Some characteristics of cytochrome f in the cyanobacterium Phormidium laminosum: its sequence and charge properties in the reaction with plastocyanin

AbstractPart of the petCA operon was cloned and the sequence of the cytochrome f gene from the moderately thermophilic cyanobacterium Phormidium laminosum determined. A partial sequence of the petC gene encoding the Rieske iron-sulphur protein was also obtained. The cytochrome f gene encodes a mature protein of 385 residues and a leader sequence of 45 residues. The mature protein contains several acidic or neutral residues corresponding to basic residues in the turnip protein. Some of the latter are thought to be important for the interaction with plastocyanin via its ‘eastern’ face. Many of the corresponding residues on the eastern face of P. laminosum plastocyanin are either basic or neutral instead of acidic. These comparisons suggested that the local charges on P. laminosum cytochrome f that are important for its interaction with the homologous plastocyanin may be negative rather than positive. The importance of acidic groups was confirmed by measuring the rates of reduction of horse heart cytochrome c and P. laminosum and spinach plastocyanins by the cytochrome bf complex isolated from P. laminosum. P. laminosum plastocyanin gave the highest rates, which decreased at high ionic strength, confirming the importance of positive local charges on this protein. When extrapolated to infinite ionic strength the rates observed with the two kinds of plastocyanin were similar, but cytochrome c became unreactive. An optimum was observed in the ionic strength response with P. laminosum plastocyanin

Transmission Properties of the oscillating delta-function potential

We derive an exact expression for the transmission amplitude of a particle moving through a harmonically driven delta-function potential by using the method of continued-fractions within the framework of Floquet theory. We prove that the transmission through this potential as a function of the incident energy presents at most two real zeros, that its poles occur at energies $n\hbar\omega+\varepsilon^*$ ($0<Re(\varepsilon^*)<\hbar\omega$), and that the poles and zeros in the transmission amplitude come in pairs with the distance between the zeros and the poles (and their residue) decreasing with increasing energy of the incident particle. We also show the existence of non-resonant "bands" in the transmission amplitude as a function of the strength of the potential and the driving frequency.Comment: 21 pages, 12 figures, 1 tabl

Infinite-Order Percolation and Giant Fluctuations in a Protein Interaction Network

We investigate a model protein interaction network whose links represent interactions between individual proteins. This network evolves by the functional duplication of proteins, supplemented by random link addition to account for mutations. When link addition is dominant, an infinite-order percolation transition arises as a function of the addition rate. In the opposite limit of high duplication rate, the network exhibits giant structural fluctuations in different realizations. For biologically-relevant growth rates, the node degree distribution has an algebraic tail with a peculiar rate dependence for the associated exponent.Comment: 4 pages, 2 figures, 2 column revtex format, to be submitted to PRL 1; reference added and minor rewording of the first paragraph; Title change and major reorganization (but no result changes) in response to referee comments; to be published in PR

Impact of long-range interactions on the disordered vortex lattice

The interaction between the vortex lines in a type-II superconductor is mediated by currents. In the absence of transverse screening this interaction is long-ranged, stiffening up the vortex lattice as expressed by the dispersive elastic moduli. The effect of disorder is strongly reduced, resulting in a mean-squared displacement correlator = characterized by a mere logarithmic growth with distance. Finite screening cuts the interaction on the scale of the London penetration depth \lambda and limits the above behavior to distances R<\lambda. Using a functional renormalization group (RG) approach, we derive the flow equation for the disorder correlation function and calculate the disorder-averaged mean-squared relative displacement \propto ln^{2\sigma} (R/a_0). The logarithmic growth (2\sigma=1) in the perturbative regime at small distances [A.I. Larkin and Yu.N. Ovchinnikov, J. Low Temp. Phys. 34, 409 (1979)] crosses over to a sub-logarithmic growth with 2\sigma=0.348 at large distances.Comment: 9 pages, no figure

Molecular Dynamics Study of Bamboo-like Carbon Nanotube Nucleation

MD simulations based on an empirical potential energy surface were used to study the nucleation of bamboo-like carbon nanotubes (BCNTs). The simulations reveal that inner walls of the bamboo structure start to nucleate at the junction between the outer nanotube wall and the catalyst particle. In agreement with experimental results, the simulations show that BCNTs nucleate at higher dissolved carbon concentrations (i.e., feedstock pressures) than those where non-bamboolike carbon nanotubes are nucleated

2-loop Functional Renormalization Group Theory of the Depinning Transition

We construct the field theory which describes the universal properties of the quasi-static isotropic depinning transition for interfaces and elastic periodic systems at zero temperature, taking properly into account the non-analytic form of the dynamical action. This cures the inability of the 1-loop flow-equations to distinguish between statics and quasi-static depinning, and thus to account for the irreversibility of the latter. We prove two-loop renormalizability, obtain the 2-loop beta-function and show the generation of "irreversible" anomalous terms, originating from the non-analytic nature of the theory, which cause the statics and driven dynamics to differ at 2-loop order. We obtain the roughness exponent zeta and dynamical exponent z to order epsilon^2. This allows to test several previous conjectures made on the basis of the 1-loop result. First it demonstrates that random-field disorder does indeed attract all disorder of shorter range. It also shows that the conjecture zeta=epsilon/3 is incorrect, and allows to compute the violations, as zeta=epsilon/3 (1 + 0.14331 epsilon), epsilon=4-d. This solves a longstanding discrepancy with simulations. For long-range elasticity it yields zeta=epsilon/3 (1 + 0.39735 epsilon), epsilon=2-d (vs. the standard prediction zeta=1/3 for d=1), in reasonable agreement with the most recent simulations. The high value of zeta approximately 0.5 found in experiments both on the contact line depinning of liquid Helium and on slow crack fronts is discussed.Comment: 32 pages, 17 figures, revtex

Expression of plastocyanin and cytochrome f of the cyanobacterium Phormidium laminosum in escherichia coli and Paracoccus denitrificans and the role of leader peptides

Macromolecular Biochemistr

Quantization of adiabatic pumped charge in the presence of superconducting lead

We investigate the parametric electron pumping of a double barrier structure in the presence of a superconducting lead. The parametric pumping is facilitated by cyclic variation of the barrier heights $x_1$ and $x_2$ of the barriers. In the weak coupling regime, there exists a resonance line in the parameter space $(x_1,x_2)$ so that the energy of the quasi-bound state is in line with the incoming Fermi energy. Levinson et al found recently that the pumped charge for each pumping cycle is quantized with $Q=2e$ for normal structure when the pumping contour encircles the resonance line. In the presence of a superconducting lead, we find that the pumped charge is quantized with the value $2e$

Optimal quantum pump in the presence of a superconducting lead

We investigate the parametric pumping of a hybrid structure consisting of a normal quantum dot, a normal lead and a superconducting lead. Using the time dependent scattering matrix theory, we have derived a general expression for the pumped electric current and heat current. We have also derived the relationship among the instantaneous pumped heat current, electric current, and shot noise. This gives a lower bound for the pumped heat current in the hybrid system similar to that of the normal case obtained by Avron et al

Rings and rigidity transitions in network glasses

Three elastic phases of covalent networks, (I) floppy, (II) isostatically rigid and (III) stressed-rigid have now been identified in glasses at specific degrees of cross-linking (or chemical composition) both in theory and experiments. Here we use size-increasing cluster combinatorics and constraint counting algorithms to study analytically possible consequences of self-organization. In the presence of small rings that can be locally I, II or III, we obtain two transitions instead of the previously reported single percolative transition at the mean coordination number $\bar r=2.4$, one from a floppy to an isostatic rigid phase, and a second one from an isostatic to a stressed rigid phase. The width of the intermediate phase $~ \bar r$ and the order of the phase transitions depend on the nature of medium range order (relative ring fractions). We compare the results to the Group IV chalcogenides, such as Ge-Se and Si-Se, for which evidence of an intermediate phase has been obtained, and for which estimates of ring fractions can be made from structures of high T crystalline phases.Comment: 29 pages, revtex, 7 eps figure