Biomedical subjects

Evgeny B Stukalin

Publications and source records attributed to Evgeny B Stukalin.

8 recordsLinked to original sources

PubMed2006

Minimal model of relaxation in an associating fluid: viscoelastic and dielectric relaxations in equilibrium polymer solutions.

Cluster formation and disintegration greatly complicate the description of relaxation processes in complex fluids. We systematically contrast the viscoelastic and dielectric properties for models of equilibrium polymers whose thermodynamic properties have previously been established. In particular, the monomer-mediated model allows chain growth to proceed only by monomer addition, while the scission-recombination model enables all particles to associate democratically, so that chain scission and fusion occur at the interior segments as well as at chain ends. The minimal models neglect hydrodynamic and entanglement interactions and are designed to explore systematically the competition between chemical reaction and internal chain relaxation and how this coupling modifies the dynamics from that of a polydisperse solution of Rouse chains with fixed lengths (i.e., "frozen" chains). As expected, the stress relaxation is nearly single exponential when the assembly-disassembly reaction is fast on the time scale of structural chain rearrangements, while multiexponential or nearly stretched exponential relaxation is obtained when this reaction rate is slow compared to the broad relaxation spectrum of almost unperturbed, nearly "dead" chains of intrinsically polydisperse equilibrium polymer solutions. More generally, a complicated intermediate behavior emerges from the interplay between the chemical kinetic events and internal chain motions.

Journal Article↗

PubMed2006

Transport of single molecules along the periodic parallel lattices with coupling.

General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period N are developed. Theoretical analysis that allows to calculate explicitly the steady-state dynamic properties of single molecules, such as mean velocity V and dispersion D, is presented for N=1 and N=2 models. For the systems with N>2 exact analytic expressions for the large-time dynamic properties are obtained in the limit of strong coupling between the lattices that leads to dynamic equilibrium between two parallel kinetic pathways. It is shown that for all systems dispersion is maximal when the coupling between channels is weak.

Algorithms↗

PubMed2006

Dynamic transitions in coupled motor proteins.

The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, which allows one to calculate explicitly the dynamic properties, is developed. It is shown that there are two dynamic regimes, depending on the interaction between the particles. For strong interactions the motor proteins move as one tight cluster, while for weak interactions there is no correlation in the motion of the proteins, and the particle separation increases steadily with time. The boundary between the two regimes is specified by a critical interaction that has a nonzero value only for the coupling of the asymmetric motor proteins, and it depends on the temperature and transition rates. At the critical interaction there is a change in slope for the mean velocities and a discontinuity in the dispersions of the motor proteins as a function of interactions.

Binding Sites↗

PubMed2006

ATP hydrolysis stimulates large length fluctuations in single actin filaments.

Polymerization dynamics of single actin filaments is investigated theoretically using a stochastic model that takes into account the hydrolysis of ATP-actin subunits, the geometry of actin filament tips, and the lateral interactions between the monomers as well as the processes at both ends of the polymer. Exact analytical expressions are obtained for the mean growth velocity, for the dispersion in the length fluctuations, and the nucleotide composition of the actin filaments. It is found that the ATP hydrolysis has a strong effect on dynamic properties of single actin filaments. At high concentrations of free actin monomers, the mean size of the unhydrolyzed ATP-cap is very large, and the dynamics is governed by association/dissociation of ATP-actin subunits. However, at low concentrations the size of the cap becomes finite, and the dissociation of ADP-actin subunits makes a significant contribution to overall dynamics. Actin filament length fluctuations reach a sharp maximum at the boundary between two dynamic regimes, and this boundary is always larger than the critical concentration for the actin filament's growth at the barbed end, assuming the sequential release of phosphate. Random and sequential mechanisms of hydrolysis are compared, and it is found that they predict qualitatively similar dynamic properties at low and high concentrations of free actin monomers with some deviations near the critical concentration. The possibility of attachment and detachment of oligomers in actin filament's growth is also discussed. Our theoretical approach is successfully applied to analyze the latest experiments on the growth and length fluctuations of individual actin filaments.

Actin Cytoskeleton↗

PubMed2005

Coupling of two motor proteins: a new motor can move faster.

We study the effect of a coupling between two motor domains in highly processive motor protein complexes. A simple stochastic discrete model, in which the two parts of the protein molecule interact through some energy potential, is presented. The exact analytical solutions for the dynamic properties of the combined motor species, such as the velocity and dispersion, are derived in terms of the properties of free individual motor domains and the interaction potential. It is shown that the coupling between the motor domains can create a more efficient motor protein that can move faster than individual particles. The results are applied to analyze the motion of RecBCD helicase molecules.

DNA↗

PubMed2005

Polymerization dynamics of double-stranded biopolymers: chemical kinetic approach.

The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the lateral interactions between the protofilaments. By considering all possible molecular configurations, the exact analytical expressions for the growth velocity and dispersion for two-stranded polymers are obtained in the case of the growing at only one end, and for the growth from both polymer ends. Exact theoretical calculations are compared with the predictions of approximate multilayer models that consider only a finite number of the most relevant polymer configurations. Our theoretical approach is applied to analyze the experimental data on the growth and fluctuations dynamics of individual single actin filaments.

Journal Article↗

PubMed2005

Understanding mechanochemical coupling in kinesins using first-passage-time processes.

Kinesins are processive motor proteins that move along microtubules in a stepwise manner, and their motion is powered by the hydrolysis of ATP. Recent experiments have investigated the coupling between the individual steps of single kinesin molecules and ATP hydrolysis, taking explicitly into account forward steps, backward steps, and detachments. A theoretical study of mechanochemical coupling in kinesins, which extends the approach used successfully to describe the dynamics of motor proteins, is presented. The possibility of irreversible detachments of kinesins from the microtubules is explicitly taken into account. Using the method of first-passage times, experimental data on the mechanochemical coupling in kinesins are fully described using the simplest two-state model. It is shown that the dwell times for the kinesin to move one step forward or backward, or to dissociate irreversibly, are the same, although the probabilities of these events are different. It is concluded that the current theoretical view-that only the forward motion of the motor protein molecule is coupled to ATP hydrolysis--is consistent with all available experimental observations for kinesins.

Adenosine Triphosphate↗

PubMed2004

Simple growth models of rigid multifilament biopolymers.

The growth dynamics of rigid biopolymers, consisting of N parallel protofilaments, is investigated theoretically using simple approximate models. In our approach, the structure of a polymer's growing end and lateral interactions between protofilaments are explicitly taken into account, and it is argued that only few configurations are important for a biopolymer's growth. As a result, exact analytic expressions for growth velocity and dispersion are obtained for any number of protofilaments and arbitrary geometry of the growing end of the biopolymer. Our theoretical predictions are compared with a full description of biopolymer growth dynamics for the simplest N=2 model. It is found that the results from the approximate theory are approaching the exact ones for large lateral interactions between the protofilaments. Our theory is also applied to analyze the experimental data on the growth of microtubules.

Biopolymers↗