Related papers: Side-chain conformational changes upon protein-pro…
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…
Planar/flat configurations of fixed-angle chains and trees are well studied in the context of polymer science, molecular biology, and puzzles. In this paper, we focus on a simple type of fixed-angle linkage: every edge has unit length…
In two nearby atoms, the dipole-dipole interaction can couple transitions with orthogonal dipole moments. This orthogonal coupling accounts for a number of interesting effects, but strongly depends on the geometry of the setup. Here, we…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
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]…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…
Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g. with the Lennard-Jones contact potentials. The folding…
The role of thermal fluctuations on the conformational dynamics of a single closed filament is studied. It is shown that, due to the interaction between charges and bending degrees of freedom, initially circular aggregates may undergo…
Dihadron and isolated direct photon-hadron angular correlations are measured in $p$$+$$p$ collisions at $\sqrt{s}=200$ GeV. The correlations are sensitive to nonperturbative initial-state and final-state transverse momentum $k_T$ and $j_T$…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
We use a smoothed particle hydrodynamics (SPH) code to examine the effects of a binary companion on a Be star disk for a range of disk viscosities and misalignment angles, i.e. the angle between the orbital plane and the primary's spin…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
BAR superfamily proteins have a banana-shaped domain that causes the local bending of lipid membranes. We study as to how such a local anisotropic curvature induces effective interaction between proteins and changes the global shape of…
We study a large data set of protein structure ensembles of very diverse sizes determined by nuclear magnetic resonance. By examining the distance-dependent correlations in the displacement of residues pairs and conducting finite size…
Electronic and optical properties of doped organic semiconductors are dominated by local interactions between donor and acceptor molecules. However, when such systems are in crystalline form, long-range order competes against short-range…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
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…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…