Protein structural dynamics of photoactive yellow protein in solution revealed by pump-probe X-ray solution scattering

Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump-probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 μs to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The reconstructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.     

Nonlinear propagation acoustics of dual-frequency wide-band excitation pulses in a focused ultrasound system

In this article, acoustic propagation effects of dual-frequency wide-band excitation pulses in a focused ultrasound system are demonstrated in vitro. A designed and manufactured dual-frequency band annular array capable of transmitting 0.9/7.5 MHz center frequency wide-band pulses was used for this purpose. The dual-frequency band annular array, has been designed using a bi-layer piezo-electric stack. Water tank measurements demonstrate the function of the array by activating the low- and high-frequency layers individually and simultaneously. The results show that the array works as intended. Activating the low- and high-frequency layers individually, results in less than -50 dB signal level from the high- and low-frequency layers respectively. Activating both layers simultaneously, produce a well defined dual-frequency pulse. The presence of the low-frequency pulse leads to compression, expansion, and a time delay of the high-frequency pulse. There is a phase shift between the low- and high-frequency pulse as it propagates from the array to the focus. This makes the latter described effects also dependent on the array configuration. By varying the low-frequency pressure, a shift of up to 0.5 MHz in center frequency of a 8.0 MHz transmitted high-frequency pulse is observed at the array focus. The results demonstrate the high propagation complexity of dual-frequency pulses.     

Limit analysis and conic programming: ‘porous Drucker–Prager’ material and Gurson's modelAnalyse limite et optimisation conique : étude d'un matériau de Drucker–Prager poreux

Extending a previous work on the Gurson model for a ‘porous von Mises’ material, the present study first focuses on the yield criterion of a ‘porous Drucker–Prager’ material with spherical cavities. On the basis of the Gurson micro-macro model and a second order conic programming (socp) formulation, calculated inner and outer approaches to the criterion are very close, providing a reliable estimate of the yield criterion. Comparison with an analytical criterion recently proposed by Barthélémy and Dormieux—from a nonlinear homogenization method—shows both excellent agreement when considering tensile average boundary conditions and substantial improvement under compressive conditions. Then the results of an analogous study in the case of cylindrical cavities in plane strain are presented. It is worth noting that obtaining these results was made possible by using mosek, a recent commercial socp code, whose impressive efficiency was already seen in our previous works. To cite this article: M. Trillat et al., C. R. Mecanique 334 (2006).     

Nonlinear propagation delay and pulse distortion resulting from dual frequency band transmit pulse complexes

A method of acoustic imaging is discussed that potentially can improve the diagnostic capabilities of medical ultrasound. The method, given the name second order ultrasound field imaging, is achieved by the processing of the received signals from transmitted dual frequency band pulse complexes with at least partly overlapping high frequency (HF) and low frequency (LF) pulses. The transmitted HF pulses are used for image reconstruction whereas the transmitted LF pulses are used to manipulate the elastic properties of the medium observed by the HF imaging pulses. In the present paper, nonlinear propagation effects observed by a HF imaging pulse due to the presence of a LF manipulation pulse is discussed. When using dual frequency band transmit pulse complexes with a large separation in center frequency (e.g., 1:10), these nonlinear propagation effects are manifested as a nonlinear HF propagation delay and a HF pulse distortion different from conventional harmonic distortion. In addition, with different transmit foci for the HF and LF pulses, nonlinear aberration will occur.     

Evaluation of the relaxation modules from the response to a constant rate of strain followed by a constant strain

The stress response σ(t) to a constant rate of strain $ \dot \varepsilon $ ε during the period 0 < t ≤ t^* and to the constant strain ε^* $ ( = \dot \varepsilon t*) $ thereafter is considered in terms of the Boltzmann superposition principle. When t ≤ t^*, the data directly give the constant-rate modulus F (t) ≡ σ(t)/ε(t), which can be converted straightforwardly into the relaxation modulus E(t). Results from illustrative calculations show that a reduction in the relaxation rate effects a decrease in [σ(t^*)/ε^*]/E(t^*) and also in the time at which [σ(t)/ε^*]/E(t) becomes essentially unity. To evaluate E(t) at t > t^*, F(t) is first obtained from σ(t) and F(t ? t^*) by using a derived equation similar to that presented by Meissner. Thereafter, F(t) is transformed into E(t). For illustration, E(t) for a rubbery solid is evaluated over some 2.5 decades of time from its response to a strain rate of 0.25 min^?1 for 0.40 min and thereafter to the attained strain of 0.10 for 5.4 min.     

Nanosecond redox equilibrium method for determining oxidation potentials in organic media

A general, nanosecond equilibrium method is described for determining thermodynamically meaningful oxidation potentials in organic media for compounds that form highly reactive cation radicals upon one-electron oxidation. The method provides oxidation potentials with unusually high precision and accuracy. Redox ladders have been constructed of appropriate reference compounds in dichloromethane and in acetonitrile that can be used to set up electron-transfer equilibria with compounds with unknown oxidation potentials. The method has been successfully applied to determining equilibrium oxidation potentials for a series of aryl-alkylcyclopropanes, whose oxidation potentials were imprecisely known previously. Structure-property trends for oxidation potentials of the cyclopropanes are discussed.     

Interactions of novel, nonhemolytic surfactants with phospholipid vesicles

PEG-12-acyloxystearates constitute a novel class of pharmaceutical solubilizers and are synthesized from polyethylene glycol and 12-hydroxystearic acid, which has been esterified with a second acyl chain. The hemolytic activity of these surfactants decreases drastically with increasing pendant acyloxy chain length, and surfactants with an acyloxy chain of 14 carbon atoms or more are essentially nonhemolytic. In this paper, the interactions of PEG-12-acyloxystearates (acyloxy chain lengths ranging from 8 to 16 carbon atoms) with phosphatidylcholine vesicles, used as a model system for erythrocyte membranes, were studied in search of an explanation for the large variations in hemolytic activity. Surfactant-induced alterations of membrane permeability were investigated by studying the leakage of vesicle-entrapped calcein. It was found that all of the surfactants within the series interact with the vesicle membranes and cause slow leakage at elevated surfactant concentrations, but with large variations in leakage kinetics. The initial leakage rate decreases rapidly with increasing pendant acyloxy chain length. After prolonged incubation, on the other hand, the leakage is not a simple function of acyloxy chain length. The effect of the surfactants on membrane integrity was also investigated by turbidity measurements and cryo-transmission electron microscopy. At a surfactant/lipid molar ratio of 0.4, the vesicle membranes are saturated with surfactant. When the surfactant/lipid molar ratio is further increased, the vesicle membranes are progressively solubilized into mixed micelles. The rate of this process decreases strongly with increasing acyloxy chain length. When comparing the results of the different experiments, it can be concluded that there is no membrane permeabilization below saturation of the vesicle membranes. The large variations in the kinetics suggest that several steps are involved in the mechanism of leakage induced by PEG-12-acyloxystearates and that their relative rates vary with acyloxy chain length. The slow kinetics may in part be explained by the low critical micelle concentrations (CMCs) exhibited by the surfactants. The CMCs were found to be in the range of 0.003-0.025 microM.     

A fluorescence polarization based screening assay for identification of small molecule inhibitors of the PICK1 PDZ domain

PDZ (PSD-95/Discs-large/ZO-1 homology) domains represent putative targets in several diseases including cancer, stroke, addiction and neuropathic pain. Here we describe the application of a simple and fast screening assay based on fluorescence polarization (FP) to identify inhibitors of the PDZ domain in PICK1 (protein interacting with C kinase 1). We screened 43,380 compounds for their ability to inhibit binding of an Oregon Green labeled C-terminal dopamine transporter peptide (OrG-DAT C13) to purified PICK1 in solution. The assay was highly reliable with excellent screening assay parameters (Z'≈0.7 and Z≈0.6). Out of ~200 compounds that reduced FP to less than 80% of the control wells, six compounds were further characterized. The apparent affinities of the compounds were determined in FP competition binding experiments and ranged from ~5.0 μM to ~193 μM. Binding to the PICK1 PDZ domain was confirmed for five of the compounds (CSC-03, CSC-04, CSC-43, FSC-231 and FSC-240) in a non-fluorescence based assay by their ability to inhibit pull-down of PICK1 by a C-terminal DAT GST fusion protein. CSC-03 displayed the highest apparent affinity (5.0 μM) in the FP assay, and was according to fluorescence resonance energy transfer (FRET) experiments capable of inhibiting the interaction between the C-terminus of the GluR2 subunit of the AMPA-type glutamate receptor and PICK1 in live cells. Additional experiments suggested that CSC-03 most likely is an irreversible inhibitor but with specificity for PICK1 since it did not bind three different PDZ domains of PSD-95. Summarized, our data suggest that FP based screening assays might be a widely applicable tool in the search for small molecule inhibitors of PDZ domain interactions.