Related papers: Cooperativity-Dependent Folding of Single-Stranded…
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the…
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,…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
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 panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
The design of hydrogels that combine mechanical robustness with dynamic reconfigurability remains a fundamental challenge, as increasing crosslink dissociation rates compromise network integrity. This limitation is addressed through the…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…