Energies consilient mechanism

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... 

Especially when seen in three dimensions, as in Figure 1.5 A, the stereo view of the myosin motor domain has the appearance of a sculpted surface. The surface contains crevices and depressions, as though formed from sandstone that had been weathered by wind and rain. Only a relatively few water molecules are seen in these surface recesses, because the majority of water molecules are too mobile to be observed by X-ray diffraction. Yet these surface crevices and depressions can be filled with water molecules that, by the consilient mechanism, contribute to the energy considerations of motor function. In this regard, it should be appreciated that only 10% to 20% of the existing water molecules are sufficiently fixed in space to be located by X-ray diffraction. ... 

The energies interconverted by both of these steps are demonstrable by model proteins designed to function by the consilient mechanism of controlling phase separation. 

It may be noted that present calculations of protein structure and function neglect the presence of so much internal water. In calculations, a quantity called the dielectric constant, required in electrostatic calculations of the energy of interaction between charges, is utilized. The value of the dielectric constant of bulk water is about 80, and commonly the assumption is made that the value shifts at the surface of the protein from 80 to 5 or less within the protein. The presence of the waters of Thales raises concern about such assumptions. Similarly, in Chapter 5, particularly in Figure 5.30, the experimental values could only be approximated by electrostatic calculations when a value of 5 or less was used, whereas direct measurement of the dielectric constant for the model protein system required that the value within the model protein motor be no less than 65. These points provide substantial support for the consilient mechanism. 

The correlations of Figure 2.6 represent one profound expression of the consilient mechanism for protein function in energy conversion that is, the data of Figure 2.6 represent a common groundwork of explanation" for protein function. 

In Chapter 8, more structural background and molecular details of contraction exhibited by the linear myosin II motor are considered after, in Chapter 5, the physical basis for the apolar (oil-like)-polar (vinegar-like) repulsive energy that controls hydrophobic association is experimentally and analytically developed. The crystal structures of the cross-bridge of scallop muscle provide remarkable examples of the consilient mechanism functioning in this protein-based machine ... 

We again draw comparison by quoting from Schrddinger s What is Life as published in 1944 What I wish to make clear in this last chapter is, in short, that from all that we have learnt about the structure of living matter, we must be prepared to find it working in a manner that cannot be reduced to the ordinary laws of physics. In the present volume, our foundation is, of course, the somewhat counterintuitive inverse temperature transition. It is by means of the inverse temperature transition that the energies essential to sustain Life can, in fact, be accessed. This efficient consilient mechanism, however, requires no new laws of physics. In fact, the seeds of this mechanism are found in a 1937 report of Butler,in which he analyzed the thermodynamic elements of the solubility of oil-like groups in water. 

In this chapter we briefly note the improbability of a protein comprised of 20 different amino acids in specified sequence. Then we step through the details whereby a protein of specified sequence comes into being, and, like the accountant, sum up the cost in terms of the biological energy currency, adenosine triphosphate (ATP), that is, in terms of the number of ATP molecules consumed in the production of a protein of unique sequence. Such an essentially ordinary exercise requires inclusion in this book in order to remove unnecessary mystery of protein production, to provide an example whereby molecular machines utilize energy to produce biological structure, and to place in perspective the ease with which new protein-based machines evolve when functioning by the consilient mechanism. 

A Consilient Mechanism Provides a Common Groundwork of Explanation for the Diverse Energy Conversions of Biology... 

Capacity to Move the T,-divide as a Measure of Energy Available to the Consilient Mechanism (That Is, Moving the Temperature Interval)... 

Living organisms function without the changes in temperatme required for thermomechanical transduction by the consilient mechanism. What makes the mechanism consilient or pervasive, however, is that many different energy... 

The position of the T,-divide that separates soluble from insoluble (hydrophobically associated) states in the phase diagram depends on seven variables on the six intensive variables of temperature, chemical potential, electrochemical potential, mechanical force, pressure, and electromagnetic radiation, and on polymer volume fraction or concentration. Therefore, diverse protein-catalyzed energy conversions by the consilient mechanism result from designs that control the location of the Tfdivide in this seven-dimensional phase transitional space. Complete mathematical description has yet to be written for representation of the T,-divide in seven-dimensional phase transitional space, but it may prove to be more relevant to... 

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

Cataloging the Energy Resources Available to the Consilient Mechanism of Energy Conversion 131... 

T, to a new value of T, caused by an energy input represented by % to provide a measure of the change in Gibbs free energy for hydrophobic association of the protein-based polymer. Therefore, Tt, the onset temperature for the inverse temperature transition, represents an intrinsic property of the hydrophobic consilient mechanism of energy conversion. 

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