Related papers: Allosteric communication mediated by protein conta…

A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…

Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned…

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…

Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit…

Using tools and concepts from contact topology we show that non-vanishing twist implies conservation of the layer structure in cholesteric liquid crystals. This leads to a number of additional topological invariants for cholesteric…

Allosterism traditionally refers to local changes in an extended object, for instance the binding of a ligand to a macromolecule, leading to a localized response at some other, possibly quite remote position. Here, we show that such…

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…

Stochastic modeling of disease dynamics has had a long tradition. Among the first epidemic models including a spatial structure in the form of local interactions is the contact process. In this article we investigate two extensions of the…

We consider a cell population structured by a positive real number, describing the number of P-glycoproteins carried by the cell. We are interested in the effect of those proteins on the growth of the population: those proteins are indeed…

We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…

Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…

We propose models describing the collective dynamics of two opposing groups of individuals with stochastic communication. Individuals from the same group are assumed to align in a stochastic manner, while individuals from different groups…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

In the current study, we demonstrated that allostery transpires by entropy transfers across time-spatial scales that actualize the conception of a molecular trap that supervises ligand interaction, selection, and migration into the…

Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a…

We investigate a driven diffusive lattice gas model with two oppositely moving species of particles. The model is motivated by bi-directional traffic of ants on a pre-existing trail. A third species, corresponding to pheromones used by the…

We propose a new dynamic stochastic blockmodel that focuses on the analysis of interaction lengths in networks. The model does not rely on a discretization of the time dimension and may be used to analyze networks that evolve continuously…

Allosteric regulation at distant sites is central to many cellular processes. In particular, allosteric sites in proteins are a major target to increase the range and selectivity of new drugs, and there is a need for methods capable of…

The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…

The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…