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Biomedical subjects

B I Shklovskii

Publications and source records attributed to B I Shklovskii.

12 recordsLinked to original sources

How does a protein search for the specific site on DNA: The role of disorder.

Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to nonspecific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such a one-dimensional route towards the target an "antenna." We studied the role of the dispersion of nonspecific binding energies within the antenna due to a quasirandom sequence of natural DNA. A random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for macroscopic and mesoscopic antennas.

Adsorption↗

Ion exchange phase transitions in water-filled channels with charged walls.

Ion transport through narrow water-filled channels is impeded by a high electrostatic barrier. The latter originates from the large ratio of the dielectric constants of the water and the surrounding media. We show that "doping," i.e., immobile charges attached to the walls of the channel, substantially reduces the barrier. This explains why most of the biological ion channels are "doped." We show that at rather generic conditions the channels may undergo ion exchange phase transitions (typically of the first order). Upon such a transition a finite latent concentration of ions may either enter or leave the channel, or be exchanged between the ions of different valences. We discuss possible implications of these transitions for the Ca-vs-Na selectivity of biological Ca channels. We also show that transport of divalent Ca ions is assisted by their fractionalization into two separate excitations.

Journal Article↗

How proteins search for their specific sites on DNA: the role of DNA conformation.

It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.

DNA↗

Conductance of ion channels and nanopores with charged walls: a toy model.

We consider ion transport through protein ion channels in lipid membranes and water-filled nanopores in silicon films. It is known that, due to the large ratio of dielectric constants of water and the surrounding material, an ion placed inside the channel faces a large electrostatic self-energy barrier. The barrier leads to an exponentially large resistance of the channel. We study reduction of the electrostatic barrier by immobile charges located on the internal walls of the channel. We show that the barrier practically vanishes already at relatively small concentration of wall charges.

Biophysics↗

Long-range polarization attraction between two different like-charged macroions.

It is known that in a water solution with multivalent counterions (Z-ions) two likely charged macroions can attract each other due to correlations of Z-ions adsorbed on their surfaces. This "correlation" attraction is short ranged and decays exponentially with increasing distance between macroions at characteristic distance A/2pi , where A is the average distance between Z -ions on the surfaces of macroions. In this work, we show that an additional long-range "polarization" attraction exists when the bare surface charge densities of the two macroions have the same sign, but are different in absolute values. The key idea is that with adsorbed Z -ions, two insulating macroions can be considered as conductors with fixed but different electric potentials. Each potential is determined by the difference between the entropic bulk chemical potential of a Z -ion and its correlation chemical potential at the surface of the macroion determined by its bare surface charge density. When the two macroions are close enough, they get polarized in such a way that their adjacent spots form a charged capacitor, which leads to attraction. In a salt-free solution this polarization attractive force is long ranged: it decays as a power of the distance between the surfaces of two macroions, d. The polarization force decays slower than the van der Waals attraction and therefore is much larger than it in a large range of distances. In the presence of large amount of monovalent salt, the polarization attraction decays exponentially at d larger than the Debye-Hückel screening radius r(s) . Still, when A/2pi<<d<<r(s), this force is much stronger than the van der Waals attraction and the correlation attraction mentioned above. The recent atomic force experiment has shown evidence for this polarization attraction.

Journal Article↗

Phase diagram of aggregation of oppositely charged colloids in salty water.

Aggregation of two oppositely charged colloids in salty water is studied. We focus on the role of Coulomb interaction in strongly asymmetric systems in which the charge and size of one colloid is much larger than the other one. In the solution, each large colloid (macroion) attracts a certain number of oppositely charged small colloids (Z-ion) to form a complex. If the concentration ratio of the two colloids is such that complexes are not strongly charged, they condense in a macroscopic aggregate. As a result, the phase diagram in a plane of concentrations of two colloids consists of an aggregation domain sandwiched between two domains of stable solutions of complexes. The aggregation domain has a central part of total aggregation and two wings corresponding to partial aggregation. A quantitative theory of the phase diagram in the presence of monovalent salt is developed. It is shown that as the Debye-Hückel screening radius r(s) decreases, the aggregation domain grows, but the relative size of the partial aggregation domains becomes much smaller. As an important application of the theory, we consider solutions of long double-helix DNA with strongly charged positive spheres (artificial chromatin). We also consider implications of our theory for in vitro experiments with the natural chromatin. Finally, the effect of different shapes of macroions on the phase diagram is discussed.

Binding Sites↗

Persistence length of a polyelectrolyte in salty water: Monte Carlo study.

We address the long standing problem of the dependence of the electrostatic persistence length l(e) of a flexible polyelectrolyte (PE) on the screening length r(s) of the solution within the linear Debye-Hückel theory. The standard Odijk, Skolnick, and Fixman (OSF) theory suggests l(e) proportional, variant r(2)s, while some variational theories and some computer simulations suggest l(e) proportional, variant r(s). In this paper, we use Monte Carlo simulations to study the conformation of a simple polyelectrolyte. Using four times longer PEs than in previous simulations and refined methods for the treatment of the simulation data, we show that the results are consistent with the OSF dependence l(e) proportional, variant r(2)s. The linear charge density of the PE, which enters in the coefficient of this dependence is properly renormalized to take into account local fluctuations.

Journal Article↗

Model of inversion of DNA charge by a positive polymer: fractionalization of the polymer charge.

We model one strand of DNA by a one-dimensional lattice (ODL) of negative charges and consider the problem of inversion of its charge by a positive polyelectrolyte (PE). In the neutral state of the ODL-PE complex, each of the ODL charges is locally compensated by a PE charge. When an additional PE molecule is adsorbed by ODL, its charge gets fractionalized into monomer charges of defects (tails and arches) on the background of the perfectly neutralized ODL. Defects spread all over the ODL, eliminating the self-energy of PE. For DNA this fractionalization mechanism leads to a substantial inversion of charge, a phenomenon which is widely used for gene delivery.

DNA↗

Kinetics of macroion coagulation induced by multivalent counterions.

Due to the strong correlations between multivalent counterions condensed on a macroion, the net macroion charge changes sign at some critical counterion concentration. This effect is known as the charge inversion. Near this critical concentration the macroion net charge is small. Therefore, short range attractive forces between macroions dominate Coulomb repulsion and lead to their coagulation. The kinetics of macroion coagulation in this range of counterion concentrations is studied. We calculate the Coulomb barrier between two approaching like charged macroions at a given counterion concentration. Two different macroion shapes (spherical and rodlike) are considered. A new "self-regulated" regime of coagulation is found. As the size of aggregates increases, their charge and Coulomb barrier also grow and diminish the sticking probability of aggregates. This leads to a slow, logarithmic increase of the aggregate size with time.

Journal Article↗

Adsorption of charged particles on an oppositely charged surface: oscillating inversion of charge.

Adsorption of multivalent counterions on the charged surface of a macroion is known to lead to inversion of the macroion charge due to the strong lateral correlations of counterions. We consider a nontrivial role of the excluded volume of counterions on this effect. It is shown analytically that when the bare charge of the macroion increases, its net charge including the adsorbed counterions oscillates with the number of their layers. Charge inversion vanishes every time the top layer of counterions is completely full and becomes incompressible. These oscillations of charge inversion are confirmed by Monte Carlo simulations. Another version of this phenomenon is studied for a metallic electrode screened by multivalent counterions when the potential of the electrode is controlled instead of its charge. In this case, oscillations of the compressibility and charge inversion lead to oscillations of capacitance of this electrode with the number of adsorbed layers of multivalent counterions.

Journal Article↗

Screening of a macroion by multivalent ions: correlation-induced inversion of charge.

Screening of a strongly charged macroion by multivalent counterions is considered. It is shown that counterions form a strongly correlated liquid at the surface of the macroion. Cohesive energy of this liquid leads to additional attraction of counterions to the surface, which is absent in conventional solutions of the Poisson-Boltzmann equation. Away from the surface this attraction can be taken into account by a new boundary condition for the concentration of counterions near the surface. The Poisson-Boltzmann equation is solved with this boundary condition for a charged flat surface, a cylinder, and a sphere. In all three cases, screening is much stronger than in the conventional approach. At some critical exponentially small concentration of multivalent counterions in the solution, they totally neutralize the surface charge at small distances from the surface. At larger concentrations they invert the sign of the net macroion charge. The absolute value of the inverted charge density can be as large as 20% of the bare one. In particular, for a cylindrical macroion it is shown that for screening by multivalent counterions, predictions of the Onsager-Manning theory are quantitatively incorrect. The net charge density of the cylinder is smaller than their theory predicts and inverts the sign with a growing concentration of counterions. Moreover, the condensation loses its universality and the net charge linear density depends on the bare one.

Journal Article↗

Negative electrostatic contribution to the bending rigidity of charged membranes and polyelectrolytes screened by multivalent counterions.

Bending rigidity of a charged membrane or polyelectrolyte screened by monovalent counterions is known to be enhanced by electrostatic effects. We show that in the case of screening by multivalent counterions the electrostatic effects reduce the bending rigidity. This inversion of the sign of the electrostatic contribution is related to the formation of two-dimensional strongly correlated liquids (SCL) of counterions at the charged surface due to strong lateral repulsion between them. When a membrane or a polyelectrolyte is bent, SCL is compressed on one side and stretched on the other so that thermodynamic properties of SCL contribute to the bending rigidity. Thermodynamic properties of SCL are similar to those of Wigner crystal and are anomalous in the sense that the pressure, compressibility and screening radius of SCL are negative. This brings about substantial negative correction to the bending rigidity. For the case of DNA this effect qualitatively agrees with experiment.

Cations↗