Competition for hydrogen bond formation in the helix-coil transition and protein folding

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 Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev

Microscopic formulation of the Zimm-Bragg model for the helix-coil transition

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field. However, the dependence on temperature of the reduced external field turns out to differ from the standard one-dimensional Ising model and hence it gives rise to different thermophysical properties, despite the exact mapping connecting them. We discuss how this point has been frequently overlooked in the recent literature.Comment: 11 pages, 2 figure

Statistical mechanics of DNA-nanotube adsorption

Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aromatic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, a phenomenon related to hybridization. We propose a Hamiltonian formulation for the zipper model that accounts for the DNA-CNT interactions and allows for the processing of experimental data, which has awaited an available theory for a decade

Helix-coil transition in terms of Potts-like spins

In the spin model of a helix-coil transition in polypeptides a preferred value of spin has to be assigned to the helical conformation, in order to account for different symmetries of the helical {\sl vs.} the coil states, leading thus to the {\sl Generalized Model of Polypeptide Chain} (GMPC) Hamiltonian as opposed to the Potts model Hamiltonian, both with many-body interactions. Comparison of explicit transfer-matrix secular equations of the Potts model and the GMPC model reveals that the largest eigenvalue of the Potts model with $\Delta$ many-body interactions {\sl coincides} with the largest eigenvalue of the GMPC model with $\Delta-1$ many-body interactions, indicating the identity of both free energies. In distinction, the second largest eigenvalues in both models do {\sl not coincide}, indicating a different behavior for the spatial correlation length that in its turn defines the width of the helix-coil transition interval. We explore in detail the thermodynamic consequences, resulting from spin models with and without the built-in spin anisotropy, that should indicate which model to favour as a more appropriate description of the equilibrium physical properties pertaining to the helix-coil transitio

Statistical mechanics of DNA adsorption on a carbon nanotube

The attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aro- matic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between them. With the goal to provide the theoretical support to numerous technologies on the basis of DNA-CNT hybrids, we propose a Hamiltonian formulation for the zipper model that accounts for relevant interactions and allows for the processing of experimental data, which has awaited an available theory for a decade

Statistical mechanics of DNA-nanotube adsorption

Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNTs) and the aromaticnucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, aphenomenon related to hybridization. We propose a Hamiltonian formulation for the zipper model that accountsfor the DNA-CNT interactions and allows for the processing of experimental data, which has awaited an availabletheory for a decade