Related papers: Simulating Mono-and Multi-Protein Phosphorylation …
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…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
Multistationarity, underlies biochemical switching and cellular decision-making. We study how multistationarity in the sequential n-site phosphorylation-dephosphorylation cycle is affected when only some species are open, meaning allowed to…
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…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
Clustering of molecules on biological membranes is a widely observed phenomenon. In some cases, such as the clustering of Ras proteins on the membranes of mammalian cells, proper cell signaling is critically dependent on the maintenance of…
Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized. Proteins that specialize in this function are called by a…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
Protein phosphorylation provides a dynamic readout of cellular signaling yet remains difficult to detect at low abundance and stoichiometry. Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) using particle-in-pore plasmonic…
Ras GTPases are lipid-anchored G proteins which play a fundamental role in cell signaling processes. Electron micrographs of immunogold-labeled Ras have shown that membrane-bound Ras molecules segregate into nanocluster domains. Several…
Multisite phosphorylation networks are encountered in many intracellular processes like signal transduction, cell-cycle control or nuclear signal integration. In this contribution networks describing the phosphorylation and…
We present a comprehensive approach to the modeling, performance analysis, and design of clustered molecular nanonetworks in which nano-machines of different clusters release an appropriate number of molecules to transmit their sensed…
In many cellular signaling pathways, key components form clusters at the cell membrane. Although much work has focused on the mechanisms behind such cluster formation, the implications for downstream signaling remain poorly understood.…
Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Phosphorelays are a class of signaling mechanisms used by cells to respond to changes in their environment. Phosphorelays (of which two-component systems constitute a special case) are particularly abundant in prokaryotes and have been…