Related papers: Conformational Biases of {\alpha}-Synuclein and Fo…
We use numerical simulations of a bead-spring model chain to investigate the evolution of the conformation of long and flexible elastic fibers in a steady shear flow. In particular, for rather open initial configurations, and by varying a…
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
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…
Knots across various length scales, from micro to macro-scales, such as polymers, DNA, shoelaces, and surgery, serving their unique mechanical properties. The shape of ideal knots has been extensively studied in the context of knot theory,…
The most tight conformation of the trefoil knot found by the SONO algorithm is presented. Structure of the set of its self-contact points is analyzed.
We perform a compare-and-contrast investigation between the equilibrium shapes of physical and ideal trefoil knots, both in closed and open configurations. Ideal knots are purely geometric abstractions for the tightest configuration tied in…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a…
Three-dimensional images of evolving numerical trefoil vortex knots are used to study the growth and decay of the enstrophy and helicity. Negative helicity density ($h<0$) plays several roles. First, sheets of oppositely-signed helicity…
We derive solutions of the Kirchhoff equations for a knot tied on an infinitely long elastic rod subjected to combined tension and twist. We consider the case of simple (trefoil) and double (cinquefoil) knots; other knot topologies can be…
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…
Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that…
We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
We report on new numerical computations of the set of self-contacts in tightly knotted tubes of uniform circular cross-section. Such contact sets have been obtained before for the trefoil and figure eight knots by simulated annealing -- we…
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…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of…
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…