Adhesive dynamics simulation of neutrophil arrest with deterministic activation

The transition from rolling to firm adhesion is a key element of neutrophil activation and essential to the inflammatory response. Although the molecular mediators of rolling and firm adhesion are known to be selectins and beta2 -integrins, respectively, the precise dynamic mechanism by which these ligands facilitate neutrophil arrest remains unknown. Recently, it has been shown that ligation of E-selectin can stimulate the firm adhesion of neutrophils via a MAP-kinase cascade. To study the possible mechanism by which neutrophil arrest could occur, we created an integrated model by combining two methodologies from computational biology: a mechanics-based modeling of leukocyte adhesion (adhesive dynamics) and signal transduction pathway modeling. Within adhesive dynamics, a computational method our group has shown to accurately recreate rolling dynamics, we include a generic, tunable integrin activation module that links selectin engagement to integrin and activity. This model allows us to relate properties of the activation function to the dynamics of rolling and the time and distance rolled before arrest. This integrated model allows us to understand how intracellular signaling activity can set the timescale of neutrophil activation, adhesion, and diapedesis.     

Adhesive dynamics simulations of the mechanical shedding of L-selectin from the neutrophil surface

Here we accurately recreate the mechanical shedding of L-selectin and its effect on the rolling behavior of neutrophils in vitro using the adhesive dynamics simulation by incorporating the shear-dependent shedding of L-selectin. We have previously shown that constitutively expressed L-selectin is cleaved from the neutrophil surface during rolling on a sialyl Lewis x-coated planar surface at physiological shear rates without the addition of exogenous stimuli. Utilizing a Bell-like model to describe a shedding rate which presumably increases exponentially with force, we were able to reconstruct the characteristics of L-selectin-mediated neutrophil rolling observed in the experiments. First, the rolling velocity was found to increase during rolling due to the mechanical shedding of L-selectin. When most of the L-selectin concentrated on the tips of deformable microvilli was cleaved by force exerted on the L-selectin bonds, the cell detached from the reactive plane to join the free stream as observed in the experiments. In summary, we show through detailed computational modeling that the force-dependent shedding of L-selectin can explain the rolling behavior of neutrophils mediated by L-selectin in vitro.     

Eradication-resolution dynamics with stochastic flare-ups

In infectious disease as well as in cancer, the ultimate outcome of the curative response, mediated by the body itself or through drug treatment, is either successful eradication or a resurgence of the disease (“flare-up” or “relapse”), depending on random fluctuations that dominate the dynamics of the system when the number of diseased cells has become very low. The presence of a low-numbers bottle-neck in the dynamics, which is unavoidable if eradication is to take place at all, renders at least one phase of the dynamics essentially stochastic. However, the eradicating agents (e.g. immune cells, drug molecules) generally remain at high numbers during the critical bottle-neck phase, sufficiently so to warrant a deterministic treatment. This leads us to consider a hybrid stochastic-deterministic approach where the infected cells are treated stochastically whereas the eradicating agents are treated deterministically. Exploiting the fact that the number of eradicating agents typically decreases monotonically during the resolution phase of the response, we derive a set of coupled first-order differential equations that describe the probability of ultimate eradication as a function of the system's state, and we consider a number of biomedical applications.     

Evolutionary dynamics of fearfulness and boldness: a stochastic simulation model

A stochastic simulation model is investigated for the evolution of anti-predator behavior in birds. The main goal is to reveal the effects of population size, predation threats, and energy lost per escape on the evolutionary dynamics of fearfulness and boldness. Two pure strategies, fearfulness and boldness, are assumed to have different responses for the predator attacks and nonlethal disturbance. On the other hand, the co-existence mechanism of fearfulness and boldness is also considered. For the effects of total population size, predation threats, and energy lost per escape, our main results show that: (i) the fearful (bold) individuals will be favored in a small (large) population, i.e. in a small (large) population, the fearfulness (boldness) can be considered to be an ESS; (ii) in a population with moderate size, fearfulness would be favored under moderate predator attacks; and (iii) although the total population size is the most important factor for the evolutionary dynamics of both fearful and bold individuals, the small energy lost per escape enables the fearful individuals to have the ability to win the advantage even in a relatively large population. Finally, we show also that the co-existence of fearful and bold individuals is possible when the competitive interactions between individuals are introduced.     

Rolling dynamics of a neutrophil with redistributed L-selectin

The most common white blood cell is the neutrophil, which slowly rolls along the walls of blood vessels due to the coordinated formation and breakage of chemical selectin-carbohydrate bonds. We show that L-selectin receptors are rapidly redistributed to form a cap at one end of the cell membrane during rolling via selectins or chemotactic stimulation. This topography significantly alters the adhesive dynamics as demonstrated by computer simulations of neutrophils rolling on a carbohydrate selectin-ligand substrate under flow. It was found that neutrophils with a redistributed L-selectin cap roll on sialyl Lewis-x with a quasi-periodic motion, as characterized by relatively low velocity intervals interspersed with regular jumps in the rolling velocity. On average, neutrophils with redistributed L-selectin rolled at a lower velocity when compared with cells having a uniform L-selectin distribution of equal average density. We speculate on the possible biological implications that these differences in adhesion dynamics will have during the inflammatory response.     

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane

Computer simulations of phospholipid membranes have been carried out by using a combined approach of molecular and stochastic dynamics and a mean field based on the Marcelja model. First, the single-chain mean field simulations of Pastor et al. [(1988) J. Chem. Phys. 89, 1112-1127] were extended to a complete dipalmitoylphosphatidylcholine molecule; a 102-ns Langevin dynamics simulation is presented and compared with experiment. Subsequently, a hexagonally packed seven-lipid array was simulated with Langevin dynamics and a mean field at the boundary and with molecular dynamics (and no mean field) in the center. This hybrid method, mean field stochastic boundary molecular dynamics, reduces bias introduced by the mean field and eliminates the need for periodic boundary conditions. As a result, simulations extending to tens of nanoseconds may be carried out by using a relatively small number of molecules to model the membrane environment. Preliminary results of a 20-ns simulation are reported here. A wide range of motions, including overall reorientation with a nanosecond decay time, is observed in both simulations, and good agreement with NMR, IR, and neutron diffraction data is found.     

N-formylpeptide-receptor dynamics, cytoskeletal activation, and intracellular calcium response in human neutrophil cytoplasts

Cytoplasts (enucleated neutrophils which are depleted of dense granules) were prepared from human neutrophils with a modified procedure which employed dihydrocytochalasin B instead of cytochalasin B. These cytoplasts retained an activatable cytoskeletal network similar to cells in that filamentous actin polymerization in response to an N-formylpeptide (fluoresceinated N-formyl-nle-leu-phe-nle-tyr-lys, FLPEP) occurred with similar dose-response characteristics and was inhibitable by cytochalasin B and dihydrocytochalasin B. Cytoplasts had the same number of receptors per surface area as cells and binding constants and dissociation kinetics were the same for cells and cytoplasts. The conversion of receptors from a rapidly dissociating form to a slowly dissociating form was comparable in cells and cytoplasts. This conversion was not inhibited by cytochalasins and thus did not require actin polymerization. Cytoplasts were capable of internalizing 30% of bound FLPEP after 3 min of binding. Cytochalasins did not block this internalization which thus did not appear to require actin polymerization. After 5 min of binding, [3H]-N-formyl-met-leu-phe cosedimented with the Golgi marker enzymes when cytoplasts were fractionated on sucrose density gradients after N2 cavitation. These results indicate that the internalization mechanism is functional in cytoplasts. The Indo-1-detectable calcium response in cytoplasts had a ED50 similar to cells, though the maximum increase in Ca2+ concentration was about one-half that of cells. The response recovered with time after stimulation and the calcium detected was primarily from intracellular stores. The decay of responses after addition of formylpeptide antagonists was parallel for cells and cytoplasts, and leukotriene B4-induced responses in both cells and cytoplasts. Thus the regulation of the responses in cells and cytoplasts was analogous.     

The activation of human neutrophil gelatinase

To study the mechanisms of activation of human neutrophil gelatinase, the enzyme has been purified using a combination of chromatography on a DEAE-Sephacel and a gelatin-peptide-Sepharose column. On reducing SDS-polyacrylamide-gel electrophoresis the purified gelatinase ran as a single band of about 94,000 Da, and had a specific activity of 5624.4 units/mg of enzyme protein. When latent gelatinase was treated with trypsin, cathepsin G, neutrophil elastase, HgCl2 or urea, its activity was enhanced and the enzyme was processed and converted into species of the lower molecular mass. Upon activation, the protein band of 94,000 Da of reduced latent gelatinase underwent a decrease of about 6,000-12,000 Da. Formation of the species of lower molecular mass during urea activation could be blocked by the addition of EDTA.     

Extracellular acidification induces human neutrophil activation

In the current work, we evaluated the effect of extracellular acidification on neutrophil physiology. Neutrophils suspended in bicarbonate-buffered RPMI 1640 medium adjusted to acidic pH values (pH 6.5-7.0) underwent: 1) a rapid transient increase in intracellular free calcium concentration levels; 2) an increase in the forward light scattering properties; and 3) the up-regulation of surface expression of CD18. By contrast, extracellular acidosis was unable to induce neither the production of H2O2 nor the release of myeloperoxidase. Acidic extracellular pH also modulated the functional profile of neutrophils in response to conventional agonists such as FMLP, precipiting immune complexes, and opsonized zymosan. It was found that not only calcium mobilization, shape change response, and up-regulation of CD18 expression but also production of H2O2 and release of myeloperoxidase were markedly enhanced in neutrophils stimulated in acidic pH medium. Moreover, extracellular acidosis significantly delayed neutrophil apoptosis and concomitantly extended neutrophil functional lifespan. Extracellular acidification induced an immediate and abrupt fall in the intracellular pH, which persisted over the 240-s analyzed. A similar abrupt drop in the intracellular pH was detected in cells suspended in bicarbonate-supplemented PBS but not in those suspended in bicarbonate-free PBS. A role for intracellular acidification in neutrophil activation is suggested by the fact that only neutrophils suspended in bicarbonate-buffered media (i.e., RPMI 1640 and bicarbonate-supplemented PBS) underwent significant shape changes in response to extracellular acidification. Together, our results support the notion that extracellular acidosis may intensify acute inflammatory responses by inducing neutrophil activation as well as by delaying spontaneous apoptosis and extending neutrophil functional lifespan.     

Early prolonged neutrophil activation in critically ill patients with sepsis

We hypothesised that plasma concentrations of biomarkers of neutrophil activation and pro-inflammatory cytokines differ according to the phase of rapidly evolving sepsis. In an observational study, we measured heparin-binding protein (HBP), myeloperoxidase (MPO), IL-6 and IL-8 in 167 sepsis patients on intensive care unit admission. We prospectively used the emergence of the first sepsis-associated organ dysfunction (OD) as a surrogate for the sepsis phase. Fifty-five patients (of 167, 33%) developed the first OD > 1 h before, 74 (44%) within ± 1 h, and 38 (23%) > 1 h after intensive care unit admission. HBP and MPO were elevated at a median of 12 h before the first OD, remained high up to 24 h, and were not associated with sepsis phase. IL-6 and IL-8 rose and declined rapidly close to OD emergence. Elevation of neutrophil activation markers HBP and MPO was an early event in the evolution of sepsis, lasting beyond the subsidence of the pro-inflammatory cytokine reaction. Thus, as sepsis biomarkers, HBP and MPO were not as prone as IL-6 and IL-8 to the effect of sample timing.     

A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations

Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. In the first place, continuous-wave EPR spectra reflect the motional freedom of the spin-label specifically linked to a desired site within the protein. EPR spectra calculations based on molecular dynamics (MD) and stochastic dynamics simulations facilitate verification or refinement of predicted computer-aided models of local protein conformations. The presented spectra simulation algorithm implies a specialized in vacuo MD simulation at 600 K with additional restrictions to sample the entire accessible space of the bound spin-label without large temporal effort. It is shown that the distribution of spin-label orientations obtained from such MD simulations at 600 K agrees well with the extrapolated motion behavior during a long timescale MD at 300 K with explicit water. The following potential-dependent stochastic dynamics simulation combines the MD data about the site-specific orientation probabilities of the spin-label with a realistic rotational diffusion coefficient yielding a set of trajectories, each more than 700 ns long, essential to calculate the EPR spectrum. Analyses of a structural model of the loop between helices E and F of bacteriorhodopsin are illustrated to demonstrate the applicability and potentials of the reported simulation approach. Furthermore, effects on the motional freedom of bound spin-labels induced by solubilization of bacteriorhodopsin with Triton X-100 are examined.     

Jumping frequencies in membrane channels. Comparison between stochastic molecular dynamics simulation and rate theory

Permeation of molecules through membrane channels involves local interactions with a limited number of ligand groups. A method for the molecular dynamics simulation of particle movement in small ligand systems is described. It is assumed that the ligand groups carry out thermal vibrations, whereas the rest of the channel molecule and the surroundings act as a heat bath which is coupled via random forces to the motions of the ligands. The simulation technique is applied to a simple system which contains some of the essential features influencing jumping rates in membrane channels, such as flexibility of ligand configuration or inertial effects in the motion of the ligands. Since the simulation is based on strictly microscopic parameters of the particle-ligand system, a rigorous test of the predictions of rate theory is possible. It is found that rate theory describes the general dependence of jumping frequency k' on temperature and on ligand binding strength rather well, although the values of k' obtained by computer simulation are 2-3 times smaller than those predicted by rate theory.     

A stochastic model of evolutionary dynamics with deterministic large-population asymptotics

An evolutionary birth-death process is proposed as a model of evolutionary dynamics. Agents residing in a continuous spatial environment X, play a game G, with a continuous strategy set S, against other agents in the environment. The agents’ positions and strategies continuously change in response to other agents and to random effects. Agents spawn asexually at rates that depend on their current fitness, and agents die at rates that depend on their local population density. Agents’ individual evolutionary trajectories in X and S are governed by a system of stochastic ODEs. When the number of agents is large and distributed in a smooth density on (X,S), the collective dynamics of the entire population is governed by a certain (deterministic) PDE, which we call a fitness-diffusion equation.     

Dynamic regulation of LFA-1 activation and neutrophil arrest on intercellular adhesion molecule 1 (ICAM-1) in shear flow

Neutrophil recruitment during acute inflammation is triggered by G-protein-linked chemotactic receptors that in turn activate beta(2) integrin (CD18), deemed a critical step in facilitating cell capture and arrest under the shear force of blood flow. A conformational switch in the I domain allosteric site (IDAS) and in CD18 regulates LFA-1 affinity for endothelial ligands including intercellular adhesion molecule 1 (ICAM-1). We examined the dynamics of CD18 activation in terms of the efficiency of neutrophil capture of ICAM-1, and we correlated this with the membrane topography of 327C, an antibody that recognizes the active conformation of CD18 I-like domain. Adhesion increased in direct proportion to chemotactic stimulus rising 7-fold over a log range of interleukin-8 (IL-8). A threshold dose of approximately 75 pm IL-8, corresponding to ligation of only approximately 10-100 receptors, was sufficient to activate approximately 20,000 CD18 and a rapid boost in the capture efficiency on ICAM-1. This was accompanied by a rapid redistribution of active LFA-1, but not Mac-1, into membrane patches, a necessary component for optimum adhesion efficiency. Shear-resistant arrest on a monolayer of ICAM-1 was reversed within minutes of chemotactic stimulation correlating with a shift from high to low affinity CD18 and dispersal of patches of active CD18. Mobility of active CD18 into high avidity patches was dependent on phosphatidylinositol 3-kinase activity and not F-actin polymerization. The data reveal that the number of chemotactic receptors bound and the topography and lifetime of high affinity LFA-1 tightly regulate the efficiency of neutrophil capture on ICAM-1.     

Multistable and multistep dynamics in neutrophil differentiation

Background  

Cell differentiation has long been theorized to represent a switch in a bistable system, and recent experimental work in micro-organisms has revealed bistable dynamics in small gene regulatory circuits. However, the dynamics of mammalian cell differentiation has not been analyzed with respect to bistability.