Related papers: A Minimal Off-Lattice Model for Alpha-helical Prot…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…
The behaviour of the one--dimensional random--forced Burgers equation is investigated in the path integral formalism, using a discrete space--time lattice. We show that by means of Monte Carlo methods one may evaluate observables, such as…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…