R. Dean Astumian

Surfactant Sealing of Membranes Permeabilized by Ionizing Radiation

Abstract Hannig, J., Zhang, D., Canaday, D. J., Beckett, M. A., Astumian, R. D., Weichselbaum, R. R. and Lee, R. C. Surfactant Sealing of Membranes Permeabilized by Ionizing Radiation. Acute tissue injury and subsequent inflammation, including tissue edema and erythema, can be caused by sufficiently high levels of exposure to γ radiation. The mechanism of this tissue injury is related to the generation of reactive oxygen intermediates (ROI) which chemically alter biological molecules and cell physiology. Cell membrane lipids are vulnerable to ROI-mediated lipid peroxidation that then leads to many of the acute tissue effects. We hypothesize that increased cell membrane permeability leading to osmotic swelling and vascular transudation is one of these effects. Thus we used adult postmitotic rhabdomyocytes in culture and microscopic fluorescence techniques to quantify radiation-induced changes in cell membrane permeability. Based on time-resolved dye flux measurements, a characteristic lag time of 34 ± 3 min was determined between exposure to 160 Gy of γ radiation and the decrease in membrane permeability. Administration of 0.1 mM nonionic surfactant Poloxamer 188 added to the cell medium after irradiation completely inhibited the dye loss over the time course of 2 h. Thus a reproducible model was developed for studying the mechanism of acute radiation injury and the efficacy of membrane-sealing agents. As only supportive measures now exist for treating the acute, nonlethal injuries from high-dose radiation exposure, agents that can restore cell membrane function after radiation damage may offer an important tool for therapy.

Thermodynamics and Kinetics of Molecular Motors

Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules.

A Chemically Reversible Brownian Motor: Application to Kinesin and Ncd

Kinesin and nonclaret disjunctional protein (ncd) are two microtubule-based molecular motors that use energy from ATP hydrolysis to drive motion in opposite directions. They are structurally very similar and bind with similar orientations on microtubule. What is the origin of the different directionality? Is it some subtle feature of the structure of the motor domains, not apparent in x-ray diffraction studies, or possibly some difference near the neck regions far from the microtubule binding site? Perhaps because the motors function as dimers, the explanation involves differences in the strength of the interaction between the two motor monomers themselves. Here we present another possibility, based on a Brownian ratchet, in which the direction of motion of the motor is controlled by the chemical mechanism of ATP hydrolysis and is an inherent property of a single head. In contrast to conventional power stroke models, dissociation of the individual heads is not obligatory in the chemomechanical cycle, and the steps during which motion and force generation occurs are best described as one-dimensional thermally activated transitions that take place while both heads are attached to the microtubule. We show that our model is consistent with experiments on kinesin in which the velocity is measured as a function of external force and with the observed stiochiometry of one ATP/8-nm step at low load. Further, the model provides a way of understanding recent experiments on the ATP dependence of the variance (randomness) of the distance moved in a given time.

Relative Unidirectional Translation in an Artificial Molecular Assembly Fueled by Light

Motor molecules present in nature convert energy inputs, such as a chemical fuel or incident photons of light, into directed motion and force biochemical systems away from thermal equilibrium. The ability not only to control relative movements of components in molecules but also to drive their components preferentially in one direction relative to each other using versatile stimuli is one of the keys to future technological applications. Herein, we describe a wholly synthetic small-molecule system that, under the influence of chemical reagents, electrical potential, or visible light, undergoes unidirectional relative translational motion. Altering the redox state of a cyclobis(paraquat-p-phenylene) ring simultaneously (i) inverts the relative heights of kinetic barriers presented by the two termini--one a neutral 2-isopropylphenyl group and the other a positively charged 3,5-dimethylpyridinium unit--of a constitutionally asymmetric dumbbell, which can impair the threading/dethreading of a [2]pseudorotaxane, and (ii) controls the rings affinity for a 1,5-dioxynaphthalene binding site located in the dumbbells central core. The formation and subsequent dissociation of the [2]pseudorotaxane by passage of the ring over the neutral and positively charged termini of the dumbbell component in one, and only one, direction relatively defined has been demonstrated by (i) spectroscopic ((1)H NMR and UV/vis) means and cyclic voltammetry as well as with (ii) DFT calculations and by (iii) comparison with control compounds in the shape of constitutionally symmetrical [2]pseudorotaxanes, one with two positively charged ends and the other with two neutral ends. The operation of the system relies solely on reversible, yet stable, noncovalent bonding interactions. Moreover, in the presence of a photosensitizer, visible-light energy is the only fuel source that is needed to drive the unidirectional molecular translation, making it feasible to repeat the operation numerous times without the buildup of byproducts.

The unreasonable effectiveness of equilibrium theory for interpreting nonequilibrium experiments

There has been much interest in applying the results of statistical mechanics to single molecule experiments. Recent work has highlighted nonequilibrium work-energy relations and fluctuation theorems that have an equilibriumlike (time independent) form. I give a simple heuristic example where an equilibrium result (the barometric law for colloidal particles in water) can be derived using the thermodynamically nonequilibrium behavior of a single colloidal particle falling through the water due to gravity. This description is possible because the particle, even while falling, is in mechanical equilibrium (the gravitational force equals the viscous drag force) at every instant. The results are generalized using Onsager’s thermodynamic action approach for stochastic processes to derive time independent equations that hold for thermodynamically nonequilibrium (and even nonstationary) systems. These relations offer great possibilities for the rapid determination of thermodynamic parameters from single molecule ...

Adiabatic operation of a molecular machine

Operation of a molecular machine is often thought of as a “far from equilibrium” process in which energy released by some high free energy fuel molecule or by light is used to drive a nonequilibrium “power stroke” to do work on the environment. Here we discuss how a molecular machine can be operated arbitrarily close to chemical equilibrium and still perform significant work at an appreciable rate: micrometer per second velocities against piconewton loads. As a specific example, we focus on a motor based on a three-ring catenane similar to that discussed by Leigh [Leigh DA, Wong JKY, Dehez F, Zerbetto F (2003) Nature 424:174–179]. The machine moves through its working cycle under the influence of external modulation of the energies of the states, where the modulation is carried out slowly enough that the state probabilities obey a Boltzmann equilibrium distribution at every instant. The mechanism can be understood in terms of the geometric phase [Berry MV (1990) Phys Today 43(12):34–40] in which the system moves adiabatically around a closed loop in parameter space, completing, on average, nearly one-half mechanical cycle each time it does so. Because the system is very close to equilibrium at every instant, the efficiency can approach 100%.

Theoretical limits on the threshold for the response of long cells to weak extremely low frequency electric fields due to ionic and molecular flux rectification.

Understanding exposure thresholds for the response of biological systems to extremely low frequency (ELF) electric and magnetic fields is a fundamental problem of long-standing interest. We consider a two-state model for voltage-gated channels in the membrane of an isolated elongated cell (Lcell = 1 mm; rcell = 25 micron) and use a previously described process of ionic and molecular flux rectification to set lower bounds for a threshold exposure. A key assumption is that it is the ability of weak physical fields to alter biochemistry that is limiting, not the ability of a small number of molecules to alter biological systems. Moreover, molecular shot noise, not thermal voltage noise, is the basis of threshold estimates. Models with and without stochastic resonance are used, with a long exposure time, texp = 10(4) s. We also determined the dependence of the threshold on the basal transport rate. By considering both spherical and elongated cells, we find that the lowest bound for the threshold is Emin approximately 9 x 10(-3) V m-1 (9 x 10(-5) V cm-1). Using a conservative value for the loop radius rloop = 0.3 m for induced current, the corresponding lower bound in the human body for a magnetic field exposure is Bmin approximately 6 x 10(-4) T (6 G). Unless large, organized, and electrically amplifying multicellular systems such as the ampullae of Lorenzini of elasmobranch fish are involved, these results strongly suggest that the biophysical mechanism of voltage-gated macromolecules in the membranes of cells can be ruled out as a basis of possible effects of weak ELF electric and magnetic fields in humans.

Detection of weak electric fields by sharks, rays, and skates

The elasmobranchs-sharks, rays, and skates-can detect very weak electric fields in their aqueous environment through a complex sensory system, the ampullae of Lorenzini. The ampullae are conducting tubes that connect the surface of the animal to its interior. In the presence of an electric field, the potential of the surface of the animal will differ from that of the interior and that potential is applied across the apical membrane of the special sensory cells that line the ampullae. The firing rate of the afferent neurons that transmit signals from the ampullae has been shown to vary with that potential. We show that those firing rates can be described quantitatively in terms of synchronous firing of the sensory cells that feed the neurons. We demonstrate that such synchronism follows naturally from a hypothetical weak cell-to-cell interaction that results in a self-organization of the sensory cells. Moreover, the pulse rates of those cells-and the neurons that service the cells-can be expected to vary with the imposed electric fields in accord with measured values through actions of voltage gated transmembrane proteins in the apical sector of the cell membranes that admit Ca(++) ions. We also present a more conjectural model of signal processing at the neuron level that could exploit small differences in firing rates of nerve fibers servicing different ampullae to send an unambiguous signal to the central nervous system of the animal. (c) 1998 American Institute of Physics.

Stochastic resonance at the single-cell level

Does the electricity with which we power our world pose significant health hazards from the resulting electromagnetic fields? Several authors, have speculated that ‘stochastic resonance’ — a nonlinear phenomenon in which the addition of noise to a system increases its response to an external signal — may allow biological cells to detect and respond to very weak external electric fields far below the thermal noise limit,, and thus possibly cause harmful effects. Here we examine this question using a recent theory of Bezrukov and Vodyanoy for the effect of non-equilibrium noise on a voltage detector (such as a biological ion channel). We show that with parameters appropriate for typical biological cells, adding noise does not make a far-from-detectable signal detectable.

DNA Polymerase as a Molecular Motor and Pump

DNA polymerase is responsible for synthesizing DNA, a key component in the running of biological machinery. Using fluorescence correlation spectroscopy, we demonstrate that the diffusive movement of a molecular complex of DNA template and DNA polymerase enhances during nucleotide incorporation into the growing DNA template. The diffusion coefficient of the complex also shows a strong dependence on its inorganic cofactor, Mg2+ ions. When exposed to gradients of either nucleotide or cofactor concentrations, an ensemble of DNA polymerase complex molecules shows collective movement toward regions of higher concentrations. By immobilizing the molecular complex on a patterned gold surface, we demonstrate the fabrication of DNA polymerase-powered fluid pumps. These miniature pumps are capable of transporting fluid and tracer particles in a directional manner with the pumping speed increasing in the presence of the cofactor. The role of DNA polymerase as a micropump opens up avenues for designing miniature fluid pumps using enzymes as engines.