Related papers: Statistical Mechanics of Membrane Protein Conforma…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
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…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
Some aspects of a recent paper about protein-membrane interaction are inadequate due to lack of structural information.
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as…
We propose an improved prediction method of the tertiary structures of $\alpha$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because…
Adsorption of proteins onto membranes can alter the local membrane curvature. This phenomenon has been observed in biological processes such as endocytosis, tubulation and vesiculation. However, it is not clear how the local surface…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
We investigate the adsorption of a flexible polymer at a hexagonally patterned monolayer. All conformational polymer phases are identified, which enables the construction of a hyperphase diagram, parameterized by temperature and monolayer…
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…
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…
Path integrals similar to those describing stiff polymers arise in the Helfrich model for membranes. We show how these types of path integrals can be evaluated and apply our results to study the thermodynamics of a minority stripe phase in…
We review recent simulation studies of interfaces between immiscible homopolymer phases. Special emphasis is given to the presentation of efficient simulation techniques and powerful methods of data analysis, such as the analysis of…
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…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
We study a homopolymer model of a protein chain, where each monomer carries a dipole moment. To mimic the geometry of the peptidic bond, these dipoles are constrained to be locally perpendicular to the chain. The tensorial character of the…
Classical theory of crystals states that a medium to be considered homogeneous must satisfy the following requirements: a) the dimension of the elementary cell must be much smaller than the incident wavelength; b) the sample must contain a…
In this paper we summarize some results of our theoretical investigations of helix-coil transition both in single-strand (polypeptides) and two-strand (polynucleotides) macromolecules. The Hamiltonian does not contain any parameter designed…
We consider the model for the distribution of a long homopolymer in a potential field. The typical shape of the polymer depends on the temperature parameter. We show that at a critical value of the temperature the transition occurs from a…