High temperature unfolding

US studies can produce informative free energy landscapes but assume that degrees of freedom orthogonal to the surface equilibrate quickly. The MD time needed for significant chain or backbone movement could exceed the length of typical US simulations (which are each typically on the nanosecond timescale). However, in spite of this caveat, US approaches have been very successful. One explanation for this success lies in the choice of initial conditions US simulations employ initial coordinates provided by high-temperature unfolding trajectories, which themselves have been found to yield predictive information about the nature of the relevant conformational space. 

Consider that at low temperatures, a lubricant is a poor solvent for polymer chains. When the temperature increases, interactions between polymer chains decrease the space occupied by the polymer ball takes on greater volume and consequently, the viscosity decrease due to the lubricant temperature increase is compensated by the unfolding of the polymer chain and the result is a reduction of the difference between the viscosities at low and high temperature, and therefore an Increase in viscosity index. 

The biologiccJ function of a protein or peptide is often intimately dependent upon the conformation(s) that the molecule can adopt. In contrast to most synthetic polymers where the individual molecules can adopt very different conformations, a protein usually exists in a single native state. These native states are found rmder conditions typically found in Uving cells (aqueous solvents near neutred pH at 20-40°C). Proteins can be unfolded (or denatured) using high-temperature, acidic or basic pH or certain non-aqueous solvents. However, this unfolding is often reversible cind so proteins can be folded back to their native structure in the laboratory. 

Fig. 12. Thermal denaturation for ribonuclease Tj as followed by VCD, from 20° to 65°C. The matrix descriptors determined for the native state and the unfolded high-temperature data are indicated. The values indicate a loss of the helix segment but maintenance of sheet segments. Also listed are the spectrally determined fractional contributions (FC) to the secondary structure. When combined with the segment analysis, this implies that the residual sheet segments must be very short. Reprinted with permission from Pancoska, P., et al. (1996). Biochemistry 35(40), 13094-13106, the American Chemical Society.

Proteins unfolded by GdmHCl or urea will have a dominant conformation, Pn- At low temperatures we find about one-third of the residues in chemically denatured proteins in the Pn-helix conformation, with two-thirds in the form of the high-temperature ensemble. Since at least one-third of the residues in this ensemble are isolated Pn residues or in Pn helices of two or three residues, the total Pn content will be 50% or greater. The Pn content of cold- and acid-denatured proteins will be substantial, probably >40%, but not as large as in chemically denatured proteins. 

The geometric properties of highly denatured states appear to be consistent with those expected for a random-coil polymer. For example, proteins unfolded at high temperatures or in high concentrations of denaturant invariably produce Kratky scattering profiles exhibiting the monotonic increase indicative of an expanded, coil-like conformation (Fig. 1) (Hagihara et al., 1998 see also Doniach et al., 1995). Consistent... 

Figure 13.5 Microcalorimetry thermograms (not concentration normalized) showing the destabilizing influence of 0.9% benzyl alcohol (dashed trace) on two high-temperature transitions associated with the Fc domains of an IgGjFc fusion protein. Note that 0.1% phenol exhibits very little influence on the unfolding behavior of the protein in comparison to the control (not containing preservative).

Gursky, O. and D. Atkinson. 1996. High- and low-temperature unfolding of human high-density apolipoprotein A-2. Protein Sci 5 1874—1882. 

As the temperature increases, the term TA5D N increases and causes the protein to unfold when it becomes greater than A D N i.e., when AGD N becomes negative. Thus, thermal unfolding is caused by the entropy of the unfolded state dominating at high temperature. 

Both the denaturation process in proteins and the melting transition (also referred to as the helix-to-coil transition) in nucleic acids have been modeled as a two-state transition, often referred to as the all-or-none or cooperative model. That is, the protein exists either in a completely folded or completely unfolded state, and the nucleic acid exists either as a fully ordered duplex or a fully dissociated monoplex. In both systems, the conformational flexibility, particularly in the high-temperature form, is great, so that numerous microstates associated with different conformers of the biopolymer are expected. However, the distinctions between the microstates are ignored and only the macrostates described earlier are considered. For small globular proteins and for some nucleic acid dissociation processes,11 the equilibrium between the two states can be represented as... 

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