Protein-based machines evolution

On the Evolution of Protein-based Machines (Toward Complexity of Structure and Diversity of Function)... 

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. 

Mutations and Evolution of Protein-based Machines Table 6.2. The genetic code. 

Biology s reversal of the much-noted arrow of time and equivalently biological evolution derive simply from fundamental reality of biosynthesis within the context of inverse temperature transitions as expressed in the hydrophobic consilient mechanism. The production of a new and improved protein-based machine occurs by chance, but most significantly it occurs at a cost in energy no greater than that required to produce the initial less useful protein-based machine. This is the nature of the biosynthesis of protein and of the other great macromolecules (the nucleic acids, DNA and RNA) of biology. 

When protein-based machines function by the hydrophobic consilient mechanism, the structure of the genetic code is ideally suited for the evolution of protein-based machines to access new forms of energy. 

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. 

Thus, from the perspective of the inverse temperature transition, evolution and natural selection become apparent consequences for protein-based machines that function by the hydrophobic and elastic consilient mechanisms. 

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