Related papers: Knots and Swelling in Protein Folding
Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics, and science. As topologically stable objects within field theories, they have been speculatively proposed as explanations for diverse persistent…
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $\Delta F_{\rm knotting}$, on polymer chains under tension. A…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a…
Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…
Entangled knots form spontaneously in flexible filaments, yet the influence of the surrounding environment on this process is poorly understood. Here we demonstrate that free-moving particles act as kinetic catalysts for spontaneous…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Knots are fascinating topological structures that have been observed in various contexts, ranging from micro-worlds to macro-systems, and are conjectured to play a fundamental role in their respective fields. In order to characterize their…
Knot theory provides a powerful tool for the understanding of topological matters in biology, chemistry, and physics. Here knot theory is introduced to describe topological phases in the quantum spin system. Exactly solvable models with…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
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.…
The study of knots and links from a probabilistic viewpoint provides insight into the behavior of "typical" knots, and opens avenues for new constructions of knots and other topological objects with interesting properties. The knotting of…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
We consider the problem of an inextensible but flexible fiber advected by a steady chaotic flow, and ask the simple question whether the fiber can spontaneously knot itself. Using a 1D Cosserat model, a simple local viscous drag model and…