Elastic-contractile model proteins hydrophobic association

Figure 5.5. Transitions, plotted as independent variable versus dependent variable, showing a response limited to a partieular range of independent variable. (A) Representation of the thermally driven contraction for an elastic-contractile model protein, such as the cross-linked poly(GVGVP), plotted as the percent contraction (dependent variable) versus temperature (independent variable). The plot shows a poorly responsive range below the onset of the transition, the temperature interval of the inverse temperature transition for hydrophobic association, and another poorly responsive region above the tem-...

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 hydrophobically associated state represents the insolubility side of the T,-(solubility/insolubility)divide. As discussed in Chapter 5, contraction of the model elastic-contractile model proteins capable of inverse temperature transitions arises due to hydrophobic association. Hydrophobic association occurs, most fundamentally, on raising the temperature, on adding acid (H" ) to protonate and neutralize carboxylates (-COO ), and on adding calcium ion to bind to and neutralize carboxylates. Most dramatically, hydrophobic association occurs on dephosphorylation of (i.e., phosphate release from) protein, and it commonly occurs with formation of ion pairs or salt bridges between associated hydrophobic domains. 

The phenomena that drive muscle contraction—thermal activation, pH activation, calcium ion activation, stretch activation in insect flight muscle, and dephosphorylation itself—have all been shown to drive contraction by hydrophobic association in the elastic-contractile model proteins discussed in Chapter 5. As concerns a pair of hydrophobic domains, all of these processes surmount the T,-divide (the cusp of insolubility in Figure 7.1) to go from a soluble state to an insoluble state either by raising the... 

Role of Ion-pair Formation in Hydrophobic Association of Elastic-contractile Model Proteins... 

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. 

Hydrophobic association within a protein chain constitutes an element of contraction. From our design and study of elastic-contractile model proteins, a contraction comprises two distinct but interlinked physical processes. They are... 

As with the elastic-contractile model proteins discussed in Chapter 5, favorable hydrophobic association (in this case of RIP globular protein tip with the Q site) stretches interconnecting chain segments. Thus, the answer to the question asked by Crofts et al. ° in the title of their article, becomes clear Interactions of quinone with iron-sulfur protein of the bci complex Is the mechanism spring-... 

Perhaps the most fundamental and certainly the most dramatic observation during the study of hydrophobic association using the elastic-contractile model proteins has been that the introduction of charge disrupts hydrophobic association. This finding and indeed the principal basis for controlling hydrophobic association, AGgp, stands out in the release of hydrophobic association at the Qo site. The transfer from ubiquinol, QH2, of one electron to the FeS center and of a second electron to the heme bL center leaves a positively charged ubiquinol, for example, QHi. ... 

Even so, crystal structures provide the best snapshots of forces in action. Crystal structures provide an unparalleled opportunity to assess relevance to the major protein-based machines of biology of the free energy transduction so dominantly displayed by elastic-contractile model proteins (as developed in Chapter 5). If the apolar-polar repulsive free energy of hydration, AG.p, the operative component of the Gibbs free energy of hydrophobic association, AGha> is active in ATP synthase, then it should become apparent in these snapshots. 

As reviewed in Chapter 7 with a focus on the issue of insolubility, extensive phenomenological correlations exist between muscle contraction and contraction by model proteins capable of inverse temperature transitions of hydrophobic association. As we proceed to examination of muscle contraction at the molecular level, a brief restatement of those correlations follows with observations of rigor at the gross anatomical level and with related physiological phenomena at the myofibril level. Each of the phenomena, seen in the elastic-contractile model proteins as an integral part of the comprehensive hydrophobic effect, reappear in the properties and behavior of muscle. More complete descriptions with references are given in Chapter 7, sections 7.2.2, and 7.2.3. 

Raising the temperature to drive contraction by hydrophobic association is the fundamental property of the consilient mechanism as demonstrated in Chapter 5 by means of designed elastic-contractile model proteins. Thermal activation of muscle contraction also correlates with contraction by hydrophobic association, but assisted in this case by the thermal instability of phosphoanhydride bonds associated with ATP, which on breakdown most dramatically drive hydrophobic association. In particular, both muscle and cross-linked elastic protein-based polymer, (GVGVP) contract on raising... 

By T,-type, we mean polymers that exhibit inverse temperature transitions in which the protein-based polymers hydrophobically associate on raising the temperature. T, represents the onset temperature for the transition. For the elastic-contractile model proteins of interest here, the inverse temperature transition is seen as a phase separation resulting from both intermolecular and intramolecular hydrophobic association. On raising the temperature... 

V in Table 5.5 with 0,2,3,4, and 5 F residues per 30-mer exhibits a systematic nonlinear increase in steepness, that is, in positive cooperativity, and an associated nonlinear increased pKa shift, as plotted in Figure 5.34. The energy required to convert from the COOH state to the COO" state systematically in a supralinear way becomes less and less, as more Phe residues replace Val residues. The energy required to convert from the hydrophobically dissociated state of COO" to the hydrophobically associated (contracted) state of COOH becomes less, as the model protein becomes more hydro-phobic. The elastic-contractile protein-based machine becomes more efficient as it becomes more hydrophobic. The cooperativity of Model Protein iv with a Hill coefficient of 2.6 is similar... 

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