Electrophysiological characterization of specific interactions between bacterial sensory rhodopsins and their transducers

The halobacterial phototaxis receptors sensory rhodopsin I and II (SRI, SRII) enable the bacteria to seek optimal light conditions for ion pumping by bacteriorhodopsin and/or halorhodopsin. The incoming signal is transferred across the plasma membrane by means of receptor-specific transducer proteins that bind tightly to their corresponding photoreceptors. To investigate the receptor/transducer interaction, advantage is taken of the observation that both SRI and SRII can function as proton pumps. SRI from Halobacterium salinarum, which triggers the positive phototaxis, the photophobic receptor SRII from Natronobacterium pharaonis (pSRII), as well as the mutant pSRII-F86D were expressed in Xenopus oocytes. Voltage-clamp studies confirm that SRI and pSRII function as light-driven, outwardly directed proton pumps with a much stronger voltage dependence than the ion pumps bacteriorhodopsin and halorhodopsin. Coexpression of SRI and pSRII-F86D with their corresponding transducers suppresses the proton transport, revealing a tight binding and specific interaction of the two proteins. These latter results may be exploited to further analyze the binding interaction of the photoreceptors with their downstream effectors.

Potent Inhibition of Ribulose-Bisphosphate Carboxylase by an Oxidized Impurity in Ribulose-1,5-Bisphosphate1

Oxidation of d-ribulose-1,5-bisphosphate (ribulose-P2) during synthesis and/or storage produces d-glycero-2,3-pentodiulose-1,5-bisphosphate (pentodiulose-P2), a potent slow, tight-binding inhibitor of spinach (Spinacia oleracea L.) ribulose-P2 carboxylase/oxygenase (Rubisco). Differing degrees of contamination with pentodiulose-P2 caused the decline in Rubisco activity seen during Rubisco assay time courses to vary between different preparations of ribulose-P2. With some ribulose-P2 preparations, this compound can be the dominant cause of the decline, far exceeding the significance of the catalytic by-product, d-xylulose-1,5-bisphosphate. Unlike xylulose-1,5-bisphosphate, pentodiulose-P2 did not appear to be a significant by-product of catalysis by wild-type Rubisco at saturating CO2 concentration. It was produced slowly during frozen storage of ribulose-P2, even at low pH, more rapidly in Rubisco assay buffers at room temperature, and particularly rapidly on deliberate oxidation of ribulose-P2 with Cu2+. Its formation was prevented by the exclusion of transition metals and O2. Pentodiulose-P2 was unstable and decayed to a variety of other less-inhibitory compounds, particularly in the presence of some buffers. However, it formed a tight, stable complex with carbamylated spinach Rubisco, which could be isolated by gel filtration, presumably because its structure mimics that of the enediol intermediate of Rubisco catalysis. Rubisco catalyzes the cleavage of pentodiulose-P2 by H2O2, producing P-glycolate.

Toward a mechanism for GroEL.GroES chaperone activity: an ATPase-gated and -pulsed folding and annealing cage.

Free GroEL binds denatured proteins very tightly: it retards the folding of barnase 400-fold and catalyzes unfolding fluctuations in native barnase and its folding intermediate. GroEL undergoes an allosteric transition from its tight-binding T-state to a weaker binding R-state on the cooperative binding of nucleotides (ATP/ADP) and GroES. The preformed GroEL.GroES.nucleotide complex retards the folding of barnase by only a factor of 4, and the folding rate is much higher than the ATPase activity that releases GroES from the complex. Binding of GroES and nucleotides to a preformed GroEL.denatured-barnase complex forms an intermediately fast-folding complex. We propose the following mechanism for the molecular chaperone. Denatured proteins bind to the resting GroEL.GroES.nucleotide complex. Fast-folding proteins are ejected as native structures before ATP hydrolysis. Slow-folding proteins enter chaperoning cycles of annealing and folding after the initial ATP hydrolysis. This step causes transient release of GroES and formation of the GroEL.denatured-protein complexes with higher annealing potential. The intermediately fast-folding complex is formed on subsequent rebinding of GroES. The ATPase activity of GroEL.GroES is thus the gatekeeper that selects for initial entry of slow-folding proteins to the chaperone action and then pumps successive transitions from the faster-folding R-states to the tighter-binding/stronger annealing T-states. The molecular chaperone acts as a combination of folding cage and an annealing machine.

A combined kinetic and modeling study of the catalytic center subsites of human angiogenin.

Kinetic analysis and molecular modeling have been used to map the ribonucleolytic center of angiogenin (Ang). Pyrimidine nucleotides were found to interact very weakly with Ang, consistent with the inaccessible B1 pyrimidine binding site revealed by x-ray crystallography. Ang also lacks an effective phosphate binding site on the 5' side of B1. Although the B2 site that preferentially binds purines on the 3' side of B1 is also weak, its associated phosphate subsites make substantial contributions: both 3',5'-ADP and 5'-ADP have Ki values 6-fold lower than for 5'-AMP, and adding a 3'-phosphate to the substrate CpA increases Kcat/Km by 9-fold. Thus Ang has a functional P2 site on the 3' side of B2 and a site for a second phosphate on the 5' side of B2. Modeling of an Ang-d(ApTpApA) complex suggested that Arg-5 forms part of the P2 site and that a 2'-phosphate might bind more tightly than a 3'-phosphate. Both predictions were confirmed kinetically. The subsite map obtained by this combined approach indicated that 5'-diphosphoadenosine 2'-phosphate might be a more potent inhibitor than any of the nucleotides tested thus far. Indeed, its Ki value of 150 microM is 50-fold lower than that for the best nucleotide previously reported and 400-fold lower than the Km for the best dinucleotide substrate. This compound may serve as a suitable starting point for the eventual design of tight-binding inhibitors of Ang as antiangiogenic agents for human therapy.

Selective repression of transcriptional activators by Pbx1 does not require the homeodomain.

PBX1 is a homeobox-containing gene identified as the chromosome 1 participant of the t(1;19) chromosomal translocation of childhood pre-B-cell acute lymphoblastic leukemia. This translocation produces a fusion gene encoding the chimeric oncoprotein E2A-Pbx1, which can induce both acute myeloid and T-lymphoid leukemia in mice. The binding of Pbx1 to DNA is weak; however, both Pbx1 and E2A-Pbx1 exhibit tight binding to specific DNA motifs in conjunction with certain other homeodomain proteins, and E2A-Pbx1 activates transcription through these motifs, whereas Pbx1 does not. In this report, we investigate potential transcriptional functions of Pbx1, using transient expression assays. While no segments of Pbx1 activated transcription, an internal domain of Pbx1 repressed transcription induced by the activation domain of Sp1, but not by the activation domains of VP16 or p53. This Pbx1 domain, which lies upstream of the homeodomain and is highly conserved among Pbx proteins, is thus predicted to bind a specific transcription factor. Surprisingly, the repression activity of Pbx1 did not require homeodomain-dependent DNA binding. Thus, Pbx1 may be able to alter gene transcription by both DNA-binding-dependent and DNA-binding-independent mechanisms.

Coherent transport in graphene nanoconstrictions

We study the effect of a structural nanoconstriction on the coherent transport properties of otherwise ideal zigzag-edged infinitely long graphene ribbons. The electronic structure is calculated with the standard one-orbital tight-binding model and the linear conductance is obtained using the Landauer formula. We find that, since the zero-bias current is carried in the bulk of the ribbon, this is very robust with respect to a variety of constriction geometries and edge defects. In contrast, the curve of zero-bias conductance versus gate voltage departs from the (2n+1)e2∕h staircase of the ideal case as soon as a single atom is removed from the sample. We also find that wedge-shaped constrictions can present nonconducting states fully localized in the constriction close to the Fermi energy. The interest of these localized states in regards to the formation of quantum dots in graphene is discussed.

Efficient intrinsic spin relaxation in graphene due to flexural distortions

We propose an intrinsic spin scattering mechanism in graphene originated by the interplay of atomic spin-orbit interaction and the local curvature induced by flexural distortions of the atomic lattice. Starting from a multiorbital tight-binding Hamiltonian with spin-orbit coupling considered non-perturbatively, we derive an effective Hamiltonian for the spin scattering of the Dirac electrons due to flexural distortions. We compute the spin lifetime due to both flexural phonons and ripples and we find values in the 1-10 ns range at room temperature. The proposed mechanism dominates the spin relaxation in high mobility graphene samples and should also apply to other planar aromatic compounds.

Graphene single-electron transistor as a spin sensor for magnetic adsorbates

We study single-electron transport through a graphene quantum dot with magnetic adsorbates. We focus on the relation between the spin order of the adsorbates and the linear conductance of the device. The electronic structure of the graphene dot with magnetic adsorbates is modeled through numerical diagonalization of a tight-binding model with an exchange potential. We consider several mechanisms by which the adsorbate magnetic state can influence transport in a single-electron transistor: tuning the addition energy, changing the tunneling rate, and in the case of spin-polarized electrodes, through magnetoresistive effects. Whereas the first mechanism is always present, the others require that the electrode has to have either an energy- or spin-dependent density of states. We find that graphene dots are optimal systems to detect the spin state of a few magnetic centers.

Anisotropic intrinsic spin relaxation in graphene due to flexural distortions

We propose an intrinsic spin scattering mechanism in graphene originated by the interplay of atomic spin-orbit interaction and the local curvature induced by flexural distortions of the atomic lattice. Starting from a multiorbital tight-binding Hamiltonian with spin-orbit coupling considered nonperturbatively, we derive an effective Hamiltonian for the spin scattering of the Dirac electrons due to flexural distortions. We compute the spin lifetime due to both flexural phonons and ripples and we find values in the microsecond range at room temperature. Interestingly, this mechanism is anisotropic on two counts. First, the relaxation rate is different for off-plane and in-plane spin quantization axis. Second, the spin relaxation rate depends on the angle formed by the crystal momentum with the carbon-carbon bond. In addition, the spin lifetime is also valley dependent. The proposed mechanism sets an upper limit for spin lifetimes in graphene and will be relevant when samples of high quality can be fabricated free of extrinsic sources of spin relaxation.

Quantum spin Hall phase in multilayer graphene

The so-called quantum spin Hall phase is a topologically nontrivial insulating phase that is predicted to appear in graphene and graphenelike systems. In this paper we address the question of whether this topological property persists in multilayered systems. We consider two situations: purely multilayer graphene and heterostructures where graphene is encapsulated by trivial insulators with a strong spin-orbit coupling. We use a four-orbital tight-binding model that includes full atomic spin-orbit coupling and we calculate the Z2 topological invariant of the bulk states as well as the edge states of semi-infinite crystals with armchair termination. For homogeneous multilayers we find that even when the spin-orbit interaction opens a gap for all possible stackings, only those with an odd number of layers host gapless edge states while those with an even number of layers are trivial insulators. For heterostructures where graphene is encapsulated by trivial insulators, it turns out that interlayer coupling is able to induce a topological gap whose size is controlled by the spin-orbit coupling of the encapsulating materials, indicating that the quantum spin Hall phase can be induced by proximity to trivial insulators.

Large spin splitting in the conduction band of transition metal dichalcogenide monolayers

We study the conduction band spin splitting that arises in transition metal dichalcogenide (TMD) semiconductor monolayers such as MoS2, MoSe2, WS2, and WSe2 due to the combination of spin-orbit coupling and lack of inversion symmetry. Two types of calculation are done. First, density functional theory (DFT) calculations based on plane waves that yield large splittings, between 3 and 30 meV. Second, we derive a tight-binding model that permits to address the atomic origin of the splitting. The basis set of the model is provided by the maximally localized Wannier orbitals, obtained from the DFT calculation, and formed by 11 atomiclike orbitals corresponding to d and p orbitals of the transition metal (W, Mo) and chalcogenide (S, Se) atoms respectively. In the resulting Hamiltonian, we can independently change the atomic spin-orbit coupling constant of the two atomic species at the unit cell, which permits to analyze their contribution to the spin splitting at the high symmetry points. We find that—in contrast to the valence band—both atoms give comparable contributions to the conduction band splittings. Given that these materials are most often n-doped, our findings are important for developments in TMD spintronics.

Edge states in graphene-like systems

The edges of graphene and graphene like systems can host localized states with evanescent wave function with properties radically different from those of the Dirac electrons in bulk. This happens in a variety of situations, that are reviewed here. First, zigzag edges host a set of localized non-dispersive state at the Dirac energy. At half filling, it is expected that these states are prone to ferromagnetic instability, causing a very interesting type of edge ferromagnetism. Second, graphene under the influence of external perturbations can host a variety of topological insulating phases, including the conventional quantum Hall effect, the quantum anomalous Hall (QAH) and the quantum spin Hall phase, in all of which phases conduction can only take place through topologically protected edge states. Here we provide an unified vision of the properties of all these edge states, examined under the light of the same one orbital tight-binding model. We consider the combined action of interactions, spin–orbit coupling and magnetic field, which produces a wealth of different physical phenomena. We briefly address what has been actually observed experimentally.

Julii Bernhards von Rohr Einleitung zu der allgemeinen Land- und Feld-Wirthschaffts-Kunst derer Teutschen : darinnen die allgemeinen Regeln und Anmerckungen die so wohl bey der Land und Feld-Oeconomie überhaupt als insonderheit [b]ey dem Ackerbau, der Viehzucht, Gärtne[re]y ... und Fischereyen fast in allen Provinzien Teutschlandes in acht zu nehmen [i]n einer guten Ordnung ohne Einmischung unnöthiger Sachen vorgetragen werden.

Goldsmiths'-Kress no. 05628.10, suppl.

Structural studies on antifolate drugs

Single crystal X-ray structure determinations are reported for eleven compounds all of which are either biologically active or potentially biologically important. The compounds fall into two distinct classes:- 1. Substituted diaminopyrimidines 2. Substituted aminopyrimidinones The first class of compounds were all selected on the basis of their common diaminopyrimidine nucleus which has been demonstrated to be a vital requirement for antifolate activity. They may all be described as non-classical or small molecule lipophilic dihydrofolate reductase (DHFR) inhibitors, as opposed to the classical folate analogues, having the ability to cross the blood-brain barrier, enter cells via a rapid passive diffusion process, and achieve high intracellular concentrations. Thus they are an excellent choice in the search for crystallography in the solid state, providing geometrical and distance data not available from any other analytical techniques to date; supporting and enhancing data obtained in the lower resolution studies of protein crystallography. The biological importance of these compounds is discussed and an attempt is made to relate/predict their pharmacological activity to observed structural features in the crystalline environment. Special attention is focussed on hydrogen bonding, confirmational flexibility and hydrophobicity of substituents; each of which appear to make contributions to tight binding in the enzyme active site. Chapter 9 describes the use of data from the literature and the solid state modelling of an observed enzyme-substrate interaction in an attempt to define it more accurately in terms of its geometric flexibility. Of the second class, one compound (ABPP) is reported; studies in two different crystal forms. In demonstrating both antiviral and high interferon inducing activity it is possible that this compound could be useful against cancer and also viral infections.

Thermalized polarization dynamics of a discrete optical-waveguide system with four-wave mixing

Statistical mechanics of two coupled vector fields is studied in the tight-binding model that describes propagation of polarized light in discrete waveguides in the presence of the four-wave mixing. The energy and power conservation laws enable the formulation of the equilibrium properties of the polarization state in terms of the Gibbs measure with positive temperature. The transition line T=∞ is established beyond which the discrete vector solitons are created. Also in the limit of the large nonlinearity an analytical expression for the distribution of Stokes parameters is obtained, which is found to be dependent only on the statistical properties of the initial polarization state and not on the strength of nonlinearity. The evolution of the system to the final equilibrium state is shown to pass through the intermediate stage when the energy exchange between the waveguides is still negligible. The distribution of the Stokes parameters in this regime has a complex multimodal structure strongly dependent on the nonlinear coupling coefficients and the initial conditions.