Related papers: Exactly Solvable Model for Helix-Coil-Sheet Transi…
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…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
Helix-coil transition in polypeptides is an example of a spin model with a preferred spin direction, in the sense that a theoretical formulation of this problem requires to assign a preferred value of spin to the helical conformation in…
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 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…
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…
In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the case of the q=4 and q=5 Potts model, i.e. systems where a…
We present a simple yet generic model for the behavior of a system of many surface-attached flexible polymers with rigid side chains. Beyond its potential application in describing the dynamics of the extracellular matrix of mammalian…
We discuss the effects of the solvent composition on the helix-coil transition of a polypeptide chain. We use a simple model to demonstrate that improving the hydrogen-bonding ability of the solvent can make the transition less cooperative,…
We study helix-coil transitions in an all-atom model of polyalanine. Molecules of up to length 30 residues are investigated by multicanonical simulations. Results from two implicit solvent models are compared with each other and with that…
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 report on multicanonical simulations of the helix-coil transition of a polypeptide. The nature of this transition was studied by calculating partition function zeros and the finite-size scaling of various quantities. Estimates for…
The similarity in the thermodynamic properties of two completely different theoretical models for the helix-coil transition is examined critically. The first model is an all-atomic representation for a poly-alanine chain, while the second…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
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…
An exact analytical solution of generalized three-state double-chain Potts model with multi-spin interactions which are invariant under cyclic shift of all spin values is obtained. The partition function in a finite cyclically closed strip…