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Biomedical subjects

S Leibler

Publications and source records attributed to S Leibler.

At least 37 records · Page 2Linked to original sources
PubMed1996

Motor protein mechanics: a stochastic model with minimal mechanochemical coupling.

A stochastic model for the action of motor proteins such as kinesin is presented. The mechanical components of the enzyme are 1) two identical head domains that bind to discrete sites on a microtubule and that are capable of undergoing a conformational change; and 2) an elastic element that connects each head to the rest of the molecule. We investigate the situation in which the strain dependence of the chemical reaction rates is minimal and the heads have independent biochemical cycles. The enzyme advances stochastically along a filament when one head detaches and diffuses to a new binding site, while the other head remains bound to the microtubule. We also investigate the case in which the chemical cycles of the heads are correlated so that the molecule shifts each head alternately. The predictions of the model are found to be in agreement with experimentally measured force-velocity relationships for kinesin-both when the force is applied externally and when the enzyme is loaded by a viscous drag. For reasonable values of the parameters, this agreement is quantitative. The molecular stepping characteristics observed in recent motility assays are also reproduced. A number of experiments are suggested that would provide a more stringent test of the model and help determine whether this simple picture is an appropriate description of motor proteins or whether models that include strain-dependent reaction rates or more complicated types of cooperation of the two heads need to be considered.

Animals↗
PubMed1996

Influence of M-phase chromatin on the anisotropy of microtubule asters.

In many eukaryotic cells going through M-phase, a bipolar spindle is formed by microtubules nucleated from centrosomes. These microtubules, in addition to being "captured" by kinetochores, may be stabilized by chromatin in two different ways: short-range stabilization effects may affect microtubules in close contact with the chromatin, while long-range stabilization effects may "guide" microtubule growth towards the chromatin (e.g., by introducing a diffusive gradient of an enzymatic activity that affects microtubule assembly). Here, we use both meiotic and mitotic extracts from Xenopus laevis eggs to study microtubule aster formation and microtubule dynamics in the presence of chromatin. In "low-speed" meiotic extracts, in the presence of salmon sperm chromatin, we find that short-range stabilization effects lead to a strong anisotropy of the microtubule asters. Analysis of the dynamic parameters of microtubule growth show that this anisotropy arises from a decrease in the catastrophe frequency, an increase in the rescue frequency and a decrease in the growth velocity. In this system we also find evidence for long-range "guidance" effects, which lead to a weak anisotropy of the asters. Statistically relevant results on these long-range effects are obtained in "high-speed" mitotic extracts in the presence of artificially constructed chromatin stripes. We find that aster anisotropy is biased in the direction of the chromatin and that the catastrophe frequency is reduced in its vicinity. In this system we also find a surprising dependence of the catastrophe and the rescue frequencies on the length of microtubules nucleated from centrosomes: the catastrophe frequency increase and the rescue frequency decreases with microtubule length.

Animals↗
PubMed1995

Diffusion and formation of microtubule asters: physical processes versus biochemical regulation.

Microtubule asters forming the mitotic spindle are assembled around two centrosomes through the process of dynamic instability in which microtubules alternate between growing and shrinking states. By modifying the dynamics of this assembly process, cell cycle enzymes, such as cdc2 cyclin kinases, regulate length distributions in the asters. It is believed that the same enzymes control the number of assembled microtubules by changing the "nucleating activity" of the centrosomes. Here we show that assembly of microtubule asters may be strongly altered by effects connected with diffusion of tubulin monomers. Theoretical analysis of a simple model describing assembly of microtubule asters clearly shows the existence of a region surrounding the centrosome depleted in GTP tubulin. The number of assembled microtubules may in some cases be limited by this depletion effect rather than by the number of available nucleation sites on the centrosome.

Animals↗
PubMed1994

Dynamic instability of microtubules as an efficient way to search in space.

During the formation of the mitotic spindle, dynamic microtubules search for chromosomes in the surrounding cytosol. The average time required to reach such "targets" is calculated within a simple model of dynamic instability. The values of the dynamic parameters that minimize this search time are also obtained. The results approximate well observations of the capture of chromosomes in prometaphase cells. Compared to usual reversible polymerization, dynamic instability reduces the time required to find a target by several orders of magnitude.

Animals↗
PubMed1993

Porters versus rowers: a unified stochastic model of motor proteins.

We present a general phenomenological theory for chemical to mechanical energy transduction by motor enzymes which is based on the classical "tight-coupling" mechanism. The associated minimal stochastic model takes explicitly into account both ATP hydrolysis and thermal noise effects. It provides expressions for the hydrolysis rate and the sliding velocity, as functions of the ATP concentration and the number of motor enzymes. It explains in a unified way many results of recent in vitro motility assays. More importantly, the theory provides a natural classification scheme for the motors: it correlates the biochemical and mechanical differences between "porters" such as cellular kinesins or dyneins, and "rowers" such as muscular myosins or flagellar dyneins.

Actins↗
PubMed1992

Control of microtubule dynamics and length by cyclin A- and cyclin B-dependent kinases in Xenopus egg extracts.

In eukaryotic cells, the onset of mitosis involves cyclin molecules which interact with proteins of the cdc2 family to produce active kinases. In vertebrate cells, cyclin A dependent kinases become active in S- and pro-phases, whereas a cyclin B-dependent kinase is mostly active in metaphase. It has recently been shown that, when added to Xenopus egg extracts, bacterially produced A- and B-type cyclins associate predominantly with the same kinase catalytic subunit, namely p34cdc2, and induce its histone H1 kinase activity with different kinetics. Here, we show that in the same cell free system, both the addition of cyclin A and cyclin B changes microtubule behavior. However, the cyclin A-dependent kinase does not induce a dramatic shortening of centrosome-nucleated microtubules whereas the cyclin B-dependent kinase does, as previously reported. Analysis of the parameters of microtubule dynamics by fluorescence video microscopy shows that the dramatic shortening induced by the cyclin B-dependent kinase is correlated with a several fold increase in catastrophe frequency, an effect not observed with the cyclin A-dependent kinase. Using a simple mathematical model, we show how the length distributions of centrosome-nucleated microtubules relate to the four parameters that describe microtubule dynamics. These four parameters define a threshold between unlimited microtubule growth and the establishment of steady-state dynamics, which implies that well defined steady-state length distributions can be produced by regulating precisely the respective values of the dynamical parameters. Moreover, the dynamical model predicts that increasing catastrophe frequency is more efficient than decreasing the rescue frequency to reduce the average steady state length of microtubules. These theoretical results are quantitatively confirmed by the experimental data.

Animals↗
PubMed1991

Computer simulations of self-assembled membranes.

Molecular dynamics simulations in three dimensions of particles that self-assemble to form two-dimensional, membrane-like objects are presented. Anisotropic, multibody forces, chosen so as to mimic real interactions between amphiphilic molecules, generate a finite rigidity and compressibility of the assembled membranes, as well as a finite line tension at their free edges. This model and its generalizations can be used to study a large class of phenomena taking place in fluctuating membranes. For instance, both fluid and solid-like phases, separated by a phase transition, are obtained and some of the large-scale properties of these membranes studied. In particular, thermal undulations of quasi-spherical fluid vesicles are analyzed, in a manner similar to recent experiments in lipid systems.

Computer Simulation↗
PubMed1991

A physical model for motor proteins.

A general stochastic theory is outlined for chemical to mechanical energy transduction by motor enzymes. In addition to ATP hydrolysis and fiber binding phenomena, thermal noise effects are taken into account. A minimal, 4-state model is identified that gives the hydrolysis rate as well as mechanical quantities such as sliding velocity and generated force, as functions of ATP concentration and the number of motors. It explains in a unified way many results of recent in vitro assays, both in myosins/actin and kinesins or dyneins/microtubule systems.

Models, Chemical↗