Related papers: Role of the dihedral angle potential in the nuclea…
In the diffusion-collision model, the unfolding or backward rates are given by the likelihood of secondary structural cluster dissociation. In this work, we introduce a backward rate calculation modeled from a Kramers-type thermal tunneling…
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…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g. with the Lennard-Jones contact potentials. The folding…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
A method that reconstructs protein residue networks using suitable node selection and edge recovery policies produced numerical observations that correlate strongly (Pearson's correlation coefficient < -0.83) with published folding rates…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…