Consilient mechanisms elastic hydrophobic

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. 

Complex III is an example of the consilient mechanism for elasticity that includes the coupling of hydrophobic association with development of an elastic force. In particular, the Rieske iron protein (RIP) of Complex III resides on the cytoplasmic side and contains a long hydrophobic a-helix that passes through the lipid bilayer from the cytoplasmic side to emerge on the matrix side with charged residues that combine to anchor the iron protein to the membrane. On the cytoplasmic side, a sequence of about 15 residues that is continuous with the transmembrane anchor... 

The focus has been on both aspects of the consilient mechanism (hydrophobic association/ dissociation and elastic force development/ relaxation) involved in the unique domain movement for electron transfer within Complex III. In what follows, the same aspect of hydrophobic association/dissociation of the consilient mechanism is proposed for facilitating proton gating. 

As shown in the hexagonal array in Figure 5.22, five different energy inputs can perform mechanical work by the consilient mechanism. The set of elastic-contractile model proteins capable of direct utilization of hydrophobic association for contraction are called protein-based molecular machines of the first kind. These are enumerated below with brief consideration of the reversibility of these machines. 

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. 

Applying what is now the consilient mechanism for hydrophobic association to the elastic fiber, the prediction became that oxidation of the elastic fiber by a natural enzyme with the biological role of producing superoxide and hydrogen peroxide would cause hydrophobic dissociation evidenced by a swelling and a loss of elastic recoil. A xanthine oxidase superoxide... 

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... 

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... 

Thus, the challenge to the consilient mechanisms posed by the electron transport chain transforms into a showcase example that includes the two distinct but interlinked physical processes of the development of entropic elastic force during hydrophobic association to bring both consilient mechanisms to bear. 

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. 

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