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.
We investigate thermodynamic and structural properties of colloidal dumbbells in the framework provided by the Reference Interaction Site Model (RISM) theory of molecular fluids and Monte Carlo simulations. We consider two different models: in the fi
rst one we set identical square-well attractions on the two tangent spheres composing the molecule (SW-SW model); in the second scheme, one of square-well interactions is switched off (HS-SW model). Appreciable differences emerge between the physical properties of the two models. Specifically, the $k to 0$ behavior of SW-SW structure factors $S(k)$ points to the presence of a gas-liquid coexistence, as confirmed by subsequent fluid phase equilibria calculations. Conversely, the HS-SW $S(k)$ develops a low-$k$ peak, signaling the presence of aggregates; such a process destabilizes the gas-liquid phase separation, promoting at low temperatures the formation of a cluster phase, whose structure depends on the system density. We further investigate such differences by studying the phase behavior of a series of intermediate models, obtained from the original SW-SW by progressively reducing the depth of one square-well interaction. RISM structural predictions positively reproduce the simulation data, including the rise of $S(k to 0$) in the SW-SW model and the low-$k$ peak in the HS-SW structure factor. As for the phase behavior, RISM agrees with Monte Carlo simulations in predicting a gas-liquid coexistence for the SW-SW model (though the critical parameters appears overestimated by the theory) and its progressive disappearance moving toward the HS-SW model.
