Related papers: Sub-residue sharpness of protein helix-coil transi…
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…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the…
We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is…
In the frameworks of algebraic topology {\alpha}-helix and different DNA-conformations are determined as the local latticed packing, confined by peculiar minimal surfaces which are similar to helicoids. These structures are defined by…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
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 present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
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 relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
The structural parameters of alpha helix and some forms of DNA-structures are determined by methods of algebraic topology. These structures are locally periodic and correspond to the bifurcation point for minimal surfaces given by…
We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
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…
The macroscopic behavior of polycrystalline materials is influenced by the local variation of properties caused by the presence of impurities and defects. The effect of these impurities at the atomic scale can either embrittle or strengthen…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…