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A Vologodskii

Publications and source records attributed to A Vologodskii.

11 recordsLinked to original sources
PubMed2001

Cooperative helix stabilization by complex Arg-Glu salt bridges.

Among the interactions that stabilize the native state of proteins, the role of electrostatic interactions has been difficult to quantify precisely. Surface salt bridges or ion pairs between acidic and basic side chains have only a modest stabilizing effect on the stability of helical peptides or proteins: estimates are roughly 0.5 kcal/mol or less. On the other hand, theoretical arguments and the occurrence of salt bridge networks in thermophilic proteins suggest that multiple salt bridges may exert a stronger stabilizing effect. We show here that triads of charged side chains, Arg(+)-Glu(-)-Arg(+) spaced at i,i+4 or i,i+3 intervals in a helical peptide stabilize alpha helix by more than the additive contribution of two single salt bridges. The free energy of the triad is more than 1 kcal/mol in excess of the sum of the individual pairs, measured in low salt concentration (10 mM). The effect of spacing the three groups is severe; placing the charges at i,i+4 or i,i+3 sites has a strong effect on stability relative to single bridges; other combinations are weaker. A conservative calculation suggests that interactions of this kind between salt bridges can account for much of the stabilization of certain thermophilic proteins.

Alanine↗
PubMed2001

Dynamics of site juxtaposition in supercoiled DNA.

Juxtaposition kinetics between specific sites in supercoiled DNA is investigated at close to physiological ionic conditions by Brownian dynamics simulations. At such conditions, supercoiled DNA is interwound, and the probability of spatial site juxtaposition is much higher than in relaxed DNA. We find, however, that supercoiling does not correspondingly increase the rate of juxtaposition at these physiological conditions. An explanation to this unexpected finding emerges on analysis of the juxtaposition dynamics. We note that although a particular site i(1) in supercoiled DNA is often in close proximity (juxtaposed) to another site i(2), the change of i(2) occurs very slowly and depends largely on internal slithering of opposite segments of the DNA superhelix. Such slithering results in long correlations between successive values of i(2); these correlations increase the average time of juxtaposition between two DNA sites. Random collisions between sites located on different superhelix branches-although increasing in importance with DNA size-contribute less substantially to site juxtaposition at high salt than slithering for DNA up to 6 kb in length.

Algorithms↗
PubMed2000

Multimerization-cyclization of DNA fragments as a method of conformational analysis.

Ligation of short DNA fragments results in the formation of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or by the presence of irregular structural elements. We have developed a more rigorous quantitative approach to the analysis of such experimental data based on determination of j-factors for different multimers from the distribution of the reaction products. j-Factors define the effective concentration of one end of a linear chain in the vicinity of the other end. To extract j-factors we assumed that kinetics of the reaction is described by a system of differential equations where j-factors appear as coefficients. The assumption was confirmed by comparison with experimental data obtained here for DNA fragments containing A-tracts. At the second step of the analysis j-factors are used to determine conformational parameters of DNA fragments: the equilibrium bend angle, the bending rigidity of the fragment axis, and the total twist of the fragments. This procedure is based on empirical equations that connect the conformational parameters with the set of j-factors. To obtain the equations, we computed j-factors for a large array of conformational parameters that describe model fragments. The approach was tested on both simulated and actual experimental data for DNA fragments containing A-tracts. A-tract DNA bend angle determined here is in good agreement with previously published data. We have established a set of experimental conditions necessary for the data analysis to be successful.

Base Sequence↗
PubMed2000

Tightness of random knotting.

Long polymers in solution frequently adopt knotted configurations. To understand the physical properties of knotted polymers, it is important to find out whether the knots formed at thermodynamic equilibrium are spread over the whole polymer chain or rather are localized as tight knots. We present here a method to analyze the knottedness of short linear portions of simulated random chains. Using this method, we observe that knot-determining domains are usually very tight, so that, for example, the preferred size of the trefoil-determining portions of knotted polymer chains corresponds to just seven freely jointed segments.

Models, Molecular↗
PubMed1999

Large-scale effects of transcriptional DNA supercoiling in vivo.

The scale of negative DNA supercoiling generated by transcription in Top(+) Escherichia coli cells was assessed from the efficiency of cruciform formation upstream of a regulated promoter. An increase in negative supercoiling upon promoter induction led to cruciform formation, which was quantitatively measured by chemical probing of intracellular DNA. By placing a cruciform-forming sequence at varying distances from the promoter, we found that the half-dissociation length of transcription supercoiling wave is approximately 800 bp. This is the first proof that transcription can affect DNA structure on such a remarkably large scale in vivo. Moreover, cooperative binding of the cI repressor to the upstream promoter DNA did not preclude efficient diffusion of transcriptional supercoiling. Finally, our plasmids appeared to contain discrete domains of DNA supercoiling, defined by the features and relative orientation of different promoters.

Chloramphenicol↗
PubMed1998

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition.

Thermal motions in supercoiled DNA are studied by Brownian dynamics (BD) simulations with a focus on the site juxtaposition process. It had been shown in the last decade that the BD approach is capable of describing actual times of large-scale DNA motion. The bead model of DNA used here accounts for bending and torsional elasticity as well as the electrostatic repulsion among DNA segments. The hydrodynamic interaction among the beads of the model chain and the aqueous solution is incorporated through the Rotne-Prager tensor. All simulations were performed for the sodium ion concentration of 0.01 M. We first showed, to test our BD procedure, that the same distributions of equilibrium conformational properties are obtained as by Monte Carlo simulations for the corresponding DNA model. The BD simulations also predict with accuracy published experimental values of the diffusion coefficients of supercoiled DNA. To describe the rate of conformational changes, we also calculated the autocorrelation functions for the writhe and radius of gyration for the supercoiled molecules. The rate of site juxtaposition was then studied for DNA molecules up to 3000 bp in length. We find that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules. By inspecting successive simulated conformations of supercoiled DNA, we conclude that slithering of opposing segments of the interwound superhelix is not an efficient mechanism to accomplish site juxtaposition, at least for conditions of low salt concentration. Instead, transient distortions of the interwound superhelix, followed by continuous reshaping of the molecule, contribute more significantly to site juxtaposition kinetics.

Algorithms↗
PubMed1997

The effect of intrinsic curvature on conformational properties of circular DNA.

Both thermal fluctuations and the intrinsic curvature of DNA contribute to conformations of the DNA axis. We looked for a way to estimate the relative contributions of these two components of the double-helix curvature for DNA with a typical sequence. We developed a model and Monte Carlo procedure to simulate the Boltzmann distribution of DNA conformations with a specific intrinsic curvature. Two steps were used to construct the equilibrium conformation of the model chain. We first specified the equilibrium DNA conformation at the base pair level of resolution, using a set of the equilibrium dinucleotide angles and DNA sequence. This conformation was then approximated by the conformation of the model chain consisting of a reduced number of longer, straight cylindrical segments. Each segment of the chain corresponded to a certain number of DNA base pairs. We simulated conformational properties of nicked circular DNA for different sets of equilibrium dinucleotide angles, different random DNA sequences, and lengths. Only random sequences of DNA generated with equal probability of appearance for all types of bases at any site of the sequence were used. The results showed that for a broad range of intrinsic curvature parameters, the radius of gyration of DNA circles should be nearly independent of DNA sequence for all DNA lengths studied. We found, however, a DNA properly that should strongly depend on DNA sequence if the double helix has essential intrinsic curvature. This property is the equilibrium distribution of the linking number for DNA circles that are 300-1000 bp in length. We found that a large fraction of the distributions corresponding to random DNA sequences should have two separate maxima. The physical nature of this unexpected effect is discussed. This finding opens new opportunities for joined experimental and theoretical studies of DNA intrinsic curvature.

Computer Simulation↗
PubMed1996

Effect of supercoiling on the juxtaposition and relative orientation of DNA sites.

There are many proteins that interact simultaneously with two or more DNA sites that are separated along the DNA contour. These sites must be brought close together to form productive complexes with the proteins. We used Monte Carlo simulation of supercoiled DNA conformations to study the effect of supercoiling and DNA length on the juxtaposition of DNA sites, the angle between them, and the branching of the interwound superhelix. Branching decreases the probability of juxtaposition of two DNA sites but increases the probability of juxtaposition of three sites at branch points. We found that the number of superhelix branches increases linearly with the length of DNA from 3 to 20 kb. The simulations showed that for all contour distances between two sites, the juxtaposition probability in supercoiled DNA is two orders of magnitude higher than in relaxed DNA. Supercoiling also results in a strong asymmetry of the angular distribution of juxtaposed sites. The effect of supercoiling on site-specific recombination and the introduction of supercoils by DNA gyrase is discussed in the context of the simulation results.

Binding Sites↗
PubMed1995

Modeling of long-range electrostatic interactions in DNA.

We used a Monte Carlo approach to compute the statistical properties of closed DNA chains with different descriptions of the electrostatic interactions. We compared these computed results with experimentally measured knotting probabilities, which are very sensitive to intersegment interactions. The calculated results based on the Debye-Hückel approximation of the solution of the Poisson-Boltzmann equation agreed very well with the published experimental data, while potential based on counterion condensation theory was clearly less satisfactory. We then compared the simpler hard-core approximation of electrostatic interactions to the Debye-Hückel potential. The hard-core approximation, specified in terms of a DNA effective diameter, gives the same conformational properties of random coils as the Debye-Hückel approximation. We found clear but relatively small differences between the two potentials for the conformational properties of supercoiled DNA.

DNA↗
PubMed1976

On the character of the thermodynamic properties distribution in DNA molecules inside the melting interval.

The variances of the distributions of DNA molecules over the degree of helicity and over the number of unwound regions inside the melting interval are calculated. The variance over the degree of helicity is expessed in terms of the values directly available from the experimental data. For the variance over the number of unwound regions a simple interpolation formula based on the machine calculations is proposed. Possible applications of the results obtained to interpolaation of the electron microscopic denaturation maps of DNA are discussed.

DNA↗