Related papers: Protein mechanical unfolding: a model with binary …

The potential energy surface of an off-lattice model protein is characterized in detail by constructing a disconnectivity graph and by examining the organisation of pathways on the surface. The results clearly reveal the frustration…

In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…

Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…

We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the…

A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…

Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…

Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…

We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…

The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion,…

A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…

With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…

Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…

A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…

Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…

We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…

Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component…