Related papers: Soliton mediated protein folding
We study the thermodynamic and kinetic consequences of the competition between single-protein folding and protein-protein aggregation using a phenomenological model, in which the proteins can be in the unfolded (U), misfolded (M) or folded…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
In the present work, we study, by means of a one-dimensional lattice model, the collective excitations corresponding to intra molecular ones of a chain like proteins. It is shown that such excitations are described by the Nonlinear…
Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape…
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…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We investigate propagation of a kink soliton along inhomogeneous chains with two different constituents, arranged either periodically, aperiodically, or randomly. For the discrete sine-Gordon equation and the Fibonacci and Thue-Morse chains…
Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion, from a relatively small number of components. Here we propose to identify the…
One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
We present and study new mechanism of interaction between the solitons based on the exchange interaction mediated by the localized fermion states. As particular examples, we consider solutions of simple 1+1 dimensional scalar field theories…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
Electric field induced collective reorientation of nematic molecules placed between two flat parallel electrodes is of importance for both fundamental science and practical applications. This reorientation is either homogeneous over the…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
It has been observed that certain classical chains admit topologically protected zero-energy modes that are localized on the boundaries. The static features of such localized modes are captured by linearized equations of motion, but the…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…