Mapping the potential energy landscape of intrinsically disordered proteins at amino Acid resolution

Intrinsically disordered regions are predicted to exist in a significant fraction of proteins encoded in eukaryotic genomes. The high levels of conformational plasticity of this class of proteins endows them with unique capacities to act in functional modes not achievable by folded proteins, but also places their molecular characterization beyond the reach of classical structural biology. New techniques are therefore required to understand the relationship between primary sequence and biological function in this class of proteins. Although dependences of some NMR parameters such as chemical shifts (CSs) or residual dipolar couplings (RDCs) on structural propensity are known, so that sampling regimes are often inferred from experimental observation, there is currently no framework that allows for a statistical mapping of the available Ramachandran space of each amino acid in terms of conformational propensity. In this study we develop such an approach, combining highly efficient conformational sampling with ensemble selection to map the backbone conformational sampling of IDPs on a residue specific level. By systematically analyzing the ability of NMR data to map the conformational landscape of disordered proteins, we identify combinations of RDCs and CSs that can be used to raise conformational degeneracies inherent to different data types, and apply these approaches to characterize the conformational behavior of two intrinsically disordered proteins, the K18 domain from Tau protein and N(TAIL) from measles virus nucleoprotein. In both cases, we identify the enhanced populations of turn and helical regions in key regions of the proteins, as well as contiguous strands that show clear and enhanced polyproline II sampling.     

Structural properties of docosahexaenoyl phospholipid bilayers investigated by solid-state 2H NMR spectroscopy.

Polyunsaturated lipids in cellular membranes are known to play key roles in such diverse biological processes as vision, neuronal signaling, and apoptosis. One hypothesis is that polyunsaturated lipids are involved in second messenger functions in biological signaling. Another current hypothesis affirms that the functional role of polyunsaturated lipids relies on their ability to modulate physical properties of the lipid bilayer. The present research has employed solid-state 2H NMR spectroscopy to acquire knowledge of the molecular organization and material properties of polyunsaturated lipid bilayers. We report measurements for a homologous series of mixed-chain phosphatidylcholines containing a perdeuterated, saturated acyl chain (n:0) at the sn-1 position, adjacent to docosahexaenoic acid (DHA, 22:6omega3) at the sn-2 position. Measurements have been performed on fluid (L(alpha))-state multilamellar dispersions as a function of temperature for saturated acyl chain lengths of n = 12, 14, 16, and 18 carbons. The saturated sn-1 chains are therefore used as an intrinsic probe with site-specific resolution of the polyunsaturated bilayer structure. The 2H NMR order parameters as a function of acyl position (order profiles) have been analyzed using a mean-torque potential model for the chain segments, and the results are discussed in comparison with the homologous series of disaturated lipid bilayers. At a given absolute temperature, as the sn-1 acyl length adjacent to the sn-2 DHA chain is greater, the order of the initial chain segments increases, whereas that of the end segments decreases, in marked contrast with the corresponding disaturated series. For the latter, the order of the end segments is practically constant with acyl length, thus revealing a universal chain packing profile. We find that the DHA-containing series, while more complex, is still characterized by a universal chain packing profile, which is shifted relative to the homologous saturated series. Moreover, we show how introduction of DHA chains translates the order profile along the saturated chains, making more disordered states accessible within the bilayer central region. As a result, the area per lipid headgroup is increased as compared to disaturated bilayers. The systematic analysis of the 2H NMR data provides a basis for studies of lipid interactions with integral membrane proteins, for instance in relation to characteristic biological functions of highly unsaturated lipid membranes.     

New methodological criteria in rapid multichannel microspectrofluorometry

Summary The application of microspectrofluorometric techniques to the study of various metabolic pathways in the dynamic context of intracellular interactions has gained further versatility through the use of better correlated microtopographic and spectral observations, rapid automatic data processing and a more accurate definition of specific conditions at fluorescence excitation and detection to minimize the action of exciting wavelengths on the stability of fluorochrome emission. The kinetic parameters of metabolic transients due to microinjection of substrate, are evaluated from 50–200 intracellular sites simultaneously at a temporal resolution of ~ 64 msec. Thus, regional asynchronicities and kinetic discrepancies of the metabolic response may be recognized in correlation with intracellular structure. Sequential changes in the topographic fluorescence pattern or in the fluorescence spectra may be used to define various intracellular pathways associated with the catabolism of natural metabolites or the intracellular distribution and conversion of exogenous molecules. The combination with automated data processing makes possible the uninterupted studies at the level of various intracellular compartments simultaneously on a topographic mode or the identification via spectral analysis of rapid intracellular conversion undergone by natural and exogenous fluorochromes.

---

Zusammenfassung Die Anwendung spektralfluorometrischer Mikromethoden für das Studium verschiedener Stoffwechselvorgänge im dynamischen Zusammenhang intrazellulärer Reaktionen hat durch besser abgestimmte mikrotopographische und spektrale Beobachtungsmöglichkeiten, rasche automatische Datenermittlung, genauere Angabe spezifischer Bedingungen zur Fluoreszenzanregung und Herabsetzung der Einwirkung bestimmter Wellenlängen auf die Stabilität der Fluorochromemission zu weiteren Fortschritten geführt. Die kinetischen Parameter metabolischer Übergänge infolge einer Mikroinjektion von Substrat wurden gleichzeitig an 50–200 intrazellulären Orten mit einer zeitlichen Auflösung von etwa 64 msec ausgewertet. So können regionale Ungleichzeitigkeiten und kinetische Diskrepanzen der metabolischen Beantwortung in Korrelation zur intrazellulären Struktur erkannt werden. Aufeinander folgende Veränderungen der topographischen Fluoreszenzmuster oder der Fluoreszenzspektren lassen sich zur Definition verschiedener intrazellulärer Vorgänge beim Abbau natürlicher Metaboliten oder der intrazellulären Verteilung und Umsetzung exogener Moleküle verwenden. Die Kombination mit automatischer Datenverarbeitung ermöglicht ununterbrochene Untersuchungen in der Größenordnung verschiedener intrazellulärer Räume gleichzeitig auf topographischem Wege oder den spektralanalytischen Nachweis rascher intrazellulärer Umsetzungen natürlicher oder exogener Fluorochrome.

     

Evolution de la caracteristique courant-tension des varistances a base d'oxyde de zinc avec la pression partielle d'oxygene de l'atmosphere de frittage

In order to decrease the resistivity of zinc oxide grains which is responsible for the intensity limitation observed at high current densities, the dependence of current-voltage characteristics of zinc oxide based varistors on oxygen partial pressure has been investigated. From these studies it appears that the conductivity increases with decreasing oxygen partial pressure, this phenomenon being more significant at low voltages than at higher ones. These results can be related to a slight increase of the donor density, while the superficial trap density decreases strongly, involving a collapse of the barrier height and of the non-linearity exponent.     

Structure of azomesobilirubin isomers

The structure of azomesobilirubin isomers as their methyl esters were determined using nmr and Eu(fod)₃ as a shift reagent. J. Chem. Soc., 14, 1101 (1977)     

Multiple emissions from charge transfer excited states of ruthenium(II)—polypyridine complexes

The complex cis-[(bpy)₂Ru

₂]⁴⁺ (bpy is 2,2′-bipyridine) has been prepared by methylation of (bpy)₂Ru

₂]²⁺. Electrochemical studies show that introduction of the bound pyridinium group creates a chemically attached electron acceptor site (E_1/2 = ?0.76 V in 0.1 M [N(n-C₄H₉)₄]PF₆-acetonitrile versus the SSCE). Evidence for a low-lying dπ — π^*

charge transfer (CT) state has been obtained by the appearance of a low energy emission at λ_max 680 nm in ecetonitrile (τ₀ = 104 ns) and for an upper dπ — π^* (bpy) state by a higher energy emission at 580 nm in a methanol glass at 77 K (τ₀ = 7.59 μs). Both emissions appear in a water—ethylene glycol solution containing 5% by weight polyvinyl alcohol at room temperature.     

Lifetime of fluorescent pyrene butyric acid probe in single living cells for measurement of oxygen fluctuation

We study the fluorescence lifetime of the well-known 1-pyrene butyric acid (PBA) to assess oxygen concentrations in living cells. The behavior of the probe is first studied in water, ethanol, protein solution and liposome suspension. The Stern-Volmer plot of these solutions is linear, and the bimolecular reaction rate constant agrees with previous observations. In single living cells, the PBA lifetime decreases with oxygen concentration (185 to 55 ns). The probe lifetime differences between living cells and liposome suspension, especially under nitrogen atmosphere, suggest a supplemental pathway for the deactivation of the probe. We simplify further the complex living cells system by stopping the cell functions and studying freshly fixed cells. In this case, we obtained an increase of PBA lifetime under nitrogen atmosphere (215 ns).     

Cellular uptake and photosensitizing properties of anticancer porphyrins in cell membranes and low and high density lipoproteins

The mechanisms of the phototoxic effect of anticancer porphyrins used in the photodynamic therapy (PDT) of tumours are not yet completely understood. Irradiation of porphyrins gives rise to singlet oxygen which reacts with key residues of proteins, polyunsaturated fatty acids and cholesterol in membranes, leading to inactivation of various enzymes and transporters. Lipoproteins, mainly low density lipoproteins (LDL), are efficient carriers of anticancer porphyrins in blood and can deliver these photosensitizers to tissues through the apolipoprotein (apo) B/E specific LDL receptor pathway. In this review, we discuss some aspects of anticancer porphyrin transport, cellular uptake and photosensitizing properties in cell membranes and lipoproteins.