Conformational Dynamics of Sensory Rhodopsin II in Nanolipoprotein and Styrene–Maleic Acid Lipid Particles

Styrene–maleic acid lipid particles (SMALPs) provide stable water‐soluble nanocontainers for lipid‐encased membrane proteins. Possible effects of the SMA‐stabilized lipid environment on the interaction dynamics between functionally coupled membrane proteins remain to be elucidated. The photoreceptor sensory rhodopsin II, NpSRII and its cognate transducer, NpHtrII, of Natronomonas pharaonis form a transmembrane complex, NpSRII₂/NpHtrII₂ that plays a key role in negative phototaxis and provides a unique model system to study the light‐induced transfer of a conformational signal between two integral membrane proteins. Photon absorption induces transient structural changes in NpSRII comprising an outward movement of helix F that cause further conformational alterations in NpHtrII. We applied site‐directed spin labeling and time‐resolved optical and EPR spectroscopy to compare the conformational dynamics of NpSRII₂/NpHtrII₂ reconstituted in SMALPs with that of nanolipoprotein particle and liposome preparations. NpSRII and NpSRII₂/NpHtrII₂ show similar photocycles in liposomes and nanolipoprotein particles. An accelerated decay of the M photointermediate found for SMALPs can be explained by a high local proton concentration provided by the carboxylic groups of the SMA polymer. Light‐induced large‐scale conformational changes of NpSRII₂/NpHtrII₂ observed in liposomes and nanolipoprotein particles are affected in SMALPs, indicating restrictions of the protein's conformational freedom.     

Functional Expression of the Signaling Complex Sensory Rhodopsin II/Transducer II from Halobacterium salinarum in Escherichia coli†

Sensory rhodopsin II, a photoreceptor from Halobacterium salinarum (HsSRII), in complex with its cognate transducer protein (HsHtrII) triggers the photophobic response via a cytoplasmic two‐component signaling cascade. HsHtrII possess in addition to the HsSRII binding and the cytoplasmic domains an extracellular serine‐receptor domain. Here we describe the properties of HsSRII and HsHtrII and those of various shortened transducer analogs, heterologously expressed in Escherichia coli. HsSRII displays the photocycle typical of archaeal photosensors with prolonged kinetics. Using an isothermal titration calorimetric analysis for this complex a dissociation constant of 1.1 μm was obtained similar to that of the corresponding transducer/receptor pair from Natronobacterium pharaonis. A shortened transducer lacking the extracellular and cytoplasmic domain is also sufficient to bind the receptor with a slightly lower affinity. The dissociation constant of serine binding to the extracellular domain was determined to be about 5 μm . This result is in line with the proposal that the extracellular domain indeed is a serine receptor.     

Biochemische Mechanismen einer einfachen Verhaltensreaktion

In active search for conditions for optimal phototrophic growth, halobacteria respond to light and to a variety of other environmental stimuli by taxis. Light reception is mediated by sensory rhodopsins, seven helix transmembrane retinal proteins that are stably complexed to specific MCP-related transducer proteins. Photoisomerization of the retinal chromophore generates a steric signal which activates the sensory rhodopsin-transducer-complex. Complex activation is relayed to a two component signaling system and transiently changes the cytoplasmic concentration of fumarate which, together with the small cytoplasmic protein CheY controls flagellar motor switching. Dual signaling by CheY and fumarate was also found in Escherichia coli where it mediates metabolic signaling and taxis in cells with disabled two-component system. Sensory integration of different environmental stimuli occurs at the level of the signaling domains of several stimulus-specific transducers constructed through combination of appropriate molecular modules. Irrespective of the complexity of the signaling network, the response to light is quantitatively predictable and stochastic. Its kinetic analysis suggests that time-dependent changes in the activity of signaling components can be resolved even in the context of a complex molecular network.     

Subtle Interactions and Electron Transfer between UIII,NpIII, or PuIII and Uranyl Mediated by the Oxo Group

A dramatic difference in the ability of the reducing An^III center in AnCp₃ (An=U, Np, Pu; Cp=C₅H₅) to oxo‐bind and reduce the uranyl(VI) dication in the complex [(UO₂)(THF)(H₂L)] (L=“Pacman” Schiff‐base polypyrrolic macrocycle), is found and explained. These are the first selective functionalizations of the uranyl oxo by another actinide cation. At‐first contradictory electronic structural data are explained by combining theory and experiment. Complete one‐electron transfer from Cp₃U forms the U^IV‐uranyl(V) compound that behaves as a U^V‐localized single molecule magnet below 4 K. The extent of reduction by the Cp₃Np group upon oxo‐coordination is much less, with a Np^III‐uranyl(VI) dative bond assigned. Solution NMR and NIR spectroscopy suggest Np^IVU^V but single‐crystal X‐ray diffraction and SQUID magnetometry suggest a Np^III‐U^VI assignment. DFT‐calculated Hirshfeld charge and spin density analyses suggest half an electron has transferred, and these explain the strongly shifted NMR spectra by spin density contributions at the hydrogen nuclei. The Pu^III–U^VI interaction is too weak to be observed in THF solvent, in agreement with calculated predictions.     

Subtle Interactions and Electron Transfer between UIII,NpIII, or PuIII and Uranyl Mediated by the Oxo Group

A dramatic difference in the ability of the reducing An^III center in AnCp₃ (An=U, Np, Pu; Cp=C₅H₅) to oxo‐bind and reduce the uranyl(VI) dication in the complex [(UO₂)(THF)(H₂L)] (L=“Pacman” Schiff‐base polypyrrolic macrocycle), is found and explained. These are the first selective functionalizations of the uranyl oxo by another actinide cation. At‐first contradictory electronic structural data are explained by combining theory and experiment. Complete one‐electron transfer from Cp₃U forms the U^IV‐uranyl(V) compound that behaves as a U^V‐localized single molecule magnet below 4 K. The extent of reduction by the Cp₃Np group upon oxo‐coordination is much less, with a Np^III‐uranyl(VI) dative bond assigned. Solution NMR and NIR spectroscopy suggest Np^IVU^V but single‐crystal X‐ray diffraction and SQUID magnetometry suggest a Np^III‐U^VI assignment. DFT‐calculated Hirshfeld charge and spin density analyses suggest half an electron has transferred, and these explain the strongly shifted NMR spectra by spin density contributions at the hydrogen nuclei. The Pu^III–U^VI interaction is too weak to be observed in THF solvent, in agreement with calculated predictions.     

Persistent homology for the quantitative prediction of fullerene stability

Persistent homology is a relatively new tool often used for qualitative analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this article, we report novel quantitative predictions of the energy and stability of fullerene molecules, the very first attempt in using persistent homology in this context. The ground‐state structures of a series of small fullerene molecules are first investigated with the standard Vietoris–Rips complex. We decipher all the barcodes, including both short‐lived local bars and long‐lived global bars arising from topological invariants, and associate them with fullerene structural details. Using accumulated bar lengths, we build quantitative models to correlate local and global Betti‐2 bars, respectively with the heat of formation and total curvature energies of fullerenes. It is found that the heat of formation energy is related to the local hexagonal cavities of small fullerenes, while the total curvature energies of fullerene isomers are associated with their sphericities, which are measured by the lengths of their long‐lived Betti‐2 bars. Excellent correlation coefficients (>0.94) between persistent homology predictions and those of quantum or curvature analysis have been observed. A correlation matrix based filtration is introduced to further verify our findings. © 2014 Wiley Periodicals, Inc.     

Influence of Arrestin on the Photodecay of Bovine Rhodopsin

Continued activation of the photocycle of the dim‐light receptor rhodopsin leads to the accumulation of all‐trans‐retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre‐activated truncated bovine visual arrestin (Arr^Tr) with rhodopsin in 1,2‐diheptanoyl‐sn‐glycero‐3‐phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin–arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr^Tr leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all‐trans‐retinal from rhodopsin.     

Photoreaction Cycle of Phoborhodopsin (Sensory Rhodopsin II) from Halobacterium salinarum Expressed in Escherichia coli

Phoborhodopsin (pR; also called sensory rhodopsin II, SRII) is a photoreceptor of negative phototaxis of halobacteria. The studies of photochemical properties of this pigment are not many because the amount of the pigment is small and the stability is low. Recently an expression system of phoborhodopsin from Halobacterium salinarum (called salinarum phoborhodopsin, spR; also HsSRII) in Escherichia coli and purification method has been developed (Mironova et al. [2005] FEBS Lett., 579, 3147–3151), which enables detailed studies on the photochemical properties of spR. In the present work, the photoreaction cycle of E. coli-expressed spR was studied by low-temperature spectroscopy and flash photolysis. Formations of K-, M-, O-like intermediates and P480 were reconfirmed as reported previously. New findings are as follows. (1) The K-like intermediate (P500) was a mixture of two photoproducts. (2) Formation of L-like intermediate (P482) was observed by low-temperature spectroscopy and flash photolysis at room temperature. (3) On long irradiation of spR at 20°C, formation of a new photoproduct P370 was observed and it decayed to the original spR in the dark with a decay half time of 190 min. Based on these results the similarities and dissimilarities between spR and ppR are discussed.     

Polytype Transformations in the SO42– Containing Layered Double Hydroxides of Zinc with Aluminum and Chromium: The Metal Hydroxide Layer as a Structural Synthon

Solid–solid inter‐polytype transformations are observed during the thermal dehydration of sulfate‐containing layered double hydroxides (LDHs). The metal hydroxide layer behaves as a “structural synthon” and the interconversion of polytypes of rhombohedral and hexagonal symmetries takes place by rigid translations of successive layers by (± 1/3, ± 2/3) relative to one another in the ab plane. These translations are selected among the many possible, as they preserve the coincidence of the symmetry elements of the individual layers and thereby conserve the threefold symmetry of the crystal across the inter‐polytype conversions. As a result, these transformations are enthalpically not expensive. These translations are facilitated at near ambient temperatures (30–60 °C) by the reversible dehydration of the LDH, which involves the deinsertion/insertion of water molecules within the restricted space of the interlayer region.     

Elucidating Diphosphoinositol Polyphosphate Function with Nonhydrolyzable Analogues

The diphosphoinositol polyphosphates (PP‐IPs) represent a novel class of high‐energy phosphate‐containing messengers which control a wide variety of cellular processes. It is thought that PP‐IPs exert their pleiotropic effects as allosteric regulators and through pyrophosphorylation of protein substrates. However, most details of PP‐IP signaling have remained elusive because of a paucity of suitable tools. We describe the synthesis of PP‐IP bisphosphonate analogues (PCP‐IPs), which are resistant to chemical and biochemical degradation. While the two regioisomers 1PCP‐IP₅ and 5PCP‐IP₅ inhibited Akt phosphorylation with similar potencies, 1PCP‐IP₅ was much more effective at inhibiting its cognate phosphatase hDIPP1. Furthermore, the PCP analogues inhibit protein pyrophosphorylation because of their inability to transfer the β‐phosphoryl group, and thus enable the distinction between PP‐IP signaling mechanisms. As such, the PCP analogues will find widespread applications for the structural and biochemical characterization of PP‐IP signaling properties.     

Mechanistic study on radiation-induced grafting into fluorinated polymer solid films using a swelling-induced detachment of grafted polymers

The radiation-induced graft polymerization (RGP) of styrene into poly(ethylene-co-tetrafluoroethylene) films was performed at various monomer concentrations and solvents at 60 °C. The grafted polystyrene (g-PS) was isolated using the swelling-induced detachment phenomenon, and the number-averaged molecular weight (Mn) and the number of g-PS (Np) were determined using gel permeation chromatography. The Mn increased consistently with an increase in the grafting time up to 2–3 hours, indicating very low termination rates, which was a result of the “gel effect”. This is the first direct evidence of the gradual Mn increase over time using RGP in thermally and chemically stable polymer films such as fluorinated polymers. When the Mn and Np were plotted as a function of the degree of grafting (DOG), sudden Np drops along with rapid Mn increases were observed in the DOG region of 80–90%, indicating negligible initiation and propagation; however, a recombination termination between two propagating g-PS radicals dominated the later part of the grafting process. Further increases in both Mn and Np were observed subsequently, implying that reinitiation and propagation events were triggered by morphological changes, as observed by small- and ultrasmall-angle X-ray scattering experiments, which liberated the dormant radicals from the lamellar crystals.     

Ca3Au6.61Ga4.39 – A New Gallide with a Three‐Dimensional Gold–Gallium Network

Ca₃Au_6.61Ga_4.39 was synthesized by reacting the elements in a glassy carbon crucible under argon in a water‐cooled sample chamber in a high‐frequency furnace. The compound crystallizes with a new hexagonal structure type, space group P6₃/mmc: Z = 2, a = 926.6(2), c = 733.1(2) pm, wR2 = 0.0832, 328 F values and 20 variables. This structure type consists of a remarkably complex three‐dimensional [Au_6.61Ga_4.39] network with significant Au–Au, Au–Ga, and Ga–Ga interactions. The calcium atoms are located within slightly distorted hexagonal channels of the gold–gallium network. The structural relations to the AlB₂ and Er₂RhSi₃ type structures are discussed.     

Semiempirical evaluation of the global hardness of the atoms of 103 elements of the periodic table using the most probable radii as their size descriptors

Relying upon the fact that the density functional computation of the global hardness of the atoms of the elements are still at large and there is some mathematical in congruency between the theory and operational formula of finite difference approximation, we have suggested a radial‐dependent ansatz for evaluating global hardness of atoms as: η=a(7.2/r)+b (in eV), where, “a” and “b” are the constants and r is the absolute radius of atoms in angstrom unit. The ansatz is invoked to evaluate the global hardness of atoms of 103 element of the periodic table. The evaluated new set of global hardness is found to satisfy the sine qua non of a reasonable scale of hardness by exhibiting perfect periodicity of periods and groups and correlating the gross physicochemical properties of elements. The inertness of Hg and extreme reactivity Cs atoms are nicely correlated. The chemical reactivity and its variation in small steps in the series of lanthanide elements are also nicely reproduced. The results of the present semiempirical calculation also have strong correlation with the result of some sophisticated DFT calculation for a set of atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Synthese und Kristallstruktur von ACu4As2 (A: Ca–Ba,Eu)

Synthesis and Crystal Structure of A Cu₄As₂ ( A : Ca–Ba, Eu) Steel‐gray single crystals of ACu₄As₂ with A = Ca–Ba and Eu respectively were synthesized by heating mixtures of the elements at about 900 °C. Structure determinations with X‐ray diffractometry data revealed, that the isotypic compounds crystallize in the rhombohedral CaCu₄P₂ type structure (R3m; Z = 3) (hexagonal axes see ”︁Inhaltsübersicht”︁”︁). Measurements of the susceptibility of EuCu₄As₂ showed divalent Eu and ferromagnetic order at 35 K.     

Swedenborgite‐Type Cobaltites and Ferrites: Tetrahedral Frameworks with Exceptional Magnetic Properties

Swedenborgite‐type cobaltites and ferrites and derivatives, represent a very important class of oxides, LnBaM₄O₇ and CaBaM₄O₇ (M = Co, Fe). They are one of the rare families of mixed valent transition metal oxides, where the transition element exhibits exclusively the tetrahedral coordination. Their complex crystal chemistry, involving closely related structures with various symmetries (orthorhombic, hexagonal cubic) and possibility of oxygen “hyperstoichiometry”, leading to LnBaM₄O_7+δ oxides is described herein, as well as their ability to exhibit structural transitions vs. temperature. It is also shown that the triangular geometry of these new strongly electron correlated systems, plays an important role in their physics, particularly in the competition that appears between the 1D magnetic ordering and the 2D magnetic frustration. The generation of new magnetodielectric properties for CaBaCo₄O₇ is also emphasized.     

Complex–Surfactant‐Assisted Hydrothermal Synthesis and Properties of Hierarchical Worm‐Like Cobalt Sulfide Microtubes Assembled by Hexagonal Nanoplates

The preparation of exquisite hierarchical worm‐like Co_1?xS (x=0.75) microtubes by a one‐pot complex–surfactant‐assisted hydrothermal method is successfully achieved for the first time. The hierarchical structures of the microtube wall are assembled from numerous interleaving hexagonal nanoplates. X‐ray diffraction, X‐ray photoelectron spectroscopy, scanning electron microscopy, transmission electron microscopy, and high‐resolution transmission electron microscopy were used to characterize the samples. The experimental results indicate that the “soft template” surfactant cetyltrimethylammonium bromide and the chelating ethylenediamine both play important roles for the formation of hierarchical Co_1?xS microtubes. A possible formation mechanism for the growth processes is proposed. Additionally, the electrochemical and magnetic properties of Co_1?xS microtubes were systematically studied.     

Interaction of AnVI with Isothiocyanate Ion in Water‐Organic Media (An = U,Np, Pu)

Behavior of U^VI, Np^VI and Pu^VI in water‐acetonitrile solutions was studied spectrophotometrically with the successive addition of the polar organic ligands (dimethyl sulfoxide or hexamethylphosphoric triamide) and the NCS^– ion. The detected spectral effects – changes in the absorption intensity, bathochromic shifts in the absorption bands, the absence of isosbestic points, a change in the color of the solution – indicate complex competitive processes occurring in the studied solutions. In the case of Np^VI, its partial reduction to Np^IV by NCS^– ion is observed. Solid U^VI complex, [UO₂(HMPA)₂(NCS)₂], was isolated, its crystal structure was determined using X‐ray diffraction. In contrast to known AnO₂²⁺ compounds with the NCS^– ion, this complex exhibits tetragonal bipyramidal environment of the U atom. [UO₂(HMPA)₂(NCS)₂] is also characterized by UV/Vis, IR and luminescence spectroscopy.     

ChemNetworks: A complex network analysis tool for chemical systems

Many intermolecular chemical interactions persist across length and timescales and can be considered to form a “network” or “graph.” Obvious examples include the hydrogen bond networks formed by polar solvents such as water or alcohols. In fact, there are many similarities between intermolecular chemical networks like those formed by hydrogen bonding and the complex and distributed networks found in computer science. Contemporary network analyses are able to dissect the complex local and global changes that occur within the network over multiple time and length scales. This work discusses the ChemNetworks software, whose purpose is to process Cartesian coordinates of chemical systems into a network/graph formalism and apply topological network analyses that include network neighborhood, the determination of geodesic paths, the degree census, direct structural searches, and the distribution of defect states of network. These properties can help to understand the network patterns and organization that may influence physical properties and chemical reactivity. The focus of ChemNetworks is to quantitatively describe intermolecular chemical networks of entire systems at both the local and global levels and as a function of time. The code is highly general, capable of converting a wide variety of systems into a chemical network formalism, including complex solutions, liquid interfaces, or even self‐assemblies. © 2013 Wiley Periodicals, Inc.     

The “Other” Inositols and Their Phosphates: Synthesis,Biology, and Medicine (with Recent Advances in myo‐Inositol Chemistry)

Cell signaling via inositol phosphates, in particular via the second messenger myo‐inositol 1,4,5‐trisphosphate, and phosphoinositides comprises a huge field of biology. Of the nine 1,2,3,4,5,6‐cyclohexanehexol isomers, myo‐inositol is pre‐eminent, with “other” inositols (cis‐, epi‐, allo‐, muco‐, neo‐, l ‐chiro‐, d ‐chiro‐, and scyllo‐) and derivatives rarer or thought not to exist in nature. However, neo‐ and d ‐chiro‐inositol hexakisphosphates were recently revealed in both terrestrial and aquatic ecosystems, thus highlighting the paucity of knowledge of the origins and potential biological functions of such stereoisomers, a prevalent group of environmental organic phosphates, and their parent inositols. Some “other” inositols are medically relevant, for example, scyllo‐inositol (neurodegenerative diseases) and d ‐chiro‐inositol (diabetes). It is timely to consider exploration of the roles and applications of the “other” isomers and their derivatives, likely by exploiting techniques now well developed for the myo series.