Consilient mechanisms elasticity, energy conversion

A diverse set of energy conversions that sustain life can be experimentally demonstrated by de novo design of elastic-contractile model proteins under the precept of a single, pervasive, mechanism, that is, by a consilient mechanism that creates a common groundwork of explanation. It is a mechanism that achieves function by controlling association of... 

Importance of the Elastic Consilient Mechanism to Efficiency of Energy Conversion... 

The consilient mechanism was bom out of controlling the hydrophobic association-dissociation of elastic-contractile model proteins to achieve the possibility of some 18 classes of pairwise energy conversions (see Chapter 5, section 5.6). In the process a set of five Axioms became the phenomenology out of which the consilient mechanism arose. For the first time a common groundwork of explanation was able to perform the diverse energy conversions of biology. 

A more complete technical description of the consilient mechanisms of concern to biological energy conversion encompasses two distinct but interlinked physical processes of hydrophobic association and of elastic force development. The latter results from a generally applicable... 

In general, then, the energy conversions of biology reduce to the production of ATP and the uses of ATP, that is, the production of ATP by the five protein-based machines of the inner mitochondrial membrane and the thousands of subsequent protein-based machines that do the necessary work of the cell. This constitutes yet an enormous task that will fill hundreds of volumes in the future of protein-based machines. The intention of this volume, however, is to add a simplifying feature of a common groundwork of explanation for each of the hydrophobic and elastic consilient mechanisms. For the function of protein-based machines of biology, this perspective recovers an attractive element of simplification. 

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 primary forces were designated hydrophobic and elastic consilient mechanisms, because each provided a common groundwork of explanation in its realm of utilization, and commonly they do so inseparably. In Chapter 8, those very consilient mechanisms were shown to be dominant in the function of specific examples of the three principal classes of energy conversions of living organisms (subsequent to the photosynthetic step itself). The three classes are... 

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). 

E.2.9.3 Bursts of Apolar-Polar Repulsive Free Energy on Hydrolysis of ATP, by the Hydrophobic Elastic Consilient Mechanism, Can Convert to Elastic Deformation for Efficient Energy Conversion... 

The phenomenological experimental foundation for the challenging new perspectives presented by the hydrophobic and elastic consilient mechanisms stands on the successful design of model proteins capable of the extraordinarily diverse set of energy conversions noted above. The mechanistic foundation derives from the need to obtain explanation for otherwise inexplicable experimental results, such as stretch-induced pKa shifts, hydrophobic-induced pKa shifts, hydrophobic-induced reduction potential shifts, and systematic increases in steepness (positive cooperativity) of the experimental curves that follow the change... 

The above three discussed protein-based machines—Complex III of the electron transport chain, ATP synthase/Fj-ATPase, and the myosin II motor of muscle contraction—represent the three major classes of energy conversion that sustain Life. Therefore, the facility with which the consilient mechanisms explain their function indeed support the thesis that biology s vital force arises from the coupled hydrophobic and elastic consilient mechanisms. 

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