Click strategies for single-molecule protein fluorescence

Single-molecule methods have matured into central tools for studies in biology. Foerster resonance energy transfer (FRET) techniques, in particular, have been widely applied to study biomolecular structure and dynamics. The major bottleneck for a facile and general application of these studies arises from the need to label biological samples site-specifically with suitable fluorescent dyes. In this work, we present an optimized strategy combining click chemistry and the genetic encoding of unnatural amino acids (UAAs) to overcome this limitation for proteins. We performed a systematic study with a variety of clickable UAAs and explored their potential for high-resolution single-molecule FRET (smFRET). We determined all parameters that are essential for successful single-molecule studies, such as accessibility of the probes, expression yield of proteins, and quantitative labeling. Our multiparameter fluorescence analysis allowed us to gain new insights into the effects and photophysical properties of fluorescent dyes linked to various UAAs for smFRET measurements. This led us to determine that, from the extended tool set that we now present, genetically encoding propargyllysine has major advantages for state-of-the-art measurements compared to other UAAs. Using this optimized system, we present a biocompatible one-step dual-labeling strategy of the regulatory protein RanBP3 with full labeling position freedom. Our technique allowed us then to determine that the region encompassing two FxFG repeat sequences adopts a disordered but collapsed state. RanBP3 serves here as a prototypical protein that, due to its multiple cysteines, size, and partially disordered structure, is not readily accessible to any of the typical structure determination techniques such as smFRET, NMR, and X-ray crystallography.     

STM manipulation of a subphthalocyanine double-wheel molecule on Au(111)

A new class of double-wheel molecules is manipulated on a Au(111) surface by the tip of a scanning tunneling microscope (STM) at low temperature. The double-wheel molecule consists of two subphthalocyanine wheels connected by a central rotation carbon axis. Each of the subphthalocyanine wheels has a nitrogen tag to monitor its intramolecular rolling during an STM manipulation sequence. The position of the tag can be followed by STM, allowing us to distinguish between the different lateral movements of the molecule on the surface when manipulated by the STM tip.     

Acoustic Radiation Force Impulse-Imaging for the evaluation of the thyroid gland: a limited patient feasibility study

Purpose

Real-time tissue elastography, a qualitative elastography method, has shown promising results in the diagnostic work up of thyroid nodules. However, to our knowledge no study has evaluated a quantitative elastography method in the thyroid gland. The present study is a feasibility study evaluating Acoustic Radiation Force Impulse-Imaging, a novel quantitative elastography method in the thyroid gland.

Methods

ARFI-imaging involves the mechanical excitation of tissue using short-duration acoustic pulses to generate localized displacements in tissue. The displacements induce a lateral shear-wave propagation which is tracked using multiple laterally positioned ultrasound “tracking“ beams. Inclusion criteria were: thyroid nodules ?1 cm, non-functioning or hypo-functioning on radionuclide scanning, and cytological/histological assessment of thyroid nodule as reference method. All patients received conventional ultrasound, and examination of the thyroid gland including Power Doppler Ultrasound using a 9 MHz linear transducer, in addition real-time elastography (RTE) was performed at 9 MHz frequency and ARFI-imaging was performed at 4 MHz using Siemens (ACUSON S2000) B-mode-ARFI combination transducer.

Results

Sixty nodules in 55 patients were analyzed. Three nodules were papillary carcinoma. The stiffer the tissue the faster the shear wave propagates. The results obtained indicated that the shear wave velocity in thyroid lobes ranged between 0.5 and 4.9 m/s. The median velocity of ARFI-imaging in the healthy nodule-free thyroid gland, as well as in benign and malignant thyroid nodules was 1.98 m/s (range: 1.20-3.63 m/s), 2.02 m/s (range: 0.92-3.97 m/s), and 4.30 m/s (range: 2.40-4.50 m/s), respectively. While no significant difference in median velocity was found between healthy thyroid tissue and benign thyroid nodules, a significant difference was found between malignant thyroid nodules on the one hand and healthy thyroid tissue (p = 0.018) or benign thyroid nodules (p = 0.014) on the other hand. Specificity of ARFI-imaging for the differentiation of benign and malignant thyroid nodules was comparable with RTE (91-95%).

Conclusions

ARFI can be performed in the thyroid tissue with reliable results.     

Stress‐Induced Melting of Crystals in Natural Rubber: a New Way to Tailor the Transition Temperature of Shape Memory Polymers

Lightly cross‐linked natural rubber (NR, cis‐1,4‐polyisoprene) was found to be an exceptional cold programmable shape memory polymer (SMP) with strain storage of up to 1000%. These networks are stabilized by strain‐induced crystals. Here, we explore the influence of mechanical stress applied perpendicular to the elongation direction of the network on the stability of these crystals. We found that the material recovers its original shape at a critical transverse stress. It could be shown that this is due to a disruption of the strain‐stabilizing crystals, which represents a completely new trigger for SMPs. The variation of transverse stress allows tuning of the trigger temperature T_trig(σ) in a range of 45 to 0 °C, which is the first example of manipulating the transition of a crystal‐stabilized SMP after programming.     

Application of the Finite Pointset Method (FPM) to the kinetic BGK model

The BGK model of rarefied gas dynamics [1] is solved numerically by using the Finite Pointset Method (FPM) [2], which is a particle method developed at the ITWM Kaiserslautern. For the implementation a semilagrangian scheme [3] is used. Numerical results are shown on the example of a Shock tube problem for different Knudsen numbers. The solutions are compared to the solutions of exact Euler in the case of small Knudsen numbers and to DSMC solutions for higher Knudsen numbers. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Investigation of sediment transport at the interface of a porous and a free flow domain

Sediment transport involves fluid flow in two different regions. In the free flow domain, the flow is governed by the viscous Newtonian fluid; sediment only occurs as suspended particles. In the porous domain however, the flow is governed by the pore geometry of the porous skeleton consisting of sedimented grains. In nature, the interface between these two domains is not a no-slip boundary for the free flow. In this study, we quantify how sediment transport is affected by the interaction of the two different flows. We do this by comparing fluid flow in no-slip bounded flow channels to fluid flow in channels containing both a free and a porous domain. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Vapor‐Based Synthesis of Poly[(4‐formyl‐p‐xylylene)‐co‐(p‐xylylene)] and Its Use for Biomimetic Surface Modifications

Summary: The vapor‐based synthesis and characterization of a reactive polymer, poly[(4‐formyl‐p‐xylylene)‐co‐(p‐xylylene)] ( 1 ), have been reported. The reactive polymer coating enables the immobilization of oligosaccharides via the chemoselective aldehyde‐hydrazide coupling reaction.

     

Molecular modeling of polymers, 14 quantitative structure-property relationship analyses of multicomponent systems containing polymers

One general class of polymer modeling applications involves materials which are large, in terms of molecular degrees of freedom, and poorly defined in terms of composition and morphology. Such materials are often multicomponent with respect to number of distinct polymers, fillers, additives, etc. Two obstacles limit the modeling of these materials. First, one normally does not have any idea about the key physicochemical molecular properties governing the system. Second, the functional dependence of the target properties of the material upon the key physicochemical molecular properties is usually totally unknown. Torsion angle unit (TAU) theory, a molecular decomposition technique, permits an arbitrarily large number of physicochemical properties to be computed in an open-ended fashion, and thus addresses the first problem. Genetic function approximation (GFA) analysis tackles the second problem by efficiently exploring any desired number of functional relationships between target properties and physicochemical molecular properties. Case studies of (TAU theory)-(GFA analysis) applications to estimate glass, Tg, and crystal-melt, Tm, transition temperatures will be described.