Related papers: Local Interactions and Protein Folding: A 3D Off-L…
Nonnative residual interactions have attracted increasing attention in recent protein folding researches. Experimental and theoretical investigations had been set out to catch nonnative contacts that might dominate key events in protein…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
We present a comprehensive study of the thermodynamic properties of the three-dimensional fermionic Hubbard model, with application to cold fermionic atoms subject to an optical lattice and a trapping potential. Our study is focused on the…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
We explore the transport properties of an interacting Fermi gas in a three-dimensional optical lattice. The center of mass dynamics of the atoms after a sudden displacement of the trap minimum is monitored for different interaction…
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…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…