TY - JOUR AB - Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard–Jones contact interactions is applied to model the protein–membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins. AU - Cieplak, Marek AU - Filipek, Sławomir AU - Harald Janovjak AU - Krzysko, Krystiana A ID - 3728 IS - 4 JF - Biochimica et Biophysica Acta (BBA) - Biomembranes TI - Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment VL - 1758 ER - TY - CHAP AU - Harald Janovjak AU - Mueller, Daniel J ID - 3722 T2 - Bioanalytik TI - Rastersondenmikroskopie ER - TY - JOUR AB - A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems. AU - Le,Thuc T. AU - Emonet,Thierry AU - Harlepp, Sébastien AU - Calin Guet AU - Cluzel,Philippe ID - 3755 IS - 9 JF - Biophysical Journal TI - Dynamical determinants of drug-inducible gene expression in a single bacterium VL - 90 ER - TY - CONF AB - Control of physical simulation has become a popular topic in the field of computer graphics. Keyframe control has been applied to simulations of rigid bodies, smoke, liquid, flocks, and finite element-based elastic bodies. In this paper, we create a framework for controlling systems of interacting particles -- paying special attention to simulations of cloth and flocking behavior. We introduce a novel integrator-swapping approximation in order to apply the adjoint method to linearized implicit schemes appropriate for cloth simulation. This allows the control of cloth while avoiding computationally infeasible derivative calculations. Meanwhile, flocking control using the adjoint method is significantly more efficient than currently-used methods for constraining group behaviors, allowing the controlled simulation of greater numbers of agents in fewer optimization iterations. AU - Wojtan, Christopher J AU - Mucha, Peter AU - Turk, Greg ID - 3758 TI - Keyframe control of complex particle systems using the adjoint method ER - TY - JOUR AB - Rigorous analysis of synaptic transmission in the central nervous system requires access to presynaptic terminals. However, cortical terminals have been largely inaccessible to presynaptic patch-clamp recording, due to their small size. Using improved patch-clamp techniques in brain slices, we recorded from mossy fiber terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm. The major steps of improvement were the enhanced visibility provided by high-numerical aperture objectives and infrared illumination, the development of vibratomes with minimal vertical blade vibrations and the use of sucrose-based solutions for storage and cutting. Based on these improvements, we describe a protocol that allows us to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings can be obtained in slices from both rats and mice. Presynaptic recordings can be also obtained in slices from transgenic mice in which terminals are labeled with enhanced green fluorescent protein. AU - Bischofberger, Josef AU - Engel, Dominique AU - Li, Liyi AU - Geiger, Jörg R AU - Peter Jonas ID - 3818 IS - 4 JF - Nature Protocols TI - Patch-clamp recording from mossy fiber terminals in hippocampal slices VL - 1 ER -