Protein-based machines efficiency

The Competition for Hydration Also Is Responsible for Large Hydrophobic-induced pKa Shifts with Positive Cooperativity That Results in Efficient Protein-based Machines... 

As was discussed in Chapter 5, for Figure 5.17, addition of electrons to a positively charged redox group increases oil-like character and drives model protein folding, which result in contraction and the performance of mechanical work. The increase in affinity for electrons of the vitamin-like molecule that occurs on replacement of Val by Phe (see Figure 5.20C) makes for a more efficient electron-driven contraction. Thus, a genetic code that would allow easy mutational steps to become more oil-like would, here again, provide for evolution of more efficient protein-based machines. 

E.7.2.3 A Refinement Step of Evolution-Natural Selection To Produce a More Efficient Protein-based Machine at No Extra Cost Using the Biased Genetic Code... 

As discussed in Chapter 5 and specifically considered in Chapter 6 in relation to evolution, the replacement of a Val residue by a phenylalanine (Phe, F) residue results in a more efficient protein-based machine for chemo-mechanical transduction or for electro-mechanical transduction (see Figures 5.20,5.34, and 5.36 and the associated discussions in Chapter 5). The mutation from Val to Phe occurs with a single base change at the DNA level of guanine to thymine. As listed in Table 6.2, a single base change in position 1 can access a more hydrophobic residue, as in Val to Phe, to provide a more efficient protein-based machine. 

Now, because it can cost just as much energy to produce an inefficient and more limited protein-based machine as it can to produce a more efficient and/or a new machine that can access a new energy source, obviously with natural selection the arrow of time for biology is toward greater complexity and diversity function (see Chapter 6). 

Due to the struggle to survive under circumstances of limited food supply, organisms evolve to use the most efficient mechanism available to their composition. The most efficient mechanism available to the proteins that sustain Life would seem to be the apolar-polar repulsive free energy of hydration as observed for the inverse temperature transitions for hydrophobic association. The efficiency of designed elastic-contractile protein-based machines and a number of additional properties make designed protein-based materials of substantial promise for the marketplace of the future. 

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

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... 

The most efficient ojjerational design would be for the machine to operate over the range of the acid-base titration curve with the steepest An/Ap slope. Because the Hill coefficient, n, as defined in Equation (5.20) is a measure of the slope, it provides for ready comparison of efficiencies. The Hill coefficients for Model Proteins I through v are listed in Figure 5.34, and the slopes are plotted in the inset. Accordingly, the comparison of the efficiencies of Model Proteins i and v simply becomes iii/liy = 1.5/8.0 = 0.19. Thus, by increasing the hydropho-bicity by the replacement of five Val (V) residues by five Phe (F) residues, as indicated in Table 5.5, increases the efficiency of the protein-based machine by just over fivefold. 

Changing the second base of two of the four triplet codons for Val, namely, GUA and GUG to GAA and GAG, respectively, are two ways to convert Val to Glu. Changing the second base of the other two triplet codons for Val, for example, GUU to GAU and GUC to GAC, converts Val to Asp. Thus, the Val triplet codons are such that a single base change of the second base from U to A results in amino acid residues with carboxylate side chains. A single mutation converts a thermally driven (and also a poor chemically driven) protein-based machine into a more efficient chemically driven protein-based machine. How trivial and likely the diversification of biology s molecular machines, especially because it costs no more energy (of biosynthesis) to produce the new or improved protein-based machine. 

The second point addresses the nature of elastic force development in relation to imder-standing efficient energy conversion. If the energy required for chain deformation during elastic force development becomes lost to other parts of the protein and to the surrounding water, then so too is efficient energy conversion lost. In other words, elastomeric force development on deformation in a protein-based machine followed by marked hysteresis on relaxation necessarily denotes an inefficient protein-based machine. 

The development of force under conditions of fixed length, as in an isometric contraction, involves the elastic deformation of a chain or chains within the protein-based machine. On relaxation, ideal elastic elements return the total energy of deformation to the protein-based machine for the performance of mechanical work. Thus, the approach toward high efficiency for the function of a protein-based linear motor, or even for the RIP domain movement in Complex III, depends on how nearly the extension of an elastomeric chain segment approaches ideal elasticity. 

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. 

When protein-based machines function by the hydrophobic consilient mechanism, the genetic code is ideally suited for their evolution toward new machines with greater efficiency. 

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