Related papers: Three-helix-bundle Protein in a Ramachandran Model
The two-vibron dynamics associated to amide-I vibrations in a 3D $\alpha$-helix is described according to a generalized Davydov model. The helix is modeled by three spines of hydrogen-bonded peptide units linked via covalent bonds. It is…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
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 prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the left-handed helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the…
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…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two…
Three-body recombination, or ternary association, is a termolecular reaction in which three particles collide, forming a bound state between two, whereas the third escapes freely. Three-body recombination reactions play a significant role…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
Phi-values are experimental measures of the effects of mutations on the folding kinetics of a protein. A central question is which structural information Phi-values contain about the transition state of folding. Traditionally, a Phi-value…
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…