Related papers: Structural entanglements in protein complexes

The dependence of the unfolding pathway of proteins on the pulling speed is investigated. This is done by introducing a simple one-dimensional chain comprising $N$ units, with different characteristic bistable free energies. These units…

In biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However,…

Current theories on the conformation and dynamics of unknotted and non-concatenated ring polymers in melt conditions describe each ring as a tree-like double-folded object. While evidence from simulations supports this picture on a single…

Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…

How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…

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 use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…

The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…

For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the…

Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…

Using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins.…

This paper considers a broadly biologically relevant question of a chain (such as a protein) binding to a sequence of receptors with matching multiple ligands distributed along the chain. This binding is critical in cell adhesion events,…

To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…

The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…

We establish a relation between entanglement of a many-body system and its diffractive properties, where the link is given by structure factors. Based on these, we provide a general analytical construction of multi-qubit entanglement…

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…

There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…