Related papers: Hydrodynamic Interactions in Protein Folding
The ballistic deposition of particles by taking hydrodynamic interactions (HI) into account has been studied by means of computer simulations. The radial distribution function of the assembly of particles deposited on a plane has been…
The coffee-ring effect is a universal feature of evaporating sessile droplets with pinned contact line, wherein solutes or particles are advected to the droplet's edge due to evaporation-driven flows. While existing models have successfully…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences,…
This article gives an overview of recent theoretical and experimental findings concerning the hydrodynamic interaction between liquid-embedded particles in various confined geometries. A simple unifying description emerges, which accounts…
Motility-Induced Phase Separation (MIPS) is a distinctive phenomenon in active matter that arises from its inherent non-equilibrium nature. Despite recent progress in understanding MIPS in dry active systems, it has been debated whether…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Lipid bilayers forming biological membranes are known to behave as viscous 2D fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it has been shown [Proc. Nat. Acad. Sci. USA 112,…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range…
The effects of randomly pinning particles in a model glass-forming fluid are studied, with a focus on the dynamically heterogeneous relaxation in the presence of pinning. We show how four-point dynamical correlations can be analysed in real…
We have studied the correlated Brownian motion of micron-sized particles suspended in water and confined between two plates. The hydrodynamic interaction between the particles exhibits three anomalies. (i) The transverse coupling is…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
Being the HIV-1 Protease (HIV-1-PR) an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local…