Related papers: Sub-residue sharpness of protein helix-coil transi…
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…
The representation of protein backbone geometry through the discrete nonlinear Schr\"odinger equation provides a theoretical connection between biological structure and integrable systems. Although the global application of this framework…
Based on the Zimm-Bragg model we study cooperative helix-coil transition driven by a finite-speed change of temperature. There is an asymmetry between the coil-to-helix and helix-to-coil transition: the latter is displayed already for…
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…
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…
Although recent spectroscopic studies of chemically denatured proteins hint at significant nonrandom residual structure, the results of extensive small angle X-ray scattering studies suggest random coil behavior, calling for a coherent…
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 intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
In view of the important role helix-sheet transitions play in protein aggregation, we introduce a simple model to study secondary structural transitions of helix-coil-sheet systems using a Potts model starting with an effective Hamiltonian.…
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…
Determining the three-dimensional structure of a protein from its amino-acid sequence remains a fundamental problem in biophysics. The discrete Frenet geometry of the C$_\alpha$ backbone can be mapped, via a Hasimoto-type transform, onto a…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…
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…
We study the equilibrium and nonequilibrium formation of four-particle complexes in a balanced two-species Bose-Hubbard model with repulsive intra- and attractive inter-species interactions. Using exact diagonalization, we characterize the…
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…
Consider the wave propagation in a two-layered medium consisting of a homogeneous compressible air or fluid on top of a homogeneous isotropic elastic solid. The interface between the two layers is assumed to be an unbounded rough surface.…