Related papers: Tightening the knot in phytochrome by single molec…
Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
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 with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…
Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…
We examine computer experiments that can be performed to understand the dynamics of knots under self-repulsion. In the course of specific computer exploration we use the knot theory of rational knots and rational tangles to produce classes…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific,…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of so-dium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water…
The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy…
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…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Single-molecule mechanical manipulation has enabled the quantitative understanding of the kinetics of bond ruptures as well as protein unfolding mechanism. Single-molecule experiments with theoretical models have allowed one to gain insight…