Related papers: How knots influence properties of proteins

We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work in protein folding. The striking differences in the predicted…

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…

Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…

Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…

We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of…

Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…

We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…

We explore free knot diagrams, which are projections of knots into the plane which don't record over/under data at crossings. We consider the combinatorial question of which free knot diagrams give which knots and with what probability.…

We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an…

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…

An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a…

Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…

While cracking is a complex dynamics that involves material intrinsic properties like grain shape and size distribution, elastic properties of grain and cementing materials, and extrinsic properties of loading, in this work, the focus has…

Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

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…

Branched actin networks exert pushing forces in eukaryotic cells, and adapt their stiffness to their environment. The physical basis for their mechanics and adaptability is however not understood. Indeed, here we show that their high…