Thermodynamical Implications of a Protein Model with Water Interactions

Abstract

We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding relative to the orientational energy of bound water, 2) ratio of degrees of freedom between the folded and unfolded protein chain and 3) the number of water molecules that can access the hydrophobic parts of the protein interior. By increasing the number of water molecules in the model, the separation between the two peaks in the heat capacity curve comes closer, which is more consistent with experimental data. In the end we show that if we, as a speculative assumption, assign only two distinct energy levels for the bound water molecules, we obtain better correspondence with experiments.

Localized heat urticaria in a patient is associated with a wealing response to heated autologous serum

“…These findings suggest that a large molecule (over 50 kDa) in the serum is modified by heat into an active form which is relatively stable. IgE is unlikely to be that factor because IgE is usually inactivated by heating at 60 °C for 2 h. Various serum proteins can be unfolded by heat 15,16 . We speculate that heat induces the unfolding of certain serum proteins, which are able to directly or indirectly activate mast cells, causing the mast cells to release chemical mediators including histamine.…”

Protein model exhibiting three folding transitions

“…In this article we will explain the physical basis of a protein model, that reformulates the water interactions proposed in earlier models by Hansen et al [5,6] and Bakk et al [8,9]. We will compare thermodynamical quantities, as the heat capacity, to experiments.…”

“…One simplified view of protein folding is that the protein is supposed to follow a specific folding pathway of conformations in a descending landscape of Gibbs free energy [2][3][4][5][6][7][8][9]. This is a picture of a folding protein that is forced to follow a specific "path" of successive conformational steps of increasing structural order.…”

Specific heat upon aqueous unfolding of the protein interior: a theoretical approach

“…The polar (ionic) forces are relatively strong and the hydrogen atom is light, which both favor quantum effects. Use of a two-level system [27,36,37] for this kind of problem can thus reflect such quantization.…”