Related papers: Allovalency revisited: an analysis of multisite ph…
We study the ultrasensitivity of multisite binding processes where ligand molecules can bind to several binding sites, considering more particularly recent models involving complex chemical reactions in phosphorylation systems such as…
Multisite phosphorylation plays an important role in intracellular signaling. There has been much recent work aimed at understanding the dynamics of such systems when the phosphorylation/dephosphorylation mechanism is distributive, that is,…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
Receptor-ligand binding is a critical first step in signal transduction and the duration of the interaction can impact signal generation. In mammalian cells, clustering of receptors may be facilitated by heterogeneous zones of lipids, known…
Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the…
Phosphorylation, the enzyme-mediated addition of a phosphate group to a molecule, is a ubiquitous chemical mechanism in biology. Multisite phosphorylation, the addition of phosphate groups to multiple sites of a single molecule, may be…
Bivalency confers several concentration-dependent phenomena, including avidity, competitive exchange and multi-site competitive exchange. Since these concepts are crucial for a wide variety of topics in cell and molecular biology, their…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of…
We study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses…
The dual phosphorylation network provides an essential component of intracellular signaling, affecting the expression of phenotypes and cell metabolism. For particular choices of kinetic parameters, this system exhibits multistationarity, a…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…
Multisite protein phosphorylation plays a prominent role in intracellular processes like signal transduction, cell-cycle control and nuclear signal integration. Many proteins are phosphorylated in a sequential and distributive way at more…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on…
Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…
The parameter region of multistationarity of a reaction network contains all the parameters for which the associated dynamical system exhibits multiple steady states. Describing this region is challenging and remains an active area of…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
We apply tools from real algebraic geometry to the problem of multistationarity of chemical reaction networks. A particular focus is on the case of reaction networks whose steady states admit a monomial parametrization. For such systems we…