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Background: Rap proteins from Bacilli directly target response regulators of bacterial two-component systems and modulate their activity. Their effects are controlled by binding of signaling peptides to an allosteric site. Hence Raps exemplify a class of monomeric signaling receptors, which we call switchable allosteric modulator proteins (SAMPs). These proteins have potential applications in diverse biomedical and biotechnical settings, but a quantitative understanding of the impact of molecular and cellular factors on signal transduction is lacking. Here we introduce mathematical models that elucidate how signals are propagated though the network upon receptor stimulation and control the level of active response regulator. Results: Based on a systematic parameter analysis of the models, we show that key features of the dose-response behavior at steady state are controlled either by the molecular properties of the modulator or the signaling context. In particular, we find that the biochemical activity (i.e. non-enzymatic vs. enzymatic) and allosteric properties of the modulator control the response amplitude. The Hill coefficient and the EC50 are controlled in addition by the relative ligand affinities. By tuning receptor properties, either graded or more switch-like (memory-less) response functions can be fashioned. Furthermore, we show that other contextual factors (e.g. relative concentrations of network components and kinase activity) have a substantial impact on the response, and we predict that there exists a modulator concentration which is optimal for response amplitude. Conclusion: We discuss data on Rap-Phr systems in B. subtilis to show how ourmodels can contribute to an integrated view of SAMP signaling by combining biochemical, structural and physiological insights. Our results also suggest that SAMPs could be evolved or engineered to implement diverse response behaviors. However—without additional regulatory controls-they can generate rather variable cellular outputs. [ABSTRACT FROM AUTHOR]

Abstract: Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behavior of single cells, we use extensive Monte Carlo simulations to predict non-trivial structure formation for cell communities on soft elastic substrates as a function of elastic moduli, cell density, noise and cell position geometry. In general, we find a disordered structure as well as ordered string-like and ring-like structures. The transition between ordered and disordered structures is controlled both by cell density and noise level, while the transition between string- and ring-like ordered structures is controlled by the Poisson ratio. Similar effects are observed in three dimensions. Our results suggest that in regard to elastic effects, healthy connective tissue usually is in a macroscopically disordered state, but can be switched to a macroscopically ordered state by appropriate parameter variations, in a way that is reminiscent of wound contraction or diseased states like contracture. [Copyright &y& Elsevier]