Protein-based machines biological

As is argued in Chapter 8, small, often reversible, energy excursions back and forth across the boundary between associated (water-insoluble) and dissociated (water-soluble) oil-like domains (clusters of oil-like groups) drive the protein-based machines of biology. Biology often achieves mobility by many linear motors comprised of protein, such... 

The consilient mechanisms in relation to protein-based machines of biology are introduced. Before the four major assertions that... 

A protein-based machine without water as an integral part of its structure could not function by the consilient mechanism. In other words, water is required in at least one of the two states in order to have a movable cusp of insolubility, and in order for competition for hydration to be relevant there must be adequate water present. The first prerequisite, therefore, in addressing the biological relevance of the consilient mechanism is to assess whether or not water exists within or between the changing structural elements of a protein motor during function. 

ATPase, Biology s Workhorse Protein-based Machine... 

Thereby, the objective of this book is to demonstrate the phase separation mechanism of oil-like domains separating from water and related controlling phenomena at the molecular level as relevant to specific biological protein-based machines. 

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). 

In this chapter we briefly note the improbability of a protein comprised of 20 different amino acids in specified sequence. Then we step through the details whereby a protein of specified sequence comes into being, and, like the accountant, sum up the cost in terms of the biological energy currency, adenosine triphosphate (ATP), that is, in terms of the number of ATP molecules consumed in the production of a protein of unique sequence. Such an essentially ordinary exercise requires inclusion in this book in order to remove unnecessary mystery of protein production, to provide an example whereby molecular machines utilize energy to produce biological structure, and to place in perspective the ease with which new protein-based machines evolve when functioning by the consilient mechanism. 

The following set of axioms provides the basis for the engineering of diverse protein-based machines and of the design of molecular machines from amphiphilic polymers in general, as considered in Chapter 9. They also open the door to new insights into the function of biology s protein-based machines, as discussed in Chapters 7 and 8. 

To the best of my knowledge, the hemoglobin oxygenation curve is historically the first example of a biologically essential positive cooperativity. Because of this, it becomes an important objective to explore the phenomenology of hemoglobin s positive cooperativity and compare it with that of the consilient mechanism due to an apolar-polar repulsive free energy of hydration (as is done in Chapter 7) and, in fact, to do so for a number of protein-based machines that exhibit positive cooperativity. 

D.W. Urry, S.Q. Peng, L.C. Hayes, D.T. McPherson, Jie Xu, T.C. Woods, D.C. Gowda, and A. Pattanaik, Engineering Protein-based Machines to Emulate Key Steps of Metabolism (Biological Energy Conversion). Biotechnol. Bioeng., 58,175-190,1998. 

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. 

More to the point, we now see biology s access to energy by means of the consilient mechanism of energy conversion, combined with readily available mutations to improve protein-based machines, as the source of increased structural order and functional diversity. 

In terms of the biological origins of protein-based machines, we have been addressing above what Prigogine and Stengers in Order Out of Chaos consider one of the two basic questions of our scientific heritage ... 

Consilient Mechanisms for Protein-based Machines of Biology... 

ATP and equivalent nucleotide triphosphates (NTPs) power essentially all subsequent protein-based machines of biology, either directly or indirectly. 

On the Relevance of Hydrophobic and Elastic Consilient Mechanisms to Biology s Protein-based Machines... 

Accordingly, the perspectives in Chapter 5, developed on elastic-contractile protein-based polymers, introduce new concepts into the functional description of biology s protein-based machines. As with the introductory comments in Chapter 7, the footnote relevant to reactions toward new concepts in science is repeated here in footnote form. ... 

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... 

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