Cross‐Reactive Sensor Arrays for the Detection of Peptides in Aqueous Solution by Fluorescence Spectroscopy

A simple but powerful method for the sensing of peptides in aqueous solution has been developed. The transition‐metal complexes [PdCl₂(en)], [{RhCl₂Cp*}₂], and [{RuCl₂(p‐cymene)}₂] were combined with six different fluorescent dyes to build a cross‐reactive sensor array. The fluorescence response of the individual sensor units was based on competitive complexation reactions between the peptide analytes and the fluorescent dyes. The collective response of the sensor array in a time‐resolved fashion was used as an input for multivariate analyses. A sensor array comprised of only six metal–dye combinations was able to differentiate ten different dipeptides in buffered aqueous solution at a concentration of 50 μM . Furthermore, the cross‐reactive sensor could be used to obtain information about the identity and the quantity of the pharmacologically interesting dipeptides carnosine and homocarnosine in a complex biological matrix, such as deproteinized human blood serum. The sensor array was also able to sense longer peptides, which was demonstrated by differentiating mixtures of the nonapeptide bradykinin and the decapeptide kallidin.     

Motif Reconstruction in Clusters and Layers: Benchmarks for the Kawska–Zahn Approach to Model Crystal Formation

A recently developed atomistic simulation scheme for investigating ion aggregation from solution is transferred to the morphogenesis of metal clusters grown from the vapor and layers deposited on a substrate surface. Both systems are chosen as benchmark models for intense motif reorganization during aggregate/layer growth. The applied simulation method does not necessarily involve global energy minimization after each growth event, but instead describes crystal growth as a series of structurally related configurations which may also include local energy minima. Apart from the particularly favorable high‐symmetry configurations known from experiments and global energy minimization, we also demonstrate the investigation of transient structures. In the spirit of Ostwald’s step rule, a continuous evolution of the aggregate/layer structure during crystal growth is observed.     

Improved measurement of the hydrogen 1S-2S transition frequency

We have measured the 1S-2S transition frequency in atomic hydrogen via two-photon spectroscopy on a 5.8 K atomic beam. We obtain f(1S-2S) = 2,466,061,413,187,035 (10) Hz for the hyperfine centroid, in agreement with, but 3.3 times better than the previous result [M. Fischer et al., Phys. Rev. Lett. 92, 230802 (2004)]. The improvement to a fractional frequency uncertainty of 4.2 × 10(-15) arises mainly from an improved stability of the spectroscopy laser, and a better determination of the main systematic uncertainties, namely, the second order Doppler and ac and dc Stark shifts. The probe laser frequency was phase coherently linked to the mobile cesium fountain clock FOM via a frequency comb.     

Single-pass high-harmonic generation at 20.8 MHz repetition rate

We report on single-pass high-harmonic generation (HHG) with amplified driving laser pulses at a repetition rate of 20.8?MHz. An Yb:YAG Innoslab amplifier system provides 35?fs pulses with 20?W average power at 1030?nm after external pulse compression. Following tight focusing into a xenon gas jet, we observe the generation of high-harmonic radiation of up to the seventeenth order. Our results show that state-of-the-art amplifier systems have become a promising alternative to cavity-assisted HHG for applications that require high repetition rates, such as frequency comb spectroscopy in the extreme UV.     

Bose-Einstein condensate coupled to a nanomechanical resonator on an atom chip

We theoretically study the coupling of Bose-Einstein condensed atoms to the mechanical oscillations of a nanoscale cantilever with a magnetic tip. This is an experimentally viable hybrid quantum system which allows one to explore the interface of quantum optics and condensed matter physics. We propose an experiment where easily detectable atomic spin flips are induced by the cantilever motion. This can be used to probe thermal oscillations of the cantilever with the atoms. At low cantilever temperatures, as realized in recent experiments, the backaction of the atoms onto the cantilever is significant and the system represents a mechanical analog of cavity quantum electrodynamics. With high but realistic cantilever quality factors, the strong coupling regime can be reached, either with single atoms or collectively with Bose-Einstein condensates. We discuss an implementation on an atom chip.     

Regulating Molecular Recognition with C‐Shaped Strips Attained by Chirality‐Assisted Synthesis

Chirality‐assisted synthesis (CAS) is a general approach to control the shapes of large molecular strips. CAS is based on enantiomerically pure building blocks that are designed to strictly couple in a single geometric orientation. Fully shape‐persistent structures can thus be created, even in the form of linear chains. With CAS, selective recognition between large host and guest molecules can reliably be designed de novo. To demonstrate this concept, three C‐shaped strips that can embrace a pillar[5]arene macrocycle were synthesized. The pillar[5]arene bound to the strips was a better host for electron‐deficient guests than the free macrocycle. Experimental and computational evidence is provided for these unique cooperative interactions to illustrate how CAS could open the door towards the precise positioning of functional groups for regulated supramolecular recognition and catalysis.     

Efficient refolding of a hydrophobic protein with multiple S-S bonds by on-resin immobilized metal affinity chromatography

The efficient refolding of recombinant proteins produced in the form of inclusion bodies (IBs) in Escherichia coli still is a complicated experimental problem especially for large hydrophobic highly disulfide-bonded proteins. The aim of this work was to develop highly efficient and simple refolding procedure for such a protein. The recombinant C-terminal fragment of human alpha-fetoprotein (rAFP-Cterm), which has molecular weight of 26 kDa and possesses 6 S-S bonds, was expressed in the form of IBs in E. coli. The C-terminal 7× His tag was introduced to facilitate protein purification and refolding. The refolding procedure of the immobilized protein by immobilized metal chelating chromatography (IMAC) was developed. Such hydrophobic highly disulfide-bonded proteins tend to irreversibly bind to traditionally used agarose-based matrices upon attempted refolding of the immobilized protein. Indeed, the yield of rAFP-Cterm upon its refolding by IMAC on agarose-based matrix was negligible with bulk of the protein irreversibly stacked to the resin. The key has occurred to be using IMAC based on silica matrix. This increased on-resin refolding yield of the target protein from almost 0 to 60% with purity 98%. Compared to dilution refolding of the same protein, the productivity of the developed procedure was two orders higher. There was no need for further purification or concentration of the renatured protein. The usage of silica-based matrix for the refolding of immobilized proteins by IMAC can improve and facilitate the experimental work for difficult-to-refold proteins.     

IDSite: An accurate approach to predict P450-mediated drug metabolism

Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.     

Development and validation of a rapid LC-ESI-MS/MS method for quantification of fluoxetine and its application to MS binding assays

In the present study, a rapid and sensitive LC-ESI-MS/MS method for quantification of (S)-fluoxetine as a native marker in mass spectrometry (MS) binding assays addressing the human serotonin transporter (hSERT) was developed and validated. The concept of MS binding assays based on mass spectrometric quantification of a nonlabeled marker recently introduced by us represents a promising alternative to conventional radioligand binding without the drawbacks inherently connected with radioisotope labeling. For high-performance liquid chromatography (HPLC), a 20 × 2-mm RP-18 column with a mobile phase composed of acetonitrile and ammonium bicarbonate buffer (5 mmol L⁻¹, pH 9.5) at a ratio of 80:20 (v/v) and a flow rate of 800 μL min⁻¹ in an isocratic mode were used, resulting in a chromatographic cycle time of 60 s. Employing [²H₅]fluoxetine as internal standard enabled ESI-MS/MS quantification of (S)-fluoxetine between 3 nmol L⁻¹ and 50 pmol L⁻¹ (LLOQ) in matrix obtained from binding experiments without the need of any sample preparation. Validation of the method showed that linearity, intra-, and inter-batch accuracy as well as precision meet the requirements of the FDA guidance for bioanalytical method validation. Considering sensitivity and speed, the established method is clearly superior to those published for biological matrices so far. Furthermore, the method was transferred to other RP-18 columns of different lengths and respective validation experiments demonstrated its versatility and chromatographic robustness. Finally, the newly developed method was successfully applied to MS binding assays for hSERT. The affinity determined for (S)-fluoxetine in saturation experiments was in good agreement with literature data obtained in respective radioligand binding assays.