Elasticity consilient mechanism

This mechanism of elasticity provides a common groundwork of explanation for the elasticity of all chain molecules regardless of composition and structure as long as there exists an internal chain motion that becomes decreased on deformation. For this reason, it too is a consilient mechanism. To delineate this consilient mechanism for elasticity from the consilient mechanism for hydrophobic association, as treated extensively in this volume, it will be referred to as the elastic consilient mechanism. 

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

On the Relevance of Hydrophobic and Elastic Consilient Mechanisms to Biology s Protein-based Machines... 

This chapter discusses key protein-based machines of biology to demonstrate the relevance of the hydrophobic and elastic consilient mechanisms. The objective in this chapter, therefore, is to investigate selected examples of biology s protein-based machines and to look at the molecular level for a coherence of phenomena with the designed elastic model... 

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. 

Part of our challenge, to assess the relevance of the hydrophobic and elastic consilient mechanisms and specifically of apolar-polar... 

The hydrophobic and elastic consilient mechanisms, two distinct but interlinked physical processes of hydrophobic association/dissocia-tion and elastic force development/relaxation, couple to achieve movement. In functional... 

Our conclusion is that dissociation of the RIP from the Q site in a single step represents a unique intersection of electron transfer and proton translocation that simultaneously employs both the hydrophobic and elastic consilient mechanisms. 

Relevance of the Hydrophobic Elastic Consilient Mechanism to the Fj-motor Functioning as an ATPase Analogy to the Internal Combustion Rotary Engine... 

Thus the fundamental predictions of the hydrophobic elastic consilient mechanism are that the rotor would exhibit asymmetric hydrophobicity, that different arrangements of nucleotide analogues representing different states of polarity at the catalytic sites would orient the rotor, and that hydrolysis of ATP in formation of the most polar state at a catalytic site of the involved protein subunit(s) would demonstrate a near-ideal elastic deformation of the y-rotor and the protein subunit(s). Of course, such a mechanism would exhibit high efficiency and reversibility. 

Demonstrations of these predictions constitute the message of this section 8.4, and its success introduces the perspective of a conjoined hydrophobic elastic consilient mechanism. With the values in Table 5.3 and the crystal structure with three different states of occupancy, empty, ATP, and ADP, the three sides of the rotor can be identified and the respective Gibbs free energies of hydrophobic association, AGha, have been estimated to be -20, 0, and +9kcal/mole. The most hydrophobic face associates with the empty site, the neutral face with the ATP bound site, and the most polar face with the ADP site which in the synthesis mode would be in position to add Pj. As expected from the magnitude of the resulting AG,p for a series of crystal structures wherein the least polar occupancy state for the catalytic site could be defined, the most hydrophobic side of the rotor resides in apposition to the least polar site. 

The rotor that is driven by the Fo-motor comprises a single y-subunit and a small e-subunit attached to the y-subunit at a point proximal to the base of the Fo-motor. This is called the y-rotor. In the hydrophobic elastic consilient mechanism, the interactions of a hydrophobi-cally asymmetric y-rotor with the housing of the Fi-motor with different occupancy states of the catalytic sites constitute the basis for mechano-chemical transduction of the Fi-motor. 

As seen from the landmark study of Noji et al. " and represented in Figure 8.42, the direction of rotation for the Fj-ATPase is indeed in the counterclockwise direction. Thus, the foundation for the hydrophobic and elastic consilient mechanisms in the function of ATP synthase and Fi-ATPase becomes increasingly compelling. 

Review of Correlations Between the Hydrophobic Elastic Consilient Mechanism and the Properties of ATP Synthase/Fj-ATPase... 

In the eighth point of correlation of the hydrophobic elastic consilient mechanism given above, the maximal stage of apolar-polar repulsion occurred when the most polar occupancy state, ADP Mg plus HPOJ", faced off against the most hydrophobic side of the y-rotor to provide the thrust for a counterclockwise... 

Hypothesis Efficient Production of Motion by Muscle Contraction Derives from the Hydrophobic and Elastic Consilient Mechanisms, Whereby Dephosphorylation Results in Hydrophobic Association Coupled to Near-ideal Elastic Force Development... 

The above perspectives are natural consequences of both the hydrophobic and the elastic consilient mechanisms as applied to the structural data on the myosin II motor. Here we briefly explore the elastic element. An ideal elastomer exhibits exactly reversible stress-strain curves with complete recovery on relaxation of the energy of deformation. On the other hand, an elastomer that exhibits hysteresis does not recover all of the energy on relaxation that was expended on deformation. Accordingly, efficient muscle contraction should involve the deformation of near-ideal elastic segments to utilize more efficiently the energy expended in driving contraction. The mechanism of elasticity that can provide such near-ideal elasticity is the damping of internal chain dynamics on extension. 

By the elastic consilient mechanism the extension of single flexible loops causes an increase in the elastic force. It appears that one such loop has been identified in Figure 8.55. Rayment et al. note a number of flexible loops in the myosin cross-bridge. Each of these becomes a candidate for elastic force... 

In Figures 8.47 through 8.58, two states of the myosin II motor are compared using specific reference conditions. In our view, these two states differ most dramatically by their extents of hydrophobic association. Clearly, the state with less polar occupanQr of the nucleotide binding site favors greater hydrophobic association, and the state with more polar occupancy of the nucleotide binding site favors hydrophobic dissociation. The differences between the two states become explicable in terms of the hydrophobic and elastic consilient mechanisms, and the difference between the two states provides for displacement of the sort required for the motion of muscle contraction. 

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. 

E.l Thesis Biology s Vital Force Arises from Coupled Hydrophobic and Elastic Consilient Mechanisms... 

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... 

In our view, the hydrophobic and elastic consilient mechanisms comprise the vital force of living matter. The forces arising out of inverse temperature transitions and elastic deformation, for example, apolar-polar repulsion and damping of backbone mobility on deformation, couple to create biology s vital force. ... 

E.2.9 The Elastic Consilient Mechanism as the Efficient Mechanical Coupler Within the Vital Force ... 

Elastic forces come into play as hydrophobic associations stretch interconnecting chain segments. Only if the elastic deformation is ideal does all of the energy of deformation become recovered on relaxation. To the extent that hysteresis occurs in the elastic deformation/ relaxation, energy is lost and the protein-based machine loses efficiency. Thus, the elastic consilient mechanism, whereby the force-extension curve can be found to overlay the force-relaxation curve becomes the efficient mechanical coupler within the vital force. The objective now becomes one of understanding the age-old problem of a reluctance to discard past idols. 

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