Hydrophobic effect comprehensive

Consilient Mechanisms for Diverse Protein-based Machines The Efficient Comprehensive Hydrophobic Effect... 

The Comprehensive Hydrophobic Effect Results from the Actual or Potential Hydrophobic Hydration That Can Occur for a Pair ofAssociable Hydrophobic Surfaces or Domains... 

Figure 5.10. An embodiment of the comprehensive hydrophobic effect in terms of a plot of the temperature for the onset of phase separation for hydrophobic association, Tb, versus AGha. the Gibbs free energy of hydrophobic association for the amino acid residues, calculated by means of Equation (5.10b) using the heats of the phase (inverse temperature) transition (AH,). Values were taken from Table 5.3. Tb and T, were determined from the onset of the phase separation as defined in Figure 5.1C,B, respectively. The estimates of AGha utilized the AH, data listed in Table 5.1 for fx = 0.2 but extrapolated to fx = 1, and the Gly (G) residue was taken as the...

Clearly, it would seem not unreasonable to propose the consilient mechanism as the dominant mechanism in protein structure formation and function. The comprehensive hydrophobic effect should be the foundation from which to engineer protein materials for medical and nonmedical uses. 

The Comprehensive Hydrophobic Effect Can ITiis Be a Consilient Mechanism for the Energy Conversions of Biology ... 

To date the sigmoid curve in Figure 5.10 offers perhaps the most effective introduction to the comprehensive hydrophobic effect. It is a plot of the reference temperature, either Tb or Tt, for the onset of the inverse temperature transi-... 

The Comprehensive Hydrophobic Effect Resolves Three Categories of Amino Acid Residues... 

Net Heat Changes for the Inverse Temperature Transitions of the Comprehensive Hydrophobic Effect Are Endothermic Due to the Conversion of Hydrophobic Hydration to Bulk Water ... 

One of the more challenging locations, therefore, for consideration of the comprehensive hydrophobic effect in the panoply of biological energy conversions is the electron transport chain embedded within the inner mitochondrial membrane. Essential parts of these protein-based machines insert into and function in very hydrophobic lipid bilayers. Here the ingress and egress of protons for develop-... 

As with hemoglobin, discussed in Chapter 7, a Bohr effect occurs with cytochrome c oxidase. Again from the viewpoint of the hydrophobic consilient mechanism, these phenomena are analogous. Formation of the less polar states on reduction of Complex IV and on forming deoxyhemoglobin result in proton uptake, whereas formation of the more polar oxidized state of Complex IV and the more polar oxygenated state of hemoglobin result in proton release. This is as expected from the AG, of the comprehensive hydrophobic effect, as discussed above. 

As noted in the introduction of this section 8.4, this is as one would intuitively expect. Some quantification of this in terms of the comprehensive hydrophobic effect of the hydrophobic consilient mechanism follows immediately below for the E. coli example. 

As reviewed in Chapter 7 with a focus on the issue of insolubility, extensive phenomenological correlations exist between muscle contraction and contraction by model proteins capable of inverse temperature transitions of hydrophobic association. As we proceed to examination of muscle contraction at the molecular level, a brief restatement of those correlations follows with observations of rigor at the gross anatomical level and with related physiological phenomena at the myofibril level. Each of the phenomena, seen in the elastic-contractile model proteins as an integral part of the comprehensive hydrophobic effect, reappear in the properties and behavior of muscle. More complete descriptions with references are given in Chapter 7, sections 7.2.2, and 7.2.3. 

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 operative component of the comprehensive hydrophobic effect arises from the competition between charged and oil-like groups. This was shown to result in a previously unknown repulsive force embodied within an interaction energy called an apolar-polar repulsive free energy of hydration, AG,p. During function, AG,p works in conjunction with elastic force development by the restriction of internal chain dynamics. These have been called the hydrophobic and elastic consilient mechanisms. In Chapters 6,7, and 8, these consilient mechanisms were demonstrated to be fundamental to understanding the functions of biology s proteins. 

Chapter 5 presents in one place, more extensively and in a more advanced state than previously, the decades long development of the comprehensive hydrophobic effect, the underpinnings of the hydrophobic consilient mechanism, whereby the control of hydrophobic association commands diverse energy conversion functions of protein-based polymers. Chapters 7 and 8 demonstrate the comprehensive hydrophobic effect and its interlinked elastic consilient mechanism to be vital aspects of protein function and dysfunction in biology. In the present chapter, we utilize this developed capacity to engineer protein-based polymers to demonstrate a few of an extraordinary range of applications. 

The energy conversions that produce motion in living organisms consist of two distinct but interlinked physical processes of hydrophobic association and elastic force development, collectively referred to as consilient mechanisms in that they each provide a common groundwork of explanation. The association of oil-like domains, hydrophobic association, has been characterized in terms of the comprehensive hydrophobic effect (CHE), and elastic force development has been described in terms of the damping of internal chain dynamics on deformation, whether deformation occurs by extension, compression or solvent-mediated repulsion (see section E.4.1.2 and Figures E.3 and E.4, below). 

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