Binding of a hairpin polyamide in the minor groove of DNA: sequence-specific enthalpic discrimination.

Hairpin polyamides are synthetic ligands for sequence-specific recognition in the minor groove of double-helical DNA. A thermodynamic characterization of the DNA-binding properties exhibited by a six-ring hairpin polyamide, ImPyPy-gamma-PyPyPy-beta-Dp (where Im = imidazole, Py = pyrrole, gamma = gamma-aminobutyric acid, beta = beta-alanine, and Dp = dimethylaminopropylamide), reveals an approximately 1-2 kcal/mol greater affinity for the designated match site, 5'-TGTTA-3', relative to the single base pair mismatch sites, 5'-TGGTA-3' and 5'-TATTA-3'. The enthalpy and entropy data at 20 degrees C reveal this sequence specificity to be entirely enthalpic in origin. Correlations between the thermodynamic driving forces underlying the sequence specificity exhibited by ImPyPy-gamma-PyPyPy-beta-Dp and the structural properties of the heterodimeric complex of PyPyPy and ImPyPy bound to the minor groove of DNA provide insight into the molecular forces that govern the affinity and specificity of pyrrole-imidazole polyamides.

Impaired cell volume regulation in intestinal crypt epithelia of cystic fibrosis mice.

Cystic fibrosis is a disease characterized by abnormalities in the epithelia of the lungs, intestine, salivary and sweat glands, liver, and reproductive systems, often as a result of inadequate hydration of their secretions. The primary defect in cystic fibrosis is the altered activity of a cAMP-activated Cl- channel, the cystic fibrosis transmembrane conductance regulator (CFTR) channel. However, it is not clear how a defect in the CFTR Cl- channel function leads to the observed pathological changes. Although much is known about the structural properties and regulation of the CFTR, little is known of its relationship to cellular functions other than the cAMP-dependent Cl- secretion. Here we report that cell volume regulation after hypotonic challenge is also defective in intestinal crypt epithelial cells isolated from CFTR -/- mutant mice. Moreover, the impairment of the regulatory volume decrease in CFTR -/- crypts appears to be related to the inability of a K+ conductance to provide a pathway for the exit of this cation during the volume adjustments. This provides evidence that the lack of CFTR protein may have additional consequences for the cellular function other than the abnormal cAMP-mediated Cl- secretion.

Identification of the overtone of the Fe-CO stretching mode in heme proteins: a probe of the heme active site.

Two CO-isotope sensitive lines have been detected in the overtone region of the resonance Raman spectra of CO-bound hemeproteins. One line is assigned as the overtone of the Fe-CO stretching mode and is located in the 1000- to 1070-cm-1 region. The other line is found in the 1180- to 1210-cm-1 region and is assigned as a combination between a porphyrin mode, nu 7, and the Fe-CO stretching mode. The high intensities of these lines, which in the terminal oxidase class of proteins are of the same order as those of the fundamental stretching mode, indicate that the mechanism of enhancement for modes involving the Fe-CO moiety is different from that for the modes of the porphyrin macrocycle and call for reexamination of Raman theory of porphyrins as applied to axial ligands. The anharmonicity of the electronic potential function was evaluated, revealing that in the terminal oxidases the anharmonicity is greater than in the other heme proteins that were examined, suggesting a distinctive interaction of the bound CO with its distal environment in this family. Furthermore, the anharmonicity correlates with the frequency of the C-O stretching mode, demonstrating that both of these parameters are sensitive to the Fe-CO bond energy. The overtone and combination lines involving the bound CO promise to be additional probes of heme protein structural properties.

La tagatose-1,6-bisphosphate aldolase et la fructose-1,6-bisphosphate aldolase de classe I : mécanisme et stéréospécificité

La tagatose-1,6-biphosphate aldolase de Streptococcus pyogenes est une aldolase qui fait preuve d'un remarquable manque de spécificité vis à vis de ses substrats. En effet, elle catalyse le clivage réversible du tagatose-1,6-bisphosphate (TBP), mais également du fructose-1,6-bisphosphate (FBP), du sorbose-1,6-bisphosphate et du psicose-1,6-bisphosphate, quatre stéréoisomères, en dihydroxyacétone phosphate (DHAP) et en glycéraldéhyde-3-phosphate (G3P). Aldolase de classe I, qui donc catalyse sa réaction en formant un intermédiaire covalent obligatoire, ou base de Schiff, avec son susbtrat, la TBP aldolase de S. pyogenes partage 14 % d’identité avec l’enzyme modèle de cette famille, la FBP aldolase de muscle de mammifère. Bien que le mécanime catalytique de la FBP aldolase des mammifères ait été examiné en détails et qu’il soit approprié d’en tirer des renseignements quant à celui de la TBP aldolase, le manque singulier de stéréospécificité de cette dernière tant dans le sens du clivage que celui de la condensation n’est toujours pas éclairci. Afin de mettre à jour les caractéristiques du mécanisme enzymatique, une étude structurale de la TBP aldolase de S. pyogenes, un pathogène humain extrêmement versatile, a été entreprise. Elle a permis la résolution des structures de l’enzyme native et mutée, en complexe avec des subtrats et des inhibiteurs compétitifs, à des résolutions comprises entre 1.8 Å et 2.5 Å. Le trempage des cristaux de TBP aldolase native et mutante dans une solution saturante de FBP ou TBP a en outre permis de piéger un authentique intermédiaire covalent lié à la Lys205, la lysine catalytique. La determination des profils pH de la TBP aldolase native et mutée, entreprise afin d'évaluer l’influence du pH sur la réaction de clivage du FBP et TBP et ìdentifier le(s) résidu(s) impliqué(s), en conjonction avec les données structurales apportées par la cristallographie, ont permis d’identifier sans équivoque Glu163 comme résidu responsable du clivage. En effet, le mode de liaison sensiblement différent des ligands utilisés selon la stéréochimie en leur C3 et C4 permet à Glu163, équivalent à Glu187 dans la FBP aldolase de classe I, d’abstraire le proton sur l’hydroxyle du C4 et ainsi d’amorcer le clivage du lien C3-C4. L’étude du mécanimse inverse, celui de la condensation, grâce par exemple à la structure de l’enzyme native en complexe avec ses substrats à trois carbones le DHAP et le G3P, a en outre permis d’identifier un isomérisme du substrat G3P comme possible cause de la synthèse des isomères en C4 par cette enzyme. Ce résultat, ainsi que la decouverte d’un possible isomérisme cis-trans autour du lien C2-C3 de la base de Schiff formée avec le DHAP, identifié précedemment, permet de cerner presque complètement les particularités du mécanisme de cette enzyme et d’expliquer comment elle est capable de synthétiser les quatres stéréoisomères 3(S/R), 4(S/R). De plus, la résolution de ces structures a permis de mettre en évidence trois régions très mobiles de la protéine, ce qui pourrait être relié au rôle postulé de son isozyme chez S. pyogenes dans la régulation de l’expression génétique et de la virulence de la bactérie. Enfin, la résolution de la structure du mutant Lys229→Met de la FBP aldolase de muscle en complexe avec la forme cyclique du FBP, de même que des études cristallographiques sur le mutant équivalent Lys205→Met de la TBP aldolase de S. pyogenes et des expériences de calorimétrie ont permis d’identifier deux résidus particuliers, Ala31 et Asp33 chez la FBP aldolase, comme possible cause de la discrimination de cette enzyme contre les substrats 3(R) et 4(S), et ce par encombrement stérique des substrats cycliques. La cristallographie par rayons X et la cinétique enzymatique ont ainsi permis d'avancer dans l'élucidation du mécanisme et des propriétés structurales de cette enzyme aux caractéristiques particulières.

A bibliography of paper testing.

Each part brought up to date by supplements.

Quantum transport and integrability of the Anderson model for a quantum dot with multiple leads

We show that an Anderson Hamiltonian describing a quantum dot connected to multiple leads is integrable. A general expression for the nonlinear conductance is obtained by combining the Bethe ansatz exact solution with Landauer-Buttiker theory. In the Kondo regime, a closed form expression is given for the matrix conductance at zero temperature and when all the leads are close to the symmetric point. A bias-induced splitting of the Kondo resonance is possible for three or more leads. Specifically, for N leads, with each at a different chemical potential, there can be N-1 Kondo peaks in the conductance.

Indications of coherence-incoherence crossover in layered metallic transport

For many strongly correlated metals with layered crystal structure the temperature dependence of the interlayer resistance is different to that of the intralayer resistance. We consider a small polaron model which exhibits this behavior, illustrating how the interlayer transport is related to the coherence of quasiparticles within the layers. Explicit results are also given for the electron spectral function, interlayer optical conductivity, and the interlayer magnetoresistance. All these quantities have two contributions: one coherent (dominant at low temperatures) and the other incoherent (dominant at high temperatures).

Entanglement of two-mode Bose-Einstein condensates

We investigate the entanglement characteristics of two general bimodal Bose-Einstein condensates-a pair of tunnel-coupled Bose-Einstein condensates and the atom-molecule Bose-Einstein condensate. We argue that the entanglement is only physically meaningful if the system is viewed as a bipartite system, where the subsystems are the two modes. The indistinguishibility of the particles in the condensate means that the atomic constituents are physically inaccessible and, thus, the degree of entanglement between individual particles, unlike the entanglement between the modes, is not experimentally relevant so long as the particles remain in the condensed state. We calculate the entanglement between the two modes for the exact ground state of the two bimodal condensates and consider the dynamics of the entanglement in the tunnel-coupled case.

The gap equations for spin singlet and triplet ferromagnetic superconductors

We derive gap equations for superconductivity in coexistence with ferromagnetism. We treat singlet and triplet states With either equal spin pairing (ESP) or opposite spin pairing (OSP) states, and study the behaviour of these states as a function of exchange splitting. For the s-wave singlet state we find that our gap equations correctly reproduce the Clogston-Chandrasekhar limiting behaviour and the phase diagram of the Baltensperger-Sarma equation (excluding the FFLO region). The singlet superconducting order parameter is shown to be independent of exchange splitting at zero temperature, as is assumed in the derivation of the Clogston-Chandrasekhar limit. P-wave triplet states of the OSP type behave similarly to the singlet state as a function of exchange splitting. On the other hand, ESP triplet states show a very different behaviour. In particular, there is no Clogston-Chandrasekhar limiting and the superconducting critical temperature, T-C, is actually increased by exchange splitting.

Competition between disorder and exchange splitting in superconducting ZrZn2

We propose a simple picture for the occurrence of superconductivity and the pressure dependence of the superconducting critical temperature, T-SC, in ZrZn2. According to our hypothesis the pairing potential is independent of pressure, but the exchange splitting, E-xc leads to a pressure dependence in the (spin dependent) density of states at the Fermi level, D-sigma (epsilon(F)). Assuming p-wave pairing T-SC is dependent on D-sigma (epsilonF) which ensures that, in the absence of non-magnetic impurities, T-SC decreases as pressure is applied until it reaches a minimum in the paramagnetic state. Disorder reduces this minimum to zero, this gives the illusion that the superconductivity disappears at the same pressure as ferromagnetism does.

Progress in silicon-based quantum computation

We review progress at the Australian Centre for Quantum Computer Technology towards the fabrication and demonstration of spin qubits and charge qubits based on phosphorus donor atoms embedded in intrinsic silicon. Fabrication is being pursued via two complementary pathways: a 'top-down' approach for near-term production of few-qubit demonstration devices and a 'bottom-up' approach for large-scale qubit arrays with sub-nanometre precision. The 'top-down' approach employs a low-energy (keV) ion beam to implant the phosphorus atoms. Single-atom control during implantation is achieved by monitoring on-chip detector electrodes, integrated within the device structure. In contrast, the 'bottom-up' approach uses scanning tunnelling microscope lithography and epitaxial silicon overgrowth to construct devices at an atomic scale. In both cases, surface electrodes control the qubit using voltage pulses, and dual single-electron transistors operating near the quantum limit provide fast read-out with spurious-signal rejection.

Strength indices of the proximal femur and shaft in prepubertal female gymnasts

Introduction/Purpose: The role of impact loading activity on bone mass is well established; however, there are little data on the effects of exercise on bone geometry and indices of bone strength. The primary purpose of this study was to compare indices of bone strength at the proximal femur (PF) between elite premenarcheal gymnasts (N = 30) and age-matched controls (N = 30). Methods: Structural properties of the proximal femur were derived from the hip analyses program and included measurement of subperiosteal width, endosteal diameter, cross-sectional area, bone mineral density, cross-section moment of inertia (CSMI), and section modulus (Z). These parameters were measured for two regions of the PF: the narrow neck (NN), and the shaft (S). In addition, a strength index (S-SI) was calculated at the shaft by dividing the Z at the shaft by the femur length. A secondary purpose was to compare bone mineral content (BMC) values at the total body, lumbar spine, and three sites at the PF (neck, trochanter, and total) between the groups. All dependent values were compared adjusting for height and weight using an ANCOVA procedure and for relative lean body mass post hoc. Results: The gymnasts had significantly greater size-adjusted strength indices (CSMI, Z, and SI) at the NN and S. Gymnasts also had significantly greater size-adjusted BMC at all sites investigated. However, these differences disappeared when adjusted for relative lean body mass. Conclusion: When adjusted for body size, gymnasts had significantly greater indices of both axial strength and bending strength at the NN region of the PF and S, as well as a greater bone SI at the femoral shaft. These differences may be related to greater relative lean body mass attained in gymnastics training.

A maximum density rule for surfaces of quasicrystals

Motivated by Bravais' rule, of wide validity for crystals, we introduce a maximum density rule for the surfaces of quasicrystals and use it to determine the 5-, 2- and 3-fold bulk terminations in a geometric icosahedral model of i-AlPdMn and i-AlCuFe that represent surfaces.

Absorption and fluorescence spectroscopy of rhodamine 6G in titanium dioxide nanocomposites

A comparison has been made between the spectroscopic properties of the laser dye rhodamine 6G (R6G) in mesostructured titanium dioxide (TiO2) and in ethanol. Steady-state excitation and emission techniques have been used to probe the dye-matrix interactions. We show that the TiO2-nanocomposite studied is a good host for R6G, as it allows high dye concentrations, while keeping dye molecules isolated, and preventing aggregation. Our findings have important implications in the context of solid state dye-lasers and microphotonic device applications. (C) 2003 Elsevier B.V. All rights reserved.