Related papers: Controlling the folding and substrate-binding of p…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…
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…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Due to the complex characteristics of bottle-brush polymers, it became a challenge to develop an efficient algorithm for studying such macromolecules under various solvent conditions or some constraints in the space by using computer…
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…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
Local chain structure and local environment play an important role in the dynamics of polymer chains in miscible blends. In general, the friction coefficients that describe the segmental dynamics of the two components in a blend differ from…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
The stretching of brushes of long polymers grafted to a planar surface is investigated byMonte Carlo simulations in the limit of very high grafting densities, as achieved in recent experiments. The monomer density profiles are shown to…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…