Transitions model proteins, water

In order to understand the effect of temperature on the water dynamics and how it leads to the glass transition of the protein, we have performed a study of a model protein-water system. The model is quite similar to the DEM, which deals with the collective dynamics within and outside the hydration layer. However, since we want to calculate the mean square displacement and diffusion coefficients, we are primarily interested in the single particle properties. The single particle dynamics is essentially the motion of a particle in an effective potential described by its neighbors and thus coupled to the collective dynamics. A schematic representation of the d)mamics of a water molecule within the hydration layer can be given by ... 

Four Phase Changes (Transitions) in Model Protein-Water Systems... 

The free energy required to overcome the transition barrier for this step is 18 and 22 kcal/mol with respect to 1NT2 for Models A and B in gas-phase respectively (Table 2). There is not much change in this barrier ( 1 kcal/mol) even in the presence of protein environment and water for Model B. Water molecules W362 and W615 maintain their coordination with calcium, and ASP303 and calcium respectively throughout this proposed reaction path until the formation of the final product (Fig. 5). 

Quite the inverse occurs for water-dissolved protein of interest here that is, by the consilient mechanism, heating from below to above the folding transition increases the order of the model protein. Because heating increases protein order, the transition is called an inverse temperature transition. 

Figure 5.2. The four phase transitions of the model protein (GVGVP)2si in water over the temperature range from -20 to 120°C. The familiar transition of the melting of ice and the vaporization of water are shown with the relative magnitudes of the heats of these transitions to those of protein heat denaturation and to the innocuous looking inverse temperature transition near 30°C that we believe to be the basis of the function of protein-based machines of Life. See text for discussion.

Despite the absorption of heat for the transition and the overall increase in entropy of -(-4.0 EU for the water plus protein, the protein component actually increases in order on raising the temperature. As unambiguously demonstrated by crystallization of a cyclic analog (see Figure 2.7), in this case the protein component of the water plus protein system becomes more ordered as the temperature is raised. For this and additional reasons, noted below in section 5.1.3, we call this transition exhibited by our model protein, poly (GVGVP), an inverse temperature transition. 

A vital property of these model proteins is that they are more ordered above the transition temperature defined by the binodal or coexistence line in Figure 5.3. The polymer component of this water-polypeptide system becomes more ordered or structured on increased temperature from below to above the transition. This behavior is the inverse of that observed for most systems, as discussed above. In particular, we developed the term inverse temperature transition when the precursor protein and chemical fragmentation products of the mammalian elastic fiber changed from a dissolved state, and therefore when molecules were randomly dispersed in solution, to a state of parallel-aligned twisted filaments as the temperature was raised from below to above the phase transition. - ... 

Thus, values of AGha should be recognized as the net result of a transition dominated by the endothermic conversion of hydrophobic hydration to bulk water attending hydrophobic association with a lesser contribution due to the exothermic association of the model protein molecules, resulting from van der Waals interactions usually calculated using the Lennard-... 

In Chapter 5, based on an inverse temperature transition due to hydrophobic association in water, a set of Axioms were derived from the phenomenological demonstration that de novo designed model proteins could efficiently interconvert the set of energies interconverted by living organisms. Then there followed a series of experimental results and analyses that defined the comprehensive hydrophobic effect. 

The most direct observation of changes in hydrophobic hydration attending the inverse temperature transition comes from following the temperature dependence of an absorption band in the microwave dielectric relaxation experiment shown in Figures 5.24 and 5.25. The water of hydrophobic hydration, with an absorption band near 5 GHz in the dissolved model protein, disappears on raising the temperature through the inverse temperature transition as the model protein hydrophobically... 

Chapter 5 is the scientific core of the book. It begins with familiar phase transitions of ice-to-water and water-to-vapor, both of which demonstrate increased disorder with increased temperature. It then brings in the unique phase transitions of the two-component system, model proteins in water, in which the protein... 

Two natural collapse processes are the folding of proteins into their compact native states in water, and the compaction of DNA molecules for insertion into virus heads and cell nuclei. While this homopolymer collapse model illustrates the principle of coil-to-globule transitions, neither protein folding nor DNA collapse follow it exactly, because both polymers also have electrostatic interactions and specific monomer sequences. 

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