Related papers: Statistically enhanced self-attraction of random p…
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
We demonstrate that Protein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
We investigate the equilibrium properties of a colloidal solution in contact with a soft interface. As a result of symmetry breaking, surface effects are generally prevailing in confined colloidal systems. In this Letter, particular…
Experimental data on proton-proton interactions in high energy collisions show quite a special and unexpected behaviour of the proportion of elastic scattering compared to inelastic processes with increasing energy. It decreases at the…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
Realistic fluid-solid interaction potentials are essential in description of confined fluids especially in the case of geometric heterogeneous surfaces. Correlated random field is considered as a model of random surface with high geometric…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
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…
Using molecular dynamic simulations we study a system of particles interacting through a continuous core-softened potentials consisting of a hard core, a shoulder at closest distances and an attractive well at further distance. We obtain…
We consider directed semiflexible polymers embedded in a fluctuating surface which is governed by either surface tension or bending rigidity. The attractive interactions induced by the fluctuations of the surface reduce the rigidity of the…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which…
We consider a variational model for a charge density $u\in\{-1,1\}$ on a (hyper)plane, with a short-range attraction coming from the interfacial energy and a long-range repulsion coming from the electrostatic energy. This competition leads…
We consider the adsorption of a random heteropolymer onto an interface within the model by Garel et al. [1] by taking into account self-interactions between the monomers. Within the replica trick and by using a self-consistent preaveraging…
We study mixing patterns in networks, meaning the propensity for nodes of different kinds to connect to one another. The phenomenon of assortative mixing, whereby nodes prefer to connect to others that are similar to themselves, has been…
Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among…