Consilient mechanisms hydrophobic

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. 

Here we describe the coupling of functions. A function involves any chemical entity that can exist in either of two states, and by the consilient mechanism the two states differently affect hydrophobic hydration to a significant extent. Two functions become coupled when the more polar state of each decreases hydrophobic hydration while the more hydrophobic state of each increases the potential for hydrophobic hydration. The two functions can be a chemical couple such as -COO /-COOH and a redox couple such as the interconvertible states of oxidized nicoti-namide/reduced nicotinamide. 

In the extramembrane component the y-rotor forms the stem and core of an orangeshaped structure comprised of six sections, three a-subunits and three P-subunits, arranged as threefold symmetrical (aP) pairs, designated as (aP)3. The key element of the consilient mechanism applied to ATP synthase is that the y-rotor exhibits three faces of very different hydrophobicity. In our view, rotation of the y-rotor by the Fo-motor causes the very hydrophobic side of the rotor to be spatially opposed, through a water-filled cleft, to the catalytic site containing the most charged state. 

From the perspective of the consilient mechanism, the assembly of filaments as required for muscle contraction and the necessary movement of components within the cell involves hydrophobic association/dissociation between composite subunits. The actin thin filament of... 

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 ... 

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

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... 

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. 

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. 

Energy Resources of the Consilient Mechanism Changing the Free Energy (AGha) for Hydrophobic Association... 

Because hydrophobic association does not occur until the temperatiu e is above T, for the phosphorylated state, the phosphate cannot be folded into a low dielectric constant site, but instead would be fully exposed to the solvent. It is fundamental to the consilient mechanism of protein-based machines to understand how this can be As discussed in section 5.7, the high-energy state of the phosphate is due to competition for hydration between the phosphate and the hydrophobic groups, as reflected in the large change in Tt. 

The term machine is a general designation for any device that converts energy from one form to another. The particular type of machine that performs mechanical work or produces motion is commonly called either a motor or an engine. Here, we summarize the capacity of protein-based machines to perform mechanical work (pump iron) by the consilient mechanism of hydrophobic association by utilizing a number of different energy inputs. 

Pwffomtance of Mechanical Work by the Consiliant Mechanism of Hydrophobic Folding and Assembly... 

Statement 1 Within the context of the hydrophobic consilient mechanism, a functional group is a chemical entity that can exist in one of two or more interconvertible states, each with a different hydrophobicity, as measured by the Trbased and AGnA based hydrophobicity scales (see Tables 5.1,5.2 and 5.3). 

Statement 2 Because the uncharged states of ionizable functional groups and the reduced states of oxidized functional groups are each more oil-like or hydrophobic than the charged and oxidized states, the formation of the more hydrophobic state of one functional group can cause the more polar state of a second kind of attached and responsive functional group to convert to its more hydrophobic state. This is the coupling of functions by the consilient mechanism ... 

Coupling of Functional Groups by Means of the Consilient Mechanism and by Means of Their Common Dependence on the Gibbs Free Energy of Hydrophobic Association, AGha... 

This axiom is the fundamental energy coupling axiom it utilizes the hydrophobic association transition common to all energy conversions by the consilient mechanism. Importantly, in doing so, it involves the performance of kinds of work in addition to mechanical work. Examples include the following ... 

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. 

Our focus now turns to the physical basis whereby the energy conversions of the hydrophobic consilient mechanism occur, and, of course, it becomes an issue of what controls the inverse temperature transition of hydrophobic association. 

Relationship of the Consilient Mechanism to Cold Denaturation and to Hydrophobic Dissociation on Being Made More Polar... 

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