ATPase cycle and DNA unwinding kinetics of RecG helicase

The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states

Magnetic field effects in few-level quantum dots: theory, and application to experiment

We examine several effects of an applied magnetic field on Anderson-type models for both single- and two-level quantum dots, and make direct comparison between numerical renormalization group (NRG) calculations and recent conductance measurements. On the theoretical side the focus is on magnetization, single-particle dynamics and zero-bias conductance, with emphasis on the universality arising in strongly correlated regimes; including a method to obtain the scaling behavior of field-induced Kondo resonance shifts over a very wide field range. NRG is also used to interpret recent experiments on spin-1/2 and spin-1 quantum dots in a magnetic field, which we argue do not wholly probe universal regimes of behavior; and the calculations are shown to yield good qualitative agreement with essentially all features seen in experiment. The results capture in particular the observed field-dependence of the Kondo conductance peak in a spin-1/2 dot, with quantitative deviations from experiment occurring at fields in excess of $\sim$ 5 T, indicating the eventual inadequacy of using the equilibrium single-particle spectrum to calculate the conductance at finite bias.Comment: 15 pages, 12 figures. Version as published in PR

Designing and managing multiple pipelines

There is now a growing recognition that supply chains should be designed from ‘the customer backwards’ rather than from ‘the company outwards’. If such a view is accepted then the implication is that since the organisation will likely be serving multiple markets or segments there will be the need to design and manage multiple ‘pipelines’ to serve those different customers. To assist decision makers in their choice of appropriate supply chain design a framework is proposed based upon multiple criteria. A case study is presented which highlights the benefits of selecting, engineering and operating multiple pipelines tailored to the needs of th

Correlated electron physics in multilevel quantum dots: phase transitions, transport, and experiment

We study correlated two-level quantum dots, coupled in effective 1-channel fashion to metallic leads; with electron interactions including on-level and inter-level Coulomb repulsions, as well as the inter-orbital Hund's rule exchange favoring the spin-1 state in the relevant sector of the free dot. For arbitrary dot occupancy, the underlying phases, quantum phase transitions (QPTs), thermodynamics, single-particle dynamics and electronic transport properties are considered; and direct comparison is made to conductance experiments on lateral quantum dots. Two distinct phases arise generically, one characterised by a normal Fermi liquid fixed point (FP), the other by an underscreened (USC) spin-1 FP. Associated QPTs, which occur in general in a mixed valent regime of non-integral dot charge, are found to consist of continuous lines of Kosterlitz-Thouless transitions, separated by first order level-crossing transitions at high symmetry points. A `Friedel-Luttinger sum rule' is derived and, together with a deduced generalization of Luttinger's theorem to the USC phase (a singular Fermi liquid), is used to obtain a general result for the T=0 zero-bias conductance, expressed solely in terms of the dot occupancy and applicable to both phases. Relatedly, dynamical signatures of the QPT show two broad classes of behavior, corresponding to the collapse of either a Kondo resonance, or antiresonance, as the transition is approached from the Fermi liquid phase; the latter behavior being apparent in experimental differential conductance maps. The problem is studied using the numerical renormalization group method, combined with analytical arguments.Comment: 22 pages, 18 figures, submitted for publicatio

Azobenzene versus 3,3',5,5'-tetra-tert-butyl-azobenzene (TBA) at Au(111): Characterizing the role of spacer groups

We present large-scale density-functional theory (DFT) calculations and temperature programmed desorption measurements to characterize the structural, energetic and vibrational properties of the functionalized molecular switch 3,3',5,5'-tetra-tert-butyl-azobenzene (TBA) adsorbed at Au(111). Particular emphasis is placed on exploring the accuracy of the semi-empirical dispersion correction approach to semi-local DFT (DFT-D) in accounting for the substantial van der Waals component in the surface chemical bond. In line with previous findings for benzene and pure azobenzene at coinage metal surfaces, DFT-D significantly overbinds the molecule, but seems to yield an accurate adsorption geometry as far as can be judged from the experimental data. Comparing the trans adsorption geometry of TBA and azobenzene at Au(111) reveals a remarkable insensitivity of the structural and vibrational properties of the -N=N- moiety. This questions the established view of the role of the bulky tert-butyl-spacer groups for the switching of TBA in terms of a mere geometric decoupling of the photochemically active diazo-bridge from the gold substrate.Comment: 9 pages including 6 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.htm

The ATPase cycle of PcrA helicase and its coupling to translocation on DNA.

The superfamily 1 bacterial helicase PcrA has a role in the replication of certain plasmids, acting with the initiator protein (RepD) that binds to and nicks the double-stranded origin of replication. PcrA also translocates single-stranded DNA with discrete steps of one base per ATP hydrolyzed. Individual rate constants have been determined for the DNA helicase PcrA ATPase cycle when bound to either single-stranded DNA or a double-stranded DNA junction that also has RepD bound. The fluorescent ATP analogue 2'(3')-O-(N-methylanthraniloyl)ATP was used throughout all experiments to provide a complete ATPase cycle for a single nucleotide species. Fluorescence intensity and anisotropy stopped-flow measurements were used to determine rate constants for binding and release. Quenched-flow measurements provided the kinetics of the hydrolytic cleavage step. The fluorescent phosphate sensor MDCC-PBP was used to measure phosphate release kinetics. The chemical cleavage step is the rate-limiting step in the cycle and is essentially irreversible and would result in the bound ATP complex being a major component at steady state. This cleavage step is greatly accelerated by bound DNA, producing the high activation of this protein compared to the protein alone. The data suggest the possibility that ADP is released in two steps, which would result in bound ADP also being a major intermediate, with bound ADP.P(i) being a very small component. It therefore seems likely that the major transition in structure occurs during the cleavage step, rather than P(i) release. ATP rebinding could then cause reversal of this structural transition. The kinetic mechanism of the PcrA ATPase cycle is very little changed by potential binding to RepD, supporting the idea that RepD increases the processivity of PcrA by increasing affinity to DNA rather than affecting the enzymatic properties per se

Helicity operators for mesons in flight on the lattice

Motivated by the desire to construct meson-meson operators of definite relative momentum in order to study resonances in lattice QCD, we present a set of single-meson interpolating fields at non-zero momentum that respect the reduced symmetry of a cubic lattice in a finite cubic volume. These operators follow from the subduction of operators of definite helicity into irreducible representations of the appropriate little groups. We show their effectiveness in explicit computations where we find that the spectrum of states interpolated by these operators is close to diagonal in helicity, admitting a description in terms of single-meson states of identified J^{PC}. The variationally determined optimal superpositions of the operators for each state give rapid relaxation in Euclidean time to that state, ideal for the construction of meson-meson operators and for the evaluation of matrix elements at finite momentum.Comment: 25 pages, 14 figures; v2: minor changes to reflect journal versio