Bioorthogonal organic chemistry in living cells: novel strategies for labeling biomolecules

The chemical labeling of biomolecules continues to be an important tool for the study of their function and cellular fate. Attention is increasingly focused on labeling of biomolecules in living cells, since cell lysis introduces many artefacts. In addition, with the advances in biocompatible synthetic organic chemistry, a whole new field of opportunity has opened up, affording high diversity in the nature of the label as well as a choice of ligation reactions. In recent years, several different two-step labeling strategies have emerged. These rely on the introduction of a bioorthogonal attachment site into a biomolecule, then ligation of a reporter molecule to this site using bioorthogonal organic chemistry. This Perspective focuses on these techniques, their implications and future directions.     

On the Integration of Dielectrometry into Electrochemical Impedance Spectroscopy to Obtain Characteristic Properties of a Dielectric Thin Film

We demonstrate a novel impedimetric approach providing unprecedented insight into characteristic properties of dielectric thin films covering electrode surfaces. The concept is based on the joint interpretation of electrochemical impedance spectroscopy (EIS) together with dielectrometry (DEM) whose informative value is mutually interconnected. The advantage lies in the synergistic compensation of individual shortcomings adversely affecting conventional impedimetric analysis strategies relying exclusively on either DEM or the traditional EIS approach, which in turn allows a reliable determination of thickness and permittivity values. The versatility of the method proposed is showcased by an in-situ growth-monitoring of a nanoporous, crystalline thin film (HKUST-1) on an interdigitated electrode geometry.     

Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations

We report on a study that combines advanced fluorescence methods with molecular dynamics (MD) simulations to cover timescales from nanoseconds to milliseconds for a large protein. This allows us to delineate how ATP hydrolysis in a protein causes allosteric changes at a distant protein binding site, using the chaperone Hsp90 as test system. The allosteric process occurs via hierarchical dynamics involving timescales from nano- to milliseconds and length scales from Ångstroms to several nanometers. We find that hydrolysis of one ATP is coupled to a conformational change of Arg380, which in turn passes structural information via the large M-domain α-helix to the whole protein. The resulting structural asymmetry in Hsp90 leads to the collapse of a central folding substrate binding site, causing the formation of a novel collapsed state (closed state B) that we characterise structurally. We presume that similar hierarchical mechanisms are fundamental for information transfer induced by ATP hydrolysis through many other proteins.

We report on a study that combines advanced fluorescence methods with molecular dynamics simulations to cover timescales from nanoseconds to milliseconds for a large protein, the chaperone Hsp90.     

Strong Electronic Communication in Linearly Elongated Rylenes Featuring Tunable Bridges

A modified synthetic pathway towards perylene-perylene dimers and a facile purification method to obtain the regioisomerically pure syn- and anti-isomers are reported. In addition, a novel perylene-naphthalene heterodimer with 30 conjugated π-electron pairs was designed and synthesized on the basis of a previously described precursor and the resulting regioisomers were separated from each other. Thereby, the opto-electronic properties of the linearly elongated chromophores could be investigated regarding the differences in length of their aromatic system and the configuration of the isomers. Further tuning of their energy gaps was realized via protonation and methylation of the dibenzimidazole-bridging unit. Extraordinary red-shifts of the absorption maxima of 62 nm for the methylated and 92 nm for the protonated perylene-perylene anti-isomer could be achieved. Moreover, the maxima for the syn-isomer could be shifted bathochromically by 87 and 113 nm, respectively.     

A comparison between elastohydrodynamic and dry hertzian line contacts with regard to their nonlinear vibration behaviour

The nonlinear dynamic behaviour of a simple system employing two different types of contact is compared: elastohydrodynamic line contact and Hertzian line contact with appropriate damping. The elastohydrodynamic problem is solved with finite elements. For the Hertzian line contact problem an analytical solution is known. It is found that for highly loaded cases Hertzian and elastohydrodynamic contacts lead to very similar frequency response curves. This means that instead of solving the computational expensive elastohydrodynamic problem the Hertzian contact can be used. However, considering weakly loaded contacts the two types of contact show very different behaviour. In particular the natural frequencies are different and the elastohydrodynamic contact exhibits rich nonlinear dynamic behaviour including jump phenomena as well as sub- and superharmonic bifurcations. (© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Stress-energy tensor for a massless spin 1/2 field in static black hole spacetimes

The stress-energy tensor for the massless spin 1/2 field is numerically computed outside and on the event horizons of both charged and uncharged static nonrotating black holes, corresponding to the Schwarzschild, Reissner-Nordstr?m, and extreme Reissner-Nordstr?m solutions of Einstein's equations. The field is assumed to be in a thermal state at the black hole temperature. Comparison is made between the numerical results and previous analytic approximations for the stress-energy tensor in these spacetimes. For the Schwarzschild (charge zero) solution, it is shown that the stress energy differs even in sign from the analytic approximation. For the Reissner-Nordstr?m and extreme Reissner-Nordstr?m solutions, divergences predicted by the analytic approximations are shown not to exist.     

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Extended Lattice Boltzmann Model

Conventional lattice Boltzmann models for the simulation of fluid dynamics are restricted by an error in the stress tensor that is negligible only for small flow velocity and at a singular value of the temperature. To that end, we propose a unified formulation that restores Galilean invariance and the isotropy of the stress tensor by introducing an extended equilibrium. This modification extends lattice Boltzmann models to simulations with higher values of the flow velocity and can be used at temperatures that are higher than the lattice reference temperature, which enhances computational efficiency by decreasing the number of required time steps. Furthermore, the extended model also remains valid for stretched lattices, which are useful when flow gradients are predominant in one direction. The model is validated by simulations of two- and three-dimensional benchmark problems, including the double shear layer flow, the decay of homogeneous isotropic turbulence, the laminar boundary layer over a flat plate and the turbulent channel flow.     

An integrated console for capsule-based,automated organic synthesis

The current laboratory practices of organic synthesis are labor intensive, impose safety and environmental hazards, and hamper the implementation of artificial intelligence guided drug discovery. Using a combination of reagent design, hardware engineering, and a simple operating system we provide an instrument capable of executing complex organic reactions with prepacked capsules. The machine conducts coupling reactions and delivers the purified products with minimal user involvement. Two desirable reaction classes – the synthesis of saturated N-heterocycles and reductive amination – were implemented, along with multi-step sequences that provide drug-like organic molecules in a fully automated manner. We envision that this system will serve as a console for developers to provide synthetic methods as integrated, user-friendly packages for conducting organic synthesis in a safe and convenient fashion.

Using a combination of reagent design, hardware engineering, and a simple operating system we provide an instrument capable of executing complex organic reactions using prepacked capsules with minimal user involvement.