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Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, differentiation…
The mitogen-activated protein kinase (MAPK) signaling cascade, an evolutionarily conserved motif present in all eukaryotic cells, is involved in coordinating critical cell-fate decisions, regulating protein synthesis, and mediating learning…
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…
Cells use signalling pathways as windows into the environment to gather information, transduce it into their interior, and use it to drive behaviours. MAPK (ERK) is a highly conserved signalling pathway in eukaryotes, directing multiple…
The mating pathway in \emph{Saccharomyces cerevisiae} is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and…
Nonlinear systems driven by recurrent signals are known to exhibit complex dynamical responses which, in the physiological context, can have important functional consequences. One of the simplest biological systems that is exposed to such…
PEBPs (PhosphatidylEthanolamine Binding Proteins) form a protein family widely present in the living world since they are encountered in microorganisms, plants and animals. In all organisms PEBPs appear to regulate important mechanisms that…
Recent experiments in epithelial wound healing have demonstrated the necessity of Mitogen-activated protein kinase (MAPK) for coordinated cell movement after damage. This MAPK activity is characterized by two wave-like phenomena. One MAPK…
Interconvertible enzyme cascades, exemplified by the mitogen activated protein kinase (MAPK) cascade, are a frequent mechanism in signal transduction pathways. There has been much speculation as to the role of these pathways, and how their…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
Biochemical networks related to similar functional pathways are often correlated due to cross-talk among the homologous proteins in the different networks. Using a stochastic framework, we address the functional significance of the…
AMP activated protein kinase (AMPK) is a critical energy sensor, regulating signaling networks involved in pathology including metabolic diseases and cancer. This increasingly recognized role of AMPK has prompted tremendous research efforts…
The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death. Here we study a polynomial dynamical system describing the dynamics of MEK/ERK proposed by Yeung et al. with their experimental…
To sustain metabolism, intracellular ATP concentration must be regulated within an appropriate range. This coordination is achieved through the function of the AMP-activated protein kinase (AMPK), a cellular "fuel gauge" that is expressed…
Bistability of MAP kinase (MAPK) activity has been suggested to contribute to several cellular processes, including differentiation and long-term synaptic potentiation. A recent model (48) predicts bistability due to interactions of the…
Adenosine 5'-triphosphate (ATP) is the nearly ubiquitous "energy currency" of living organisms, and thus is a crucial participant in the majority of enzymatic reactions. The standard models in enzyme kinetics generally ignore the temporal…
The response of cell populations to external stimuli plays a central role in biological mechanical processes such as epithelial wound healing and developmental morphogenesis. Wave-like propagation of a signal of ERK MAP kinase has been…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
Many cellular processes are tightly connected to the dynamics of microtubules (MTs). While in neuronal axons MTs mainly regulate intracellular trafficking, they participate in cytoskeleton reorganization in many other eukaryotic cells,…
We consider a model of extracellular signal-regulated kinase (ERK) regulation by dual-site phosphorylation and dephosphorylation, which exhibits bistability and oscillations, but loses these properties in the limit in which the mechanisms…