZFE was studied over 96 h, and three different patterns were distinguished, on the basis of the speed and extent of uptake and whether or not a steady state was reached. Decreasing internal concentrations may be due to metabolism in the ZFE.

Fatty acid desaturation index in human plasma: comparison of different analytical methodologies for the evaluation of diet effects

Stearoyl-CoA desaturase 1 (SCD1) plays a role in the development of obesity and related conditions, such as insulin resistance, and potentially also in neurological and heart diseases. The activity of SCD1 can be monitored using the desaturation index (DI), the ratio of product (16:1n-7 and 18:1n-9) to precursor (16:0 and 18:0) fatty acids. Here, different analytical strategies were applied to identify the method which best supports SCD1 biology. A novel effective approach was the use of the SCD1-independent fatty acid (16:1n-10) as a negative control. The first approach was based on a simple extraction followed by neutral loss triglyceride fatty acid analysis. The second approach was based on the saponification of triglycerides followed by fatty acid analysis (specific for the position of the double bond within monounsaturated fatty acids (MUFAs)). In addition to the analytical LC-MS assays, different matrices (plasma total triglyceride fraction and the very low-density lipoprotein (VLDL) fraction) were investigated to identify the best for studying changes in SCD1 activity. Samples from volunteers on a high-carbohydrate diet were analyzed. Both ultra HPLC (UHPLC)-MS-based assays showed acceptable accuracies (75–125 % of nominal) and precisions (<20 %) for the analysis of DI-specific fatty acids in VLDL and plasma. The most specific assay for the analysis of the liver SCD activity was then validated for specificity and selectivity, intra- and interday accuracy and precision, matrix effects, dilution effects, and analyte stability. After 3 days of high-carbohydrate diet, only the specific fatty acids in human plasma VLDL showed a significant increase in DI and associated SCD1 activity.     

Highly Selective Dimerization and Trimerization of Isobutene to Linearly Linked Products by Using Nickel Catalysts

The unique linear linkage of isobutene to generate highly valuable C₈ precursors for plasticizers is feasible by using special nickel catalysts. (4‐Cyclooctene‐1‐yl)(1,1,1,5,5,5‐hexafluoro‐2,4‐acetylacetonato)nickel and aluminum‐alkyl‐activated nickel acetylacetonates produce isobutene dimers with high selectivities of up to 95 %. Moreover, selectivity for the head‐to‐head products (2,5‐dimethylhexenes) is remarkably high at up to 99 %. Additionally, novel C₁₂ isobutene trimers are also formed with a very high selectivity of up to 99 % for the linear linkage. The trimer structure (2,5,8‐trimethylnonenes) reflects the stepwise characteristic of the reaction mechanism. Pathways of insertion and activation and the deactivation processes of the catalyst are discussed in detail.     

A regularization approach for damage models based on a displacement gradient

Common material models that take into account softening effects due to damage encounter the problem of ill-posed boundary value problems if no regularization is applied. This condition leads to a non-unique solution for the resulting algebraic system and a strong mesh dependence of the numerical results. A possible solution approach to prevent this problem is to apply regularization techniques that take into account the non-local behavior of the damage [1]. For this purpose a field function is used to couple the local damage parameter to a non-local level, in which differences between the local and non-local parameter as well as the gradient of the non-local parameter can be penalized. In contrast, we present a novel approach to regularization in which no field function is needed [2]. Hereto, the regularization is carried out by means of the divergence of the displacements and no additional quantity is necessary since the displacements are already defined on a non-local level. The idea is that with an increasing value of the damage the element's volume will increase as well. This is a result of the softening due to the occurring damage. The increasing volume can be measured by the divergence of the displacements which can be penalized by an additional energy part. The lack of any field function and the regularization by the use of the divergence of the displacements entails several numerical advantages: the computational effort is considerably reduced and the convergence behavior is improved as well. Naturally, the numerical results are mesh independent due to the regularization. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Application of a cohesive zone element for the prediction of damage in nano/micro coating

Many tools in production technology are nowadays coated to obtain a satisfactory lifetime and degradation resistance. Therefore, the main goal of this study is to investigate antiadhesive and wear resistant coatings made of ceramics, plastics and metals produced by High Power Pulsed Magnetron Sputtering (HPPMS) technique [1]. A cohesive zone element technique (CZ) is applied to model the interactions of the coatings and the substrate surfaces (see [2]). This goes along with the investigations of the delamination and failure behavior of the involved surfaces. To illustrate the applicability of the model, several structural simulations are performed. The developed CZ element model is capable of modeling the separation, the contact and also the irreversible reloading conditions in both normal and tangential directions [3]. The model is further developed to be applicable for different structures including different bonding behaviors, with a higher stability. The talk concludes with a detailed discussion of the numerical results of different material and interface properties. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Characterization of Ni/Al hybrid foam from atomic to microscale

In this paper, the Ni/Al hybrid open-cell foams are characterized on different hierarchical levels by means of experiments and numerical modeling from the atomic to the microscale. In this case, it is possible to compare the elastic-plastic behavior at different scales in order to attain a deeper understanding of the multiscale properties of the Ni/Al hybrid foams. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)