Three-dimensional molecular modeling with single molecule FRET

Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When combined with a known structure of the macromolecule(s) to which the fluorophores are attached, a three-dimensional model of the system can be determined. However, care has to be taken to properly derive distance from fluorescence energy transfer efficiency and to recognize the systematic or random errors for this relationship. Here we review the experimental and computational methods used for three-dimensional modeling based on single molecule fluorescence resonance transfer, and describe recent progress in pushing the limits of this approach to macromolecular complexes.     

Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport

Nonsymbiotic hemoglobins AHb1 and AHb2 discovered in Arabidopsis thaliana are likely to carry out distinct physiological roles, in consideration of their differences in sequence, structure, expression pattern, and tissue localization. Despite a relatively fast autoxidation in the presence of O(2) , we were able to collect O(2) -binding curves for AHb2 in the presence of a reduction enzymatic system. AHb2 binds O(2) noncooperatively with a p50 of 0.021 ± 0.003 Torr, a value consistent with a recently proposed role in O(2) transport. The analysis of the internal cavities derived from the structures sampled in molecular dynamics simulations confirms strong differences with AHb1, proposed to work as a NO deoxygenase in vivo. Overall, our results are consistent with a role for AHb2 as an oxygen carrier, as recently proposed on the basis of experiments on AHb2-overexpressing mutants of A. thaliana.     

Magnetic and fluorescent glycopolymer hybrid nanoparticles for intranuclear optical imaging

The synthesis of galactose-displaying core-shell nanospheres exhibiting both fluorescent and magnetic properties by grafting a glycocopolymer consisting of 6-O-methacryloylgalactopyranose (MAGal) and 4-(pyrenyl)butyl methacrylate (PyMA) onto magnetic silica particles via thiol-ene chemistry is reported. Magnetization measurements indicated that neither the encapsulation of the iron oxide particles into silica nor the grafting of the glycocopolymer chains had a significant influence on the superparamagnetic properties. This not only simplifies the purification of the particles but may facilitate the use of the particles in applications such as hyperthermia or magnetic resonance imaging (MRI). Furthermore, the hydrophilic glycopolymer shell provided solubility of the particles in aqueous medium and enabled the uptake of the particles into the cytoplasm and nucleus of lung cancer cells via carbohydrate-lectin recognition effects.     

Circulation times of prostate cancer and hepatocellular carcinoma cells by in vivo flow cytometry

In metastasis, the cancer cells that travel through the body are capable of establishing new tumors in locations remote from the site of the original disease. To metastasize, a cancer cell must break away from its tumor and invade either the circulatory or lymphatic system, which will carry it to a new location, and establish itself in the new site. Once in the blood stream, the cancer cells now have access to every portion of the body. Here, we have used the "in vivo flow cytometer" to study if there is any relationship between metastatic potential and depletion kinetics of circulating tumor cells. The in vivo flow cytometer has the capability to detect and quantify continuously the number and flow characteristics of fluorescently labelled cells in vivo. We have improved the counting algorithm and measured the depletion kinetics of cancer cells with different metastatic potential. Interestingly, more invasive PC-3 prostate cancer cells are depleted faster from the circulation than LNCaP cells. In addition, we have measured the depletion kinetics of two related human hepatocellular carcinoma (liver cancer) cell lines, high-metastatic HCCLM3 cells, and low-metastatic HepG2 cells. More than 60% HCCLM3 cells are depleted within the first hour. Interestingly, the low-metastatic HepG2 cells possess noticeably slower depletion kinetics. In comparison, <40% HepG2 cells are depleted within the first hour. The differences in depletion kinetics might provide insights into early metastasis processes.     

Transcatheter aortic valve implantation and hybrid coronary artery revascularization: time to combine them

We report on simultaneous off-pump coronary artery bypass grafting to the left anterior descending artery, modified transapical aortic valve implantation, and stenting of the circumflex and right coronary arteries in an 84-year-old patient. The poly-morbid patient with a logistic EuroSCORE of 85% experienced recent myocardial infarction; the left ventricular ejection fraction was reduced to 20%. Postoperative recovery was fast and short. The strategy described is the next logical step in broadening the indication for transcatheter aortic valve interventions.     

Novel bioinspired control approaches to increase the stiffness variability in multi-muscle driven joints

Antagonistic muscle pairs pulling on a joint are in general able to modulate stiffness through co-activation. Closer analysis of the stiffness, however, shows that, depending on the muscle and joint parameters, domains might occur in joint angle space for which stiffness variation is limited (low stiffness variability) or even impossible (stiffness nodes). As a consequence, stiffness control utilizing pure co-activation might fail. This work presents novel strategies for simultaneous control of torque and stiffness in a hinge joint actuated by two antagonistic muscle pairs. One strategy handles stiffness nodes by shifting them away from the current joint position and thus regaining stiffness controllability. To prevent domains of low stiffness variation, an optimal muscle configuration is sought and finally defined which allows for a maximal stiffness variation across a wide joint angle range. Based on this optimal configuration, four additional control strategies are proposed and tested which deliver stiffnesses and torques comparable to those obtained in the optimal case. The strategies combine torque control and stiffness control by co-activation with novel ideas like activation overflow and an inverse model approach. All strategies are tested in simulation and the results are compared with those of the optimal setup.     

Interaction of Bcl-2 with the Autophagy-related GABAA Receptor-associated Protein (GABARAP): BIOPHYSICAL CHARACTERIZATION AND FUNCTIONAL IMPLICATIONS*

Apoptosis and autophagy are fundamental homeostatic processes in eukaryotic organisms fulfilling essential roles in development and adaptation. Recently, the anti-apoptotic factor Bcl-2 has been reported to also inhibit autophagy, thus establishing a potential link between these pathways, but the mechanistic details are only beginning to emerge. Here we show that Bcl-2 directly binds to the phagophore-associated protein GABARAP. NMR experiments revealed that the interaction critically depends on a three-residue segment (EWD) of Bcl-2 adjacent to the BH4 region, which is anchored to one of the two hydrophobic pockets on the GABARAP molecule. This is at variance with the majority of GABARAP interaction partners identified previously, which occupy both hydrophobic pockets simultaneously. Bcl-2 affinity could also be detected for GEC1, but not for other mammalian Atg8 homologs. Finally, we provide evidence that overexpression of Bcl-2 inhibits lipidation of GABARAP, a key step in autophagosome formation, possibly via competition with the lipid conjugation machinery. These results support the regulatory role of Bcl-2 in autophagy and define GABARAP as a novel interaction partner involved in this intricate connection.