Biomedical subjects

A E Carlsson

Publications and source records attributed to A E Carlsson.

15 recordsLinked to original sources

PubMed2006

Energetics and dynamics of constrained actin filament bundling.

The formation of filopodia-like bundles from a dendritic actin network has been observed to occur in vitro as a result of branching induced by Arp2/3 complex. We study both the energetics and dynamics of actin filament bundling in such a network to evaluate their relative importance in bundle formation processes. Our model considers two semiflexible actin filaments fixed at one end and free at the other, described using a normal-mode approximation. This model is studied by both Brownian dynamics and free-energy minimization methods. Remarkably, even short filaments can bundle at separations comparable to their lengths. In the dynamic simulations, we evaluate the time required for the filaments to interact and bind, and examine the dependence of this bundling time on the filament length, the distance between the filament bases, and the cross-linking energy. In most cases, bundling occurs in a second or less. Beyond a certain critical distance, we find that the bundling time increases very rapidly with increasing interfilament separation and/or decreasing filament length. For most of the cases we have studied, the energetics results for this critical distance are similar to those obtained from dynamics simulations run for 10 s, suggesting that beyond this timescale, energetics, rather than kinetic constraints, determine whether or not bundling occurs. Over a broad range of conditions, we find that the times required for bundling from a network are compatible with experimental observations.

Actin Cytoskeleton↗

PubMed2006

Growth of attached actin filaments.

In several studies of actin-based cellular motility, the barbed ends of actin filaments have been observed to be attached to moving obstacles. Filament growth in the presence of such filament-obstacle interactions is studied via Brownian dynamics simulations of a three-dimensional energy-based model. We find that with a binding energy greater than 24k B T and a highly directional force field, a single actin filament is able to push a small obstacle for over a second at a speed of half of the free filament elongation rate. These results are consistent with experimental observations of plastic beads in cell extracts. Calculations of an external force acting on a single-filament-pushed obstacle show that for typical in vitro free-actin concentrations, a 3pN pulling force maximizes the obstacle speed, while a 4pN pushing force almost stops the obstacle. Extension of the model to treat beads propelled by many filaments suggests that most of the propulsive force could be generated by attached filaments.

Actin Cytoskeleton↗

PubMed2005

Stimulation of actin polymerization by filament severing.

The extent and dynamics of actin polymerization in solution are calculated as functions of the filament severing rate, using a simple model of in vitro polymerization. The model is solved by both analytic theory and stochastic-growth simulation. The results show that severing essentially always enhances actin polymerization by freeing up barbed ends, if barbed-end cappers are present. Severing has much weaker effects if only pointed-end cappers are present. In the early stages of polymerization, the polymerized-actin concentration grows exponentially as a function of time. The exponential growth rate is given in terms of the severing rate, and the latter is given in terms of the maximum slope in a polymerization time course. Severing and branching are found to act synergistically.

Actin Depolymerizing Factors↗

PubMed2005

The effect of branching on the critical concentration and average filament length of actin.

The dependences of the steady-state critical concentration and average filament length of actin solutions, on the filament branching and capping rates, are calculated using a rate methodology based on the total number of actin filaments. The methodology generalizes calculations of the "treadmilling" actin concentration at which an average filament has net zero growth rate. The predictions of the rate methodology are validated by comparison with stochastic-growth simulations that track the positions of all filament subunits over time. For side branching, the critical concentration drops proportionally to the square root of the branching rate; for end branching the drop is linear. The polymerization response to branching has a maximum as a function of the capping-protein concentration. The average filament length drops with increasing branching, because the critical concentration drops. Even small rates of filament uncapping have a large impact on the average filament length in vitro. The potential significance of these phenomena for cell behavior is evaluated.

Actin Cytoskeleton↗

PubMed2004

Kinetics of filament bundling with attractive interactions.

We study the kinetics of filament bundling by variable time-step Brownian-dynamics simulations employing a simplified attractive potential based on earlier atomic-level calculations for actin filaments. Our results show that collisions often cluster in time, due to memory in the random walk. The clustering increases the bundling opportunities. Small-angle collisions and collisions with short center-to-center distance are more likely to lead to bundling. Increasing the monomer-monomer attraction decreases the bundling time to a diffusional limit, which is determined by the capture cross-section and diffusion coefficients. The simulations clearly show that the bundling process consists of two sequential phases: rotation, by which two filaments align parallel to each other; and sliding, by which they maximize their contact length. Whether two filaments bundle or not is determined by the competition between rotation to a parallel state and escape. Increasing the rotational diffusion coefficient and attraction enhances rotation; decreasing attraction and increasing the translational diffusion coefficients enhance escape. Because of several competing effects, the filament length only affects the bundling time weakly.

Actin Cytoskeleton↗

PubMed2004

Structure of autocatalytically branched actin solutions.

The average branching number and cluster size in branched actin solutions with filament capping are evaluated using analytic theory and simulation methods. The average number of daughter branches per filament in steady state is much less than unity, regardless of the concentration of branching stimulant. Much more highly branched structures are obtained in the initial stages of polymerization.

Actin Cytoskeleton↗

PubMed2004

Model study of protein unfolding by interfaces.

We study interface-induced protein unfolding on hydrophobic and polar interfaces by means of a two-dimensional lattice model and an exhaustive enumeration ground-state structure search, for a set of model proteins of length 20 residues. We compare the effects of the two types of interfaces, and search for criteria that influence the retention of a protein's native-state structure upon adsorption. We find that the unfolding proceeds by a large, sudden loss of native contacts. The unfolding at polar interfaces exhibits similar behavior to that at hydrophobic interfaces but with a much weaker interface coupling strength. Further, we find that the resistance of proteins to unfolding in our model is positively correlated with the magnitude of the folding energy in the native-state structure, the thermal stability (or energy gap) for that structure, and the interface energy for native-state adsorption. We find these factors to be of roughly equal importance.

Adsorption↗

PubMed2004

End versus side branching by Arp2/3 complex.

We investigate the issue of end versus side branching of actin filaments by Arp2/3 complex, using a combination of analytic theory, polymerization assays, and quantitative modeling. The analytic theory shows that the effect of capping protein on the initial stages of actin polymerization in the presence of Arp2/3 complex depends strongly on whether new Arp2/3 complex-induced branches grow from the sides or ends of existing filaments. Motivated by these results, we measure and quantitatively model the kinetics of actin polymerization in the presence of activated Arp2/3 complex, for a range of concentrations of capping protein. Our model includes the most important types of events involving actin and actin-binding proteins, and can be adjusted to include end branching, side branching, or both. The side-branching model gives a better fit to the experimental data than the end-branching model. An end-plus-side model including both types of branching gives a moderate improvement in the quality of the fit. Another side-branching model, based on aging of subunits' capacity for branch formation, gives a significantly better fit than the end-plus-side model. We discuss implications for actin polymerization in cells.

Actin Cytoskeleton↗

PubMed2003

Growth velocities of branched actin networks.

The growth of an actin network against an obstacle that stimulates branching locally is studied using several variants of a kinetic rate model based on the orientation-dependent number density of filaments. The model emphasizes the effects of branching and capping on the density of free filament ends. The variants differ in their treatment of side versus end branching and dimensionality, and assume that new branches are generated by existing branches (autocatalytic behavior) or independently of existing branches (nucleation behavior). In autocatalytic models, the network growth velocity is rigorously independent of the opposing force exerted by the obstacle, and the network density is proportional to the force. The dependence of the growth velocity on the branching and capping rates is evaluated by a numerical solution of the rate equations. In side-branching models, the growth velocity drops gradually to zero with decreasing branching rate, while in end-branching models the drop is abrupt. As the capping rate goes to zero, it is found that the behavior of the velocity is sensitive to the thickness of the branching region. Experiments are proposed for using these results to shed light on the nature of the branching process.

Actin Depolymerizing Factors↗

PubMed2003

Multiscale study of counterion-induced attraction and bundle formation of F-actin using an Ising-like mean-field model.

An Ising-like counterion-binding model is developed and solved by a mean-field method. For G-actin, the calculated affinity constants of all the binding sites ranging from loose to tight binding match the experimental data. The model is used to calculate the interaction energy between two F-actin filaments. Within a certain counterion concentration range, a rapidly decaying attractive force between two parallel filaments is produced not only by the correlation of the counterion distributions on the two filaments, but also by the correlation of the configurations of the two filaments with fixed counterion positions, which has been ignored in previous calculations. The bundling energy depends strongly on the configuration of the filaments. Upon bundling, the tightly bound counterion site is not affected, but the medium and loosely bound ones are. The model reproduces the observed minimal divalent counterion concentration for bundling, and naturally predicts the resolubilization of bundles which is seen in recent experiments. At the optimal counterion concentration, we obtain a bundling energy of approximately -0.01 eV per monomer along the filament. The counterion valence strongly affects the optimal counterion concentration, but has only minor effects on the optimal bundling energy. We show that the attractive potential between filaments can be simplified as the sum of interactions between their monomers. This simplification makes it possible to calculate the exact free energy of a two-F-actin-filament system. We are thus able to probe the effects of filament length on F-actin bundling and obtain a critical length for bundling of 59 monomers at 1 microM monomer concentration and pH=7.2.

Actin Cytoskeleton↗

PubMed2002

Quantitative analysis of actin patch movement in yeast.

To investigate the mechanism of cortical actin patch movement in yeast, we implement a method for computer tracking the motion of the patches. Digital images from fluorescence microscope movies of living cells are fed into an image-processing program, which generates two-dimensional patch coordinates in the plane of focus for each movie frame via an algorithm based on detection of rapid intensity variations. The patch coordinates in neighboring frames are connected by a minimum-distance algorithm. The method is used to analyze control cells and cells treated with the actin-depolymerizing agent latrunculin. The motion of the patches in both cases, as analyzed by mean-square patch displacements, is found to be a random walk on average, with a much lower diffusion coefficient for the latrunculin-treated cells. The mean-squared patch travel distances for all of the latrunculin-treated cells are lower than those for all of the control cells. The patches move independently of one another. We develop a quantitative criterion for the presence of directed motion, and show that numerous patches in the control cells display directed motion to a very high degree of certainty. A small number of patches in the latrunculin-treated cells display directed motion.

Actins↗

PubMed2001

The functional form of angular forces around transition metal ions in biomolecules.

A method for generating angular forces around sigma-bonded transition metal ions is generalized to treat pi-bonded configurations. The theoretical approach is based on an analysis of ligand-field and small-cluster Hamiltonians based on the moments of the electron state distribution. The functional forms that are obtained involve a modification of the usual expression of the binding energy as a sum of ligand-ligand interactions, which, however, requires very little increase in CPU time. The angular interactions have simple forms involving sin and cos functions, whose relative weights depend on whether the ligands are sigma- or pi-bonded. They describe the ligand-field stabilization energy to an accuracy of about 10%, and the interaction energy of covalently bonded systems to an accuracy of better than 4%. The resulting functional forms for the force field are used to model the structure of small clusters, including fragments of the copper blue protein structure. Large deviations from the typical square copper coordination are found when pi-bonded ligands are present.

DNA↗

PubMed2001

Growth of branched actin networks against obstacles.

A method for simulating the growth of branched actin networks against obstacles has been developed. The method is based on simple stochastic events, including addition or removal of monomers at filament ends, capping of filament ends, nucleation of branches from existing filaments, and detachment of branches; the network structure for several different models of the branching process has also been studied. The models differ with regard to their inclusion of effects such as preferred branch orientations, filament uncapping at the obstacle, and preferential branching at filament ends. The actin ultrastructure near the membrane in lamellipodia is reasonably well produced if preferential branching in the direction of the obstacle or barbed-end uncapping effects are included. Uncapping effects cause the structures to have a few very long filaments that are similar to those seen in pathogen-induced "actin tails." The dependence of the growth velocity, branch spacing, and network density on the rate parameters for the various processes is quite different among the branching models. An analytic theory of the growth velocity and branch spacing of the network is described. Experiments are suggested that could distinguish among some of the branching models.

Actin Depolymerizing Factors↗

PubMed2000

Force-velocity relation for growing biopolymers.

The process of force generation by the growth of biopolymers is simulated via a Langevin-dynamics approach. The monomer-monomer interaction forces are taken to have simple forms that favor the growth of straight fibers from solution, and they are taken to grow against a flat obstacle. The force-velocity relation is obtained from the simulations for two versions of the monomer-monomer force field. We evaluate corrections to the simplest analytic theory based on thermal motion of the obstacle, which yields an exponential velocity decay with applied force. For most orientations of the growing fiber tip, the corrections are small. However, for orientations in which the surface of the growing fiber is parallel to the obstacle, large corrections are obtained in the direction of reduced fiber velocity. These results are explained on the basis of the diffusion properties of monomers near the fiber tip. It is also found that the mobility of the obstacle has little effect on the growth rate over a broad range of possible values.

Actins↗

PubMed1999

Simplified calculation of folding energies and residue coordination numbers in random heteropolymers.

I develop a formalism for calculating effective pair and higher-order interactions between residues in random heteropolymers that approximately predict the folding enthalpy and the coordination numbers of individual residues. In a simple model heteropolymer with additive couplings between residues, the folding enthalpy is written in terms of two-, three-, and four-body interactions between residues. The coordination numbers are expressed in terms of interactions between up to three residues. Application to a 6x6 square model shows that the folding enthalpy is obtained to an accuracy of better than 1%. The coordination numbers are obtained with a rms error of 1.2 neighbors.

Biopolymers↗