Helicase processivity and not the unwinding velocity exhibits universal increase with force

Helicases, involved in a number of cellular functions, are motors that translocate along singlestranded nucleic acid and couple the motion to unwinding double-strands of a duplex nucleic acid. The junction between double and single strands creates a barrier to the movement of the helicase, which can be manipulated in vitro by applying mechanical forces directly on the nucleic acid strands. Single molecule experiments have demonstrated that the unwinding velocities of some helicases increase dramatically with increase in the external force, while others show little response. In contrast, the unwinding processivity always increases when the force increases. The differing responses of the unwinding velocity and processivity to force has lacked explanation. By generalizing a previous model of processive unwinding by helicases, we provide a unified framework for understanding the dependence of velocity and processivity on force and the nucleic acid sequence. We predict that the sensitivity of unwinding processivity to external force is a universal feature that should be observed in all helicases. Our prediction is illustrated using T7 and NS3 helicases as case studies. Interestingly, the increase in unwinding processivity with force depends on whether the helicase forces base pair opening by direct interaction or if such a disruption occurs spontaneously due to thermal uctuations. Based on the theoretical results, we propose that proteins like single-strand binding proteins associated with helicases in the replisome, may have co-evolved with helicases to increase the unwinding processivity even if the velocity remains unaffected

Refolding dynamics of stretched biopolymers upon force quench

Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench, using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, $\tau_F$, depends asymmetrically on $\delta f_S = f_S - f_m$ and $\delta f_Q = f_m - f_Q$ where $f_S$ ($f_Q$) is the stretch (quench) force, and $f_m$ is the transition mid-force of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, $R(t)$, occurs in three stages: a rapid initial decrease in the extension is followed by a plateau, and finally an abrupt reduction in $R(t)$ that occurs as the native state is approached. The duration of the plateau increases as $\lambda =\tau_Q/\tau_F$ decreases (where $\tau_Q$ is the time in which the force is reduced from $f_S$ to $f_Q$). Variations in the mechanisms of force quench relaxation as $\lambda$ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in $R(t)$. The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding.Comment: 31 pages 11 figure

Fluctuations of a driven membrane in an electrolyte

We develop a model for a driven cell- or artificial membrane in an electrolyte. The system is kept far from equilibrium by the application of a DC electric field or by concentration gradients, which causes ions to flow through specific ion-conducting units (representing pumps, channels or natural pores). We consider the case of planar geometry and Debye-H\"{u}ckel regime, and obtain the membrane equation of motion within Stokes hydrodynamics. At steady state, the applied field causes an accumulation of charges close to the membrane, which, similarly to the equilibrium case, can be described with renormalized membrane tension and bending modulus. However, as opposed to the equilibrium situation, we find new terms in the membrane equation of motion, which arise specifically in the out-of-equilibrium case. We show that these terms lead in certain conditions to instabilities.Comment: 7 pages, 2 figures. submitted to Europhys. Let

Charge-Fluctuation-Induced Non-analytic Bending Rigidity

In this Letter, we consider a neutral system of mobile positive and negative charges confined on the surface of curved films. This may be an appropriate model for: i) a highly charged membrane whose counterions are confined to a sheath near its surface; ii) a membrane composed of an equimolar mixture of anionic and cationic surfactants in aqueous solution. We find that the charge fluctuations contribute a non-analytic term to the bending rigidity that varies logarithmically with the radius of curvature. This may lead to spontaneous vesicle formation, which is indeed observed in similar systems.Comment: Revtex, 9 pages, no figures, submitted to PR

Screening by symmetry of long-range hydrodynamic interactions of polymers confined in sheets

Hydrodynamic forces may significantly affect the motion of polymers. In sheet-like cavities, such as the cell's cytoplasm and microfluidic channels, the hydrodynamic forces are long-range. It is therefore expected that that hydrodynamic interactions will dominate the motion of polymers in sheets and will be manifested by Zimm-like scaling. Quite the opposite, we note here that although the hydrodynamic forces are long-range their overall effect on the motion of polymers vanishes due to the symmetry of the two-dimensional flow. As a result, the predicted scaling of experimental observables such as the diffusion coefficient or the rotational diffusion time is Rouse-like, in accord with recent experiments. The effective screening validates the use of the non-interacting blobs picture for polymers confined in a sheet.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/Macromolecules2006.pdf http://pubs.acs.org/doi/abs/10.1021/ma060251

Surface Shape and Local Critical Behaviour in Two-Dimensional Directed Percolation

Two-dimensional directed site percolation is studied in systems directed along the x-axis and limited by a free surface at y=\pm Cx^k. Scaling considerations show that the surface is a relevant perturbation to the local critical behaviour when k<1/z where z=\nu_\parallel/\nu is the dynamical exponent. The tip-to-bulk order parameter correlation function is calculated in the mean-field approximation. The tip percolation probability and the fractal dimensions of critical clusters are obtained through Monte-Carlo simulations. The tip order parameter has a nonuniversal, C-dependent, scaling dimension in the marginal case, k=1/z, and displays a stretched exponential behaviour when the perturbation is relevant. The k-dependence of the fractal dimensions in the relevant case is in agreement with the results of a blob picture approach.Comment: 13 pages, Plain TeX file, epsf, 6 postscript-figures, minor correction

Adiabatic-antiadiabatic crossover in a spin-Peierls chain

We consider an XXZ spin-1/2 chain coupled to optical phonons with non-zero frequency $\omega_0$. In the adiabatic limit (small $\omega_0$), the chain is expected to spontaneously dimerize and open a spin gap, while the phonons become static. In the antiadiabatic limit (large $\omega_0$), phonons are expected to give rise to frustration, so that dimerization and formation of spin-gap are obtained only when the spin-phonon interaction is large enough. We study this crossover using bosonization technique. The effective action is solved both by the Self Consistent Harmonic Approximation (SCHA)and by Renormalization Group (RG) approach starting from a bosonized description. The SCHA allows to analyze the lowfrequency regime and determine the coupling constant associated with the spin-Peierls transition. However, it fails to describe the SU(2) invariant limit. This limit is tackled by the RG. Three regimes are found. For $\omega_0\ll\Delta_s$, where $\Delta_s$ is the gap in the static limit $\omega_0\to 0$, the system is in the adiabatic regime, and the gap remains of order $\Delta_s$. For $\omega_0>\Delta_s$, the system enters the antiadiabatic regime, and the gap decreases rapidly as $\omega_0$ increases. Finally, for $\omega_0>\omega_{BKT}$, where $\omega_{BKT}$ is an increasing function of the spin phonon coupling, the spin gap vanishes via a Berezinskii-Kosterlitz-Thouless transition. Our results are discussed in relation with numerical and experimental studies of spin-Peierls systems.Comment: Revtex, 21 pages, 5 EPS figures (v1); 23 pages, 6 EPS figures, more detailed comparison with ED results, referenes added (v2