Related papers: Tightening the knot in phytochrome by single molec…
An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to knot itself during the folding process to form these highly…
A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost…
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of $f_S$ and the loading rate ($r_f$). The simulations and theoretical analysis have been done without and with the handles that are explicitly…
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring,…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…