English

A unified description of solvent effects in the helix-coil transition

Biomolecules 2015-06-18 v1 Soft Condensed Matter Biological Physics

Abstract

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 hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background \emph{in vacuo} Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be {\sl explicitly} and {\sl exactly} traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of Intrinsically Disordered Proteins and their analogues.

Keywords

Cite

@article{arxiv.1401.0281,
  title  = {A unified description of solvent effects in the helix-coil transition},
  author = {Artem Badasyan and Shushanik A. Tonoyan and Achille Giacometti and Rudolf Podgornik and V. Adrian Parsegian and Yevgeni Sh. Mamasakhlisov and Vladimir F. Morozov},
  journal= {arXiv preprint arXiv:1401.0281},
  year   = {2015}
}

Comments

12 pages, 12 figures, to be submitted to PRE