Related papers: How knots influence properties of proteins
We illustrate schematically a possible traversing along the path of trefoil-type and $8_{18}$ knots during a specific time period by considering a quantum-mechanic system which satisfies a specific kind of phase dynamics of quantum…
Cell motility and tissue morphogenesis depend crucially on the dynamic remodelling of actomyosin networks. An actomyosin network consists of an actin polymer network connected by crosslinker proteins and motor protein myosins that generate…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
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…
Molecules provide the smallest possible circuits in which quantum interference and electron correlation can be engineered to perform logical operations, including the universal NAND gate. We investigate a chemically encoded quantum NAND…
We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We…
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.…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also…
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 study of a certain class of matrix integrals can be motivated by their interpretation as counting objects of knot theory such as alternating prime links, tangles or knots. The simplest such model is studied in detail and allows to…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Recent biological experiments have shown that certain types of cells are able to move in structured and confined environment even without the activation of focal adhesion. Focusing on this particular phenomenon and based on previous works,…
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…
In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under…
Protein-protein interaction networks are useful for studying human diseases and to look for possible health care through a holistic approach. Networks are playing an increasing and important role in the understanding of physiological…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely,…