A nonequilibrium allosteric model for receptor-kinase complexes: The role of energy dissipation in chemotaxis signaling.

The chemotaxis signaling pathway has served as a model system for the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the extracellular ligand concentration and adapt across a wide concentration range by undergoing methylation and demethylation. Methylation shifts the kinase response curve by orders of magnitude in ligand concentration while incurring a much smaller change in the ligand binding curve.

Resolving the binding-kinase discrepancy in bacterial chemotaxis: A nonequilibrium allosteric model and the role of energy dissipation.

The Escherichia coli chemotaxis signaling pathway has served as a model system for studying the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the extracellular ligand concentration and adapt across a wide concentration range by undergoing methylation and demethylation. Methylation shifts the kinase response curve by orders of magnitude in ligand concentration while incurring a much smaller change in the ligand binding curve.

Sequential modification of bacterial chemoreceptors is key for achieving both accurate adaptation and high gain.

Many regulatory and signaling proteins have multiple modification sites. In bacterial chemotaxis, each chemoreceptor has multiple methylation sites that are responsible for adaptation. However, whether the ordering of the multisite methylation process affects adaptation remains unclear.

A dual regulation mechanism of histidine kinase CheA identified by combining network-dynamics modeling and system-level input-output data.

It is challenging to decipher molecular mechanisms in biological systems from system-level input-output data, especially for complex processes that involve interactions among multiple components. We addressed this general problem for the bacterial histidine kinase CheA, the activity of which is regulated in chemotaxis signaling complexes by bacterial chemoreceptors. We developed a general network model to describe the dynamics of the system, treating the receptor complex with coupling protein CheW and the P3P4P5 domains of kinase CheA as a regulated enzyme with two substrates, ATP and P1, the phosphoryl-accepting domain of CheA.

Pendular behavior of public transport networks.

In this paper, we propose a methodology that bears close resemblance to the Fourier analysis of the first harmonic to study networks subjected to pendular behavior. In this context, pendular behavior is characterized by the phenomenon of people's dislocation from their homes to work in the morning and people's dislocation in the opposite direction in the afternoon. Pendular behavior is a relevant phenomenon that takes place in public transport networks because it may reduce the overall efficiency of the system as a result of the asymmetric utilization of the system in different directions.

Analysis of etching at a solid-solid interface.

We present a method to derive an analytical expression for the roughness of an eroded surface whose dynamics are ruled by cellular automaton. Starting from the automaton, we obtain the time evolution of the height average and height variance (roughness). We apply this method to the etching model in 1+1 dimensions, and then we obtain the roughness exponent.

Physiological aging as an infinitesimally ratcheted random walk.

The distribution of a population throughout the physiological age of the individuals is very relevant information in population studies. It has been modeled by the Langevin and the Fokker-Planck equations. A major problem with these equations is that they allow the physiological age to move back in time.

Effects of adaptation in maintaining high sensitivity over a wide range of backgrounds for Escherichia coli chemotaxis.

An allosteric model is developed to study the cooperative kinase response of wild-type (wt) Escherichia coli cells to the chemoattractant MeAsp in different ambient MeAsp concentrations. The model, together with wt dose response data, reveals the underlying mechanism for E. coli's ability to maintain high sensitivity over a wide range of backgrounds.

An allosteric model for heterogeneous receptor complexes: understanding bacterial chemotaxis responses to multiple stimuli.

The classical Monod-Wyman-Changeux model for homogeneous allosteric protein complex is generalized in this article to model the responses of heterogeneous receptor complexes to multiple types of ligand stimulus. We show that the recent in vivo experimental data of Escherichia coli chemotaxis responses for mutant strains with different expression levels of the chemo-receptors to different types of stimulus [Sourjik, V. & Berg, H.

Effects of receptor interaction in bacterial chemotaxis.

Signaling in bacterial chemotaxis is mediated by several types of transmembrane chemoreceptors. The chemoreceptors form tight polar clusters whose functions are of great biological interest. Here, we study the general properties of a chemotaxis model that includes interaction between neighboring chemoreceptors within a receptor cluster and the appropriate receptor methylation and demethylation dynamics to maintain (near) perfect adaptation.

Quantitative modeling of sensitivity in bacterial chemotaxis: the role of coupling among different chemoreceptor species.

We propose a general theoretical framework for modeling receptor sensitivity in bacterial chemotaxis, taking into account receptor interactions, including those among different receptor species. We show that our model can quantitatively explain the recent in vivo measurements of receptor sensitivity at different ligand concentrations for both mutant and wild-type strains. For mutant strains, our model can fit the experimental data exactly.

Perfect and near-perfect adaptation in a model of bacterial chemotaxis.

The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent external stimuli. In many cases, the bacterial activity returns to its prestimulus level exactly, and this perfect adaptability is robust against variations in various chemotaxis protein concentrations. We model the bacterial chemotaxis signaling pathway, from ligand binding to CheY phosphorylation.