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arXiv · 1401.0281

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

Artem Badasyan·Shushanik A. Tonoyan·Achille Giacometti·Rudolf Podgornik·V. Adrian Parsegian·Yevgeni Sh. Mamasakhlisov·Vladimir F. Morozov
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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.

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Artem Badasyan, Shushanik A. Tonoyan, Achille Giacometti, Rudolf Podgornik, V. Adrian Parsegian, Yevgeni Sh. Mamasakhlisov, Vladimir F. Morozov. 2014-01-01. A unified description of solvent effects in the helix-coil transition. https://doi.org/10.1103/physreve.89.022723

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