Protein-protein interaction of a Pharaonis halorhodopsin mutant forming a complex with Pharaonis halobacterial transducer protein II detected by Fourier-transform infrared spectroscopy

Pharaonis halorhodopsin (pHR) functions as a light-driven inward chloride ion pump in Natoronomonas pharaonis, while pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, pSRII), is a light sensor for negative phototaxis. ppR forms a 2:2 complex with its cognate transducer protein (pHtrII) through intramembranous hydrogen bonds: Tyr199(ppR)-Asn74(pHtrII) and Thr189(ppR)-Glu43 (pHtrII), Ser62(pHtrII). It was reported that a pHR mutant (P240T/F250Y), which possesses the hydrogen-bonding sites, impairs its pumping activity upon complexation with pHtrII. In this study, effect of the complexation with pHtrII on the structural changes upon formation of the K, L(1) and L(2) intermediates of pHR was investigated by use of Fourier-transform infrared spectroscopy. The vibrational changes of Tyr250(pHR) and Asn74(pHtrII) were detected for the L(1) and L(2) intermediates, supporting that Tyr250(pHR) forms a hydrogen bond with Asn74(pHtrII) as similarly to Tyr199(ppR). The conformational changes of the retinal chromophore were never affected by complexation with pHtrII, but amide-I vibrations were clearly different in the absence and presence of pHtrII. The molecular environment around Asp156(pHR) in helix D is also slightly affected. These additional structural changes are probably related to blocking of translocation of a chloride ion from the extracellular to the cytoplasmic side during the photocycle.     

水滑石限域空间中Cl-与H2O的超分子作用

构建水滑石(LDHs-Cl-yH2O)周期性计算模型, 选用密度泛函理论-赝势平面波法对模型进行几何全优化, 从结构参数、Mulliken电荷布居、态密度(DOS)、能量等角度研究层间Cl-和水分子的分布形态以及与LDHs层板间的超分子作用. 计算结果表明, LDHs-Cl主客体间存在着较强的超分子作用, 主要包括静电和氢键作用. LDHs-Cl层间引入水分子后, 随着水分子数的增加, 层间距逐渐增大后趋于平衡. 水合过程中氢键作用比静电作用更占优势, layer-water型氢键要略强于anoin-water型氢键. 当y=1, 2时, Cl-与水分子所在平面以平行层板的方式存在于LDHs层板间, 并且与两层板的距离基本相等; 当y=3, 4时, Cl-与水分子则以偏向某一层的方式随机地存在于LDHs 层板间. 随着层间水分子增加, LDHs-Cl-yH2O由离子型晶体向分子型晶体转化, LDHs-Cl的水合具有饱和量.     

Microstorms in cellular polymers: a route to soft piezoelectric transducer materials with engineered macroscopic dipoles.

Cellular polymers can be internally charged by "microstorms" (silent or partial discharges) within the voids of the polymer foam. The resulting material, which carries positive and negative charges on the internal void surfaces, is called a ferroelectret. Ferroelectrets behave like typical ferroelectrics, hence they provide a novel class of ferroic materials. The soft foams are strongly piezoelectric and can be used, in a wide range of applications, as transducers for interconverting mechanical and electrical signals. Herein, an overview is provided on the preparation of cellular polymers by physical foaming (extrusion, biaxial stretching, and controlled inflation by pressure treatments), on their charging by "microstorms", on their piezo- and pyroelectricity, and on analogies to ferroelectrics. Finally, a survey of selected applications is presented.     

Hybridization of DNA to bead-immobilized probes confined within a microfluidic channel

We report the factors influencing the capture of DNA by DNA-modified microbeads confined within a microfluidic channel. Quantitative correlation of target capture efficiency to probe surface concentration, solution flow rate, and target concentration are discussed. The results indicate that the microfluidic system exhibits a limit of detection of approximately 10(-10) M (approximately 10(-16) mol) DNA and a selectivity factor of approximately 8 x 10(3). Typical hybridization times are on the order of minutes.     

Towards unnatural xylan based polysaccharides: reductive amination as a tool to access highly engineered carbohydrates

Low molecular weight xylan was modified at the reducing end with mono and bifunctional amines. Characterization by means of elemental analysis, nmr spectroscopy and mass spectrometry proved the success of the highly selective reaction. Modified xylan containing amino groups at the reducing end are capable to react with unmodified xylan and cellodextrins. The structure of the products obtained was proved by NMR spectroscopy. Size exclusion chromatography and mass spectrometry verified the increased molar mass of the head-head linked polysaccharides.     

Native bromoperoxidases do not bind to nitrocellulose: use of DEAE-cellulose as an alternative in blotting

Bromoperoxidases were investigated by protein blotting after polyacrylamide gel electrophoresis. While the denatured proteins bound to nitrocellulose, the native enzymes did not. Instead, they could be transferred successfully to DEAE-cellulose. Procedures for immunostaining and glycoprotein detection with concanavalin A on DEAE-cellulose are described. The results indicate that binding of native proteins to nitrocellulose can not necessarily be assumed. DEAE-cellulose is suitable both to investigate this phenomenon or as a substitute for nitrocellulose in blotting of native proteins.     

Cation-pi interactions as a tool to enhance the power of a chiral auxiliary during asymmetric photoreactions within zeolites

Owing to the existence of cation-pi interactions, aryl chiral auxiliaries perform far better than alkyl chiral auxiliaries during asymmetric photoreaction.     

Interaction matrices as a first step toward a general model of radionuclide cycling: Application to the 137Cs behavior in a grassland ecosystem

Summary Interaction matrices, an expert semi quantitative method to identify multiple interactions among biotic and abiotic components of the ecosystem can be considered as a useful tool to develop conceptual models of the behavior of radionuclides in the environment. This systematic approach facilitates a comprehensible identification of the pathways of the main radionuclides and permits classification of the role of different ecosystem components in terms of cause-effect relationships. The method was applied to study the radiocesium migration in grassland ecosystem affected by the Chernobyl ¹³⁷Cs deposition. Interaction matrices have been simultaneously utilized to explore the dynamic changes on the radiocesium migration pathways and to compare the consequences of the various radiation exposure paths to living organisms.     

On the Supra-LUMO Interaction: Case Study of a Sudden Change of Electronic Structure as a Functional Emergence

The synergistic functioning of redox-active components that emerges from prototypical 2,2′-di(N-methylpyrid-4-ylium)-1,1′-biphenyl is described. Interestingly, even if a trans conformation of the native assembly is expected, due to electrostatic repulsion between cationic pyridinium units, we demonstrate that cis conformation is equally energy-stabilized on account of a peculiar LUMO (SupLUMO) that develops through space, encompassing the two pyridiniums in a single, made-in-one-piece, electronic entity (superelectrophoric behavior). This SupLUMO emergence, with the cis species as superelectrophore embodiment, originates in a sudden change of electronic structure. This finding is substantiated by insights from solid state (single-crystal X-ray diffraction) and solution (NOE NMR and UV-vis-NIR spectroelectrochemistry) studies, combined with electronic structure computations. Electrochemistry shows that electron transfers are so strongly correlated that two-electron reduction manifests itself as a single-step process with a large potential inversion consistent with inner creation of a carbon-carbon bond (digital simulation). Besides, absence of reductive formation of dimers is a further indication of a preferential intramolecular reactivity determined by the SupLUMO interaction (cis isomer pre-organization). The redox-gated covalent bond, serving as electron reservoir, was studied via atropisomerism of the reduction product (VT NMR study). The overall picture derived from this in-depth study of 2,2′-di(N-methylpyrid-4-ylium)-1,1′-biphenyl proves that trans and cis species are worth considered as intrinsically sharply different, that is, as doubly-electrophoric and singly-superelectrophoric switchable assemblies, beyond conformational isomerism. Most importantly, the through-space-mediated SupLUMO may come in complement of other weak interactions encountered in Supramolecular Chemistry as a tool for the design of electroactive architectures.     

Ultracentrifuge as a Versatile Tool to Study Preferential Interaction of Polymers in Mixed Solvents

Abstract

Over the past five decades the analytical ultracentrifuge has been a versatile tool in the study of macromolecules and colloidal particles. Several textbooks [1–4] and review articles [5–10] deal with experimental techniques and theories for complete characterization of macromolecular species. However, the first published articles on the analytical ultracentrifuge dealt with the analysis of particle size distributions in suspensions of inorganic colloids. The emphasis has now shifted to organic polymers following the discovery that a large number of such polymers exist in nature. Before the development of the ultracentrifuge, the existence of such giant molecules was not recognized; the molecular kinetic units of proteins and of high organic polymers in solution were simply thought of as clusters of much smaller molecules, forming particles of undefined mass. Beginning with the elegant investigations of Svedberg [11, 12] on ultracentrifugation, such substances were revealed to be macromolecules, large because they contain a huge number of atoms connected together by primary chemical bonds [13]. Following a long and fruitful series of investigations in the early twenties and thirties, Svedberg wrote in one of his articles [12], “the proteins are built up of particles possessing the hallmark of individuality and therefore are in reality giant molecules. We have reason to believe that the particles in the protein solutions and the protein crystals are built up according to a plan which makes every atom in them indispensable for the completion of the structure.” Almost at the same time, it was Staudinger [14] who clearly demonstrated that substances such as polystyrene and natural rubber exist in solution without change in molecular weight regardless of the solvent employed .     

Primer extension reactions as a tool to uncover folding motifs within complex G-rich sequences: analysis of the human KRAS NHE

We employed primer extension reactions to uncover folding motifs in a nuclease hypersensitive element (NHE) with a complex guanine pattern, located in the human KRAS promoter. We also identified and characterized a new G-rich motif of 21 nt capable of forming a parallel G-quadruplex that is disrupted by protein UP1.     

Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel

The structure and function of the influenza A M2 proton channel have been the subject of intensive investigations in recent years because of their critical role in the life cycle of the influenza virus. Using a truncated version of the M2 proton channel (i.e., M2TM) as a model, here we show that fluctuations in the fluorescence intensity of a dye reporter that arise from both fluorescence quenching via the mechanism of photoinduced electron transfer (PET) by an adjacent tryptophan (Trp) residue and local motions of the dye molecule can be used to probe the conformational dynamics of membrane proteins. Specifically, we find that the dynamics of the conformational transition between the N-terminal open and C-terminal open states of the M2TM channel occur on a timescale of about 500 μs and that the binding of either amantadine or rimantadine does not inhibit the pH-induced structural equilibrium of the channel. These results are consistent with the direct occluding mechanism of inhibition which suggests that the antiviral drugs act by sterically occluding the channel pore.     

Activation of protein phosphatase 1 by a small molecule designed to bind to the enzyme's regulatory site

The activity of protein phosphatase 1 (PP1), a serine-threonine phosphatase that participates ubiquitously in cellular signaling, is controlled by a wide variety of regulatory proteins that interact with PP1 at an allosteric regulatory site that recognizes a "loose" consensus sequence (usually designated as RVXF) found in all such regulatory proteins. Peptides containing the regulatory consensus sequence have been found to recapitulate the binding and PP1 activity modulation of the regulatory proteins, suggesting that it might be possible to design small-molecule surrogates that activate PP1 rather than inhibiting it. This prospect constitutes a largely unexplored way of controlling signaling pathways that could be functionally complementary to the much more extensively explored stratagem of kinase inhibition. Based on these principles, we have designed a microcystin analog that activates PP1.     

Monitoring the Interaction of Albumin with a Paclitaxel-Polymer Conjugate: Complex with Warfarin as Local Probe

Summary: We have used warfarin as a local probe to investigate the orientation of paclitaxel and water soluble polymer conjugates of paxlitaxel in albumin. The relative orientation of warfarin and paclitaxel in a 1:1 complex in solution was investigated by ¹H-NMR-spektroskopy (NOESY) and the results are used for the interpretation of the steric situation of paclitaxel respectively the polymer conjugate in albumin.     

Facile synthesis of polypyrrole coated copper nanowires: a new concept to engineered core-shell structures

Polypyrrole coated copper nanowires were synthesized in a one-pot manner in the presence of cupric precursor and pyrrole. They displayed ultra-high sensitivity as a potentiometric sensor with considerable environmental stability comparable to noble metals.     

Pharaonis phoborhodopsin binds to its cognate truncated transducer even in the presence of a detergent with a 1:1 stoichiometry

Pharaonis phoborhodopsin (ppR) (also pharaonis sensory rhodopsin II) is a receptor of the negative phototaxis of Natronobacterium pharaonis. ppR forms a complex with its pharaonis halobacterial transducer (pHtrII), and this complex transmits the light signal to the sensory system in the cytoplasm. The expressed C-terminal-His tagged ppR and C-terminal-His tagged truncated pHtrII (t-Htr) in Escherichia coli (His means the 6x histidine tag) form a complex even in the presence of 0.1% of n-dodecyl-beta-D-maltoside, and the M-decay of the complex became about twice slower than that of ppR alone. The photocycling rates under varying concentration ratios of ppR to t-Htr in the presence of detergent were measured. The data were analyzed on the following assumptions: (1) the M-decay of both ppR alone and the complex followed a single exponential decay with different time constants; and (2) the M-decay under varying concentration ratios of ppR to t-Htr, therefore, followed a biexponential decay function which combined the decay of the free ppR and that of the complex as photoreactive species. From these analyses we estimated the dissociation constant (15.2 +/- 1.8 microM) and the number of binding sites (1.2 +/- 0.08).     

Incorporation of organic groups within the channel wall of spin-on mesostructured silica films by a vapor infiltration technique

Organically functionalized mesoporous silica films have been prepared by a novel synthetic procedure that involves spin-coating of mesostructured silica films and a vapor infiltration (VI) technique, using organosiloxanes, before the removal of surfactant. The VI-treated mesostructured films were characterized using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and a field emission scanning electron microscope (FE-SEM). Nitrogen adsorption/desorption measurements were performed using films attached with a silicon substrate. The XRD and FE-SEM measurements show that the mesochannel wall, densified and modified with organosilyl groups by the VI treatment, hardly contracts under calcination. FE-SEM observations for the films' cross section support the view that organosiloxane vapor is not deposited on the surface of the film. These results show that organosiloxane molecules penetrate the film and are selectively incorporated into the silica wall. Thus, hydrophobic mesoporous silica films can be synthesized without a reduction in pore size, a result that cannot be attained by conventional grafting and co-condensation methods. The excellent high porosity and hydrophobicity of the mesostructured composite films may be of advantage for next-generation low-k dielectric films.     

Dynamics change of phoborhodopsin and transducer by activation: study using D75N mutant of the receptor by site-directed solid-state 13C NMR

Pharaonis phoborhodopsin (ppR or sensory rhodopsin II) is a negative phototaxis receptor of Natronomonas pharaonis, and forms a complex, which transmits the photosignal into cytoplasm, with its cognate transducer (pHtrII). We examined a possible local dynamics change of ppR and its D75N mutant complexed with pHtrII, using solid-state (13)C NMR of [3-(13)C]Ala- and [1-(13)C]Val-labeled preparations. We distinguished Ala C(beta) (13)C signals of relatively static stem (Ala221) in the C-terminus of the receptors from those of flexible tip (Ala228, 234, 236 and 238), utilizing a mutant with truncated C-terminus. The local fluctuation frequency at the C-terminal tip was appreciably decreased when ppR was bound to pHtrII, while it was increased when D75N, that mimics the signaling state because of disrupted salt bridge between C and G helices prerequisite for the signal transfer, was bound to pHtrII. This signal change may be considered with the larger dissociation constant of the complex between pHtrII and M-state of ppR. At the same time, it turned out that fluctuation frequency of cytoplasmic portion of pHtrII is lowered when ppR is replaced by D75N in the complex with pHtrII. This means that the C-terminal tip partly participates in binding with the linker region of pHtrII in the dark, but this portion might be released at the signaling state leading to mutual association of the two transducers in the cytoplasmic regions within the ppR/pHtrII complex.     

How to choose one-dimensional basis functions so that a very efficient multidimensional basis may be extracted from a direct product of the one-dimensional functions: energy levels of coupled systems with as many as 16 coordinates

In this paper we propose a scheme for choosing basis functions for quantum dynamics calculations. Direct product bases are frequently used. The number of direct product functions required to converge a spectrum, compute a rate constant, etc., is so large that direct product calculations are impossible for molecules or reacting systems with more than four atoms. It is common to extract a smaller working basis from a huge direct product basis by removing some of the product functions. We advocate a build and prune strategy of this type. The one-dimensional (1D) functions from which we build the direct product basis are chosen to satisfy two conditions: (1) they nearly diagonalize the full Hamiltonian matrix; (2) they minimize off-diagonal matrix elements that couple basis functions with diagonal elements close to those of the energy levels we wish to compute. By imposing these conditions we increase the number of product functions that can be removed from the multidimensional basis without degrading the accuracy of computed energy levels. Two basic types of 1D basis functions are in common use: eigenfunctions of 1D Hamiltonians and discrete variable representation (DVR) functions. Both have advantages and disadvantages. The 1D functions we propose are intermediate between the 1D eigenfunction functions and the DVR functions. If the coupling is very weak, they are very nearly 1D eigenfunction functions. As the strength of the coupling is increased they resemble more closely DVR functions. We assess the usefulness of our basis by applying it to model 6D, 8D, and 16D Hamiltonians with various coupling strengths. We find approximately linear scaling.