Unified description of solvent effects in the helix-coil transition.

Phys Rev E Stat Nonlin Soft Matter Phys

Department of Molecular Physics, Yerevan State University, A. Manougian Str. 1, 375025, Yerevan, Armenia.

Published: February 2014

AI Article Synopsis

  • The study analyzes the helix-coil transition in biopolymers using spin-based models that incorporate both explicit and implicit solvent actions, focusing on how solvent interactions affect hydrogen bonding.
  • The spin Hamiltonian developed combines a basic model of polypeptide chains with terms representing solvent effects, allowing for a comprehensive understanding of how solvents influence biopolymer configurations.
  • This framework is applicable to various biopolymer behaviors, including cold denaturation and osmotic pressure effects, and helps explain the characteristics of intrinsically disordered proteins.

Article 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 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 explicitly and 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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Source
http://dx.doi.org/10.1103/PhysRevE.89.022723DOI Listing

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