Folding transitions, assembly

T[ and Tj, are the on-set temperature for the hydrophobic folding and assembly transition, that is, inverse temperature transition, in pbs (0.15 N NaCl, 0.01 M phosphate) as determined by light scattering and in water as determined by DSC, respectively. Both values are linearly extrapolated tofx = 1 and rounded to a number divisible by 5. AH and AS are the values at/x = 0.2 on the curve for a linear fit of the DSC derived endothermic heats and entropies of the transitions for die polymers in water. 

The Inverse Temperature Transition A Hydrophobic Folding and Assembly Transition... 

The protein-based polymer is soluble in water at temperatures below its coexistence line where the hydrophobic residues are surrounded by hydrophobic hydration. As the positive (-TAS) term due to hydrophobic hydration becomes larger than the negative AH term, simply due to increasing the value of T, solubility of a protein-based polymer is lost, and it hydrophobicaUy folds and assembles. The inverse temperature transition is a hydrophobic association transition. 

Axiom 1 The change in temperature interval, over which occurs the oil-like folding and assembly transition of a host model protein on introduction of different guest substituents, becomes a functional measure of relative oil-like character of the substituents, that is, of their relative hydrophobicity, and it provides a measure of the change in free energy of the hydrophobi-cally associated state. 

Axiom S At constant temperature, an energy input that changes the temperature interval for thermally driven hydrophobic association in a model protein can drive contraction, that is, oillike folding and assembly, with the performance of mechanical work in other words, the energy input moves the system through the transition zone for contraction due to hydrophobic association. 

More oil-like R-groups in our model protein studies resulted in lower temperatures for the onset of the inverse temperature transition of hydrophobic folding and assembly (see section 5.3.2). We argued that more oil-like R-groups in... 

Now, it has been shown for materials such as poly(propylene diol) (wherein both the absorption maximum for loss shear modulus and loss permittivity overlap near the frequency of IHz) that their normalized curves perfectly superimpose over their frequency band width. - As shown in Figure 9.15, the lower frequency loss shear modulus curves uniquely overlap with the loss permittivity data at higher frequency. As such the former is melded to calibrate the loss permittivity data to obtain a coarse estimate of the elastic modulus values. This provides an independent demonstration of the mechanic il resonance near 3 kHz and also allows reference to the 5 MHz dielectric relaxation as a mechanical resonance. Thus, as the folding and assembly of the elastic protein-based polymers proceed through the phase (inverse temperature) transition, the pentamers wrap up into a structurally repeating helical arrangement like that represented in Figure 9.17. 

Figure 1 A. Temperature versus normalized turbidity curves for a series of guest amino acid residues occurring at the frequency of 4 guest residues per 100 residues, i.e., fx = 0.2. The value of Tj, the temperature for the onset of the inverse temperature transition for hydrophobic folding and assembly, is defined as the temperature for 50% of maximal turbidity. Note that more hydrophobic guest residues lower the value of T,. and less hydrophobic, more polar residues raise the value of Ti.

All these studies established that the folding of RNA molecules is organized in a hierarchical manner. The assembly of complex RNA structures occurs in discrete transitions which build upon the folding of sub-systems that can then self-organize to even bigger and more complex structures [38-40]. 

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