Abstract
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.
Highlights
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data
The order parameter is expressed through the first derivative of thermodynamic potential, while the second derivative is related to the heat capacity
Experimental data are usually processed either with the help of the two-state[9] or the Zimm–Bragg[10] approach. Each of these phenomenological thermodynamical theories has its benefits and drawbacks, but the most relevant is that they are both weak in describing the interactions between the polypeptide chain and the water molecules that are essential for proteins
Summary
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. We show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intramolecular H-bonds, unavailable with other processing methods. Once the expression for thermodynamic potential (usually Gibbs free energy) is accepted, a theoretical expression is derived and fitted to experimental data points in order to estimate the (temperature-independent) enthalpic, entropic, and heat capacity costs of (un)folding Experimental data are usually processed either with the help of the two-state[9] or the Zimm–Bragg[10] approach Each of these phenomenological thermodynamical theories has its benefits and drawbacks, but the most relevant is that they are both weak in describing the interactions between the polypeptide chain and the water molecules that are essential for proteins. Succeeded by Taylor expansions of enthalpy and entropy, truncated at second term[13,14,15,16], it leads to a quadratic dependence of
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