Related papers: On Hydrophobicity Correlations in Protein Chains
This work tests the statistical mechanical theory of hydrophobic interactions, isolates consequences of excluded volume interactions, and obtains B2 for those purposes. Cavity methods that are particularly appropriate for study of…
A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
We develop a simple correspondence between hydrophobic surface topology of globular proteins and and an effective protein-protein adhesiveness parameter of the Baxter type. We discuss within this framework analytical interpretation of the…
The physics of air-water interfaces plays a central role in modern theories of the hydrophobic effect. Implementing these theories, however, has been hampered by the difficulty of addressing fluctuations in the shape of such soft…
Colloidal aggregation could be implemented in various fields ranging from purely colloidal thermodynamics to protein interactions, their stability, and maybe folding. Indeed, colloidal aggregation is closely linked to the so-called…
We calculate the ion distributions around an interface in fluid mixtures of highly polar and less polar fluids (water and oil) for two and three ion species. We take into account the solvation and image interactions between ions and…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
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…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
By enumerating all sequences of length 20, we study the designability of structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide range of inter-monomer interaction parameters. We find that although the histogram of…
Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend…
A lattice model of the directed self-avoiding walk is used to estimate the possibility on the formation of an infinitely long linear semi-flexible copolymer chain. The copolymer chain is assumed to composed of four different types of the…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
We calculate potentials of the mean force for twenty amino acids in the vicinity of the (111) surface of gold, for several dipeptides, and for some analogs of the side chains, using molecular dynamics simulations and the umbrella sampling…
Histogram-reweighting grand canonical Monte Carlo simulations are used to obtain the critical properties of lattice chains composed of solvophilic and solvophobic monomers. The model is a modification of one proposed by Larson \emph{et al.}…
The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
We present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of…